基本情報

所属

• 情報科学研究院　生命人間情報科学部門　バイオインフォマティクス分野

職名

• 准教授

学位

• 博士（理学）（東京大学）

ホームページURL

https://sites.google.com/view/nosada17/

科研費研究者番号

• 70416270

J-Global ID

• 200901034194227400

プロフィール

• 分子生物学実験，集団遺伝学，バイオインフォマティクスなどの方法を用いて進化の問題に答えようと思っています．ヒトを含めた霊長類を中心に，ショウジョウバエや植物のデータも扱っています．興味がわけば何でもやります．

研究キーワード

• 遺伝子重複   遺伝子発現調節   再編   カニクイザル   CXCL1L   ケモカイン   偽遺伝子   ゲノム進化   翻訳   CXCL1   グノム   種分化   生態学   霊長類   進化   遺伝学   遺伝子交流   

研究分野

• ライフサイエンス / システムゲノム科学
• ライフサイエンス / ゲノム生物学
• ライフサイエンス / 多様性生物学、分類学
• ライフサイエンス / 進化生物学

職歴

• 2019年04月 - 現在 北海道大学 大学院情報科学研究院 准教授
• 2012年05月 - 現在 放射線医科学総合研究所 客員研究員
• 2017年09月 - 2021年03月 北海道大学 国際連携研究教育局 准教授
• 2015年04月 - 2019年03月 北海道大学 大学院情報科学研究科 准教授
• 2010年01月 - 2015年03月 国立遺伝学研究所・総合研究大学院大学 助教
• 2011年12月 - 2011年12月 台湾国立成功大学 客員助理教授
• 2009年01月 - 2009年12月 台湾国立成功大学 兼任助理教授
• 2005年04月 - 2009年12月 独立行政法人医薬基盤研究所 研究員
• 2004年10月 - 2005年03月 国立感染症研究所 研究官
• 2003年03月 - 2004年10月 シカゴ大学 リサーチアソシエイト
• 2002年04月 - 2002年12月 東京大学 特別研究員

学歴

• 1997年04月 - 2002年03月   東京大学大学院   理学系研究科   生物科学専攻
• 1993年04月 - 1997年03月   東京大学   理学部   生物学科

所属学協会

• 生き物文化誌学会   日本バイオインフォマティクス学会   日本人類学会   日本分子生物学会   日本霊長類学会   日本進化学会   日本遺伝学会   

研究活動情報

論文

• Genealogical characterization of regional populations and dorsal coat color variation in the house mouse Mus musculus from Asia based on haplotype structure analysis of a gene-rich region harboring Mc1r

  Kazuhiro Zakoh, Kazumichi Fujiwara, Toyoyuki Takada, Naoki Osada, Hitoshi Suzuki

  Genes & Genetic Systems 2023年
• Whole-genome sequencing analysis of wild house mice (Mus musculus) captured in Madagascar

  Kazumichi Fujiwara, Marie C. Ranorosoa, Satoshi D. Ohdachi, Satoru Arai, Yuki Sakuma, Hitoshi Suzuki, Naoki Osada

  Genes & Genetic Systems 97 4 193 - 207 2022年08月01日
• A New Approach to Drug Repurposing with Two-Stage Prediction, Machine Learning, and Unsupervised Clustering of Gene Expression

  Yi Cong, Misaki Shintani, Fuga Imanari, Naoki Osada, Toshinori Endo

  OMICS: A Journal of Integrative Biology 26 6 339 - 347 2022年06月01日
• Insights into Mus musculus Population Structure across Eurasia Revealed by Whole-Genome Analysis

  Kazumichi Fujiwara, Yosuke Kawai, Toyoyuki Takada, Toshihiko Shiroishi, Naruya Saitou, Hitoshi Suzuki, Naoki Osada

  Genome Biology and Evolution 14 5 2022年05月03日 [査読有り][通常論文]
   

  Abstract For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies have suggested that they originated in South Asia and diverged into three major subspecies, almost simultaneously, approximately 110,000–500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and historic times (∼10,000 years ago to the present day) and have undergone secondary contact, which has complicated the genetic landscape of wild house mice. In this study, we sequenced the whole-genome sequences of 98 wild house mice collected from Eurasia, particularly East Asia, Southeast Asia, and South Asia. Although wild house mice were found to consist of three major genetic groups corresponding to the three major subspecies, individuals representing admixtures between subspecies were more prevalent in East Asia than has been previously recognized. Furthermore, several samples exhibited an incongruent pattern of genealogies between mitochondrial and autosomal genomes. Using samples that likely retained the original genetic components of subspecies with the least admixture, we estimated the pattern and timing of divergence among the subspecies. The estimated divergence time of the three subspecies was 187,000–226,000 years ago. These results will help us to understand the genetic diversity of wild mice on a global scale, and the findings will be particularly useful in future biomedical and evolutionary studies involving laboratory mice established from such wild mice.
• Whole-Genome Sequencing of Vero E6 (VERO C1008) and Comparative Analysis of Four Vero Cell Sublines

  Kazuhiro Konishi, Toshiyuki Yamaji, Chisato Sakuma, Fumio Kasai, Toshinori Endo, Arihiro Kohara, Kentaro Hanada, Naoki Osada

  Frontiers in Genetics 13 1 - 9 2022年03月22日 [査読有り][通常論文]
   

  The Vero cell line is an immortalized cell line established from kidney epithelial cells of the African green monkey. A variety of Vero sublines have been developed and can be classified into four major cell lineages. In this study, we determined the whole-genome sequence of Vero E6 (VERO C1008), which is one of the most widely used cell lines for the proliferation and isolation of severe acute respiratory syndrome coronaviruses (SARS-CoVs), and performed comparative analysis among Vero JCRB0111, Vero CCL-81, Vero 76, and Vero E6. Analysis of the copy number changes and loss of heterozygosity revealed that these four sublines share a large deletion and loss of heterozygosity on chromosome 12, which harbors type I interferon and CDKN2 gene clusters. We identified a substantial number of genetic differences among the sublines including single nucleotide variants, indels, and copy number variations. The spectrum of single nucleotide variants indicated a close genetic relationship between Vero JCRB0111 and Vero CCL-81, and between Vero 76 and Vero E6, and a considerable genetic gap between the former two and the latter two lines. In contrast, we confirmed the pattern of genomic integration sites of simian endogenous retroviral sequences, which was consistent among the sublines. We identified subline-specific/enriched loss of function and missense variants, which potentially contribute to the differences in response to viral infection among the Vero sublines. In particular, we identified four genes (IL1RAP, TRIM25, RB1CC1, and ATG2A) that contained missense variants specific or enriched in Vero E6. In addition, we found that V739I variants of ACE2, which functions as the receptor for SARS-CoVs, were heterozygous in Vero JCRB0111, Vero CCL-81, and Vero 76; however, Vero E6 harbored only the allele with isoleucine, resulting from the loss of one of the X chromosomes.
• Predicting PRDM9 Binding Sites by a Convolutional Neural Network and Verification Using Genetic Recombination Map

  Takahiro Nakamura, Toshinori Endo, Naoki Osada

  IPSJ Transactions on Bioinformatics 15 9 - 16 2022年03月 [査読有り][通常論文]
  
• Phylogeographic study using nuclear genome sequences of Asip to infer the origins of ventral fur color variation in the house mouse Mus musculus

  Toki Takeishi, Kazumichi Fujiwara, Naoki Osada, Akihiko Mita, Toyoyuki Takada, Toshihiko Shiroishi, Hitoshi Suzuki

  Genes & Genetic Systems 96 1 - 14 2022年03月 [査読有り][通常論文]
  
• Whole-genome sequencing analysis reveals the population history of Mus musculus in Madagascar

  Kazumichi Fujiwara, Marie C Ranorosoa, Satoshi D Ohdachi, Satoru Arai, Yuki Sakuma, Hitoshi Suzuki, Naoki Osada

  2021年09月10日 [査読無し]
   

  In Madagascar, the house mouse (Mus musculus) is thought to have colonized along with humans and is now one of the most successfully colonized rodents on the island. In this study, we determined the whole-genome sequences of the Madagascar house mouse captured from the wild. We examined the evolutionary history of its population regarding the mitochondrial and autosomal genomes. We confirmed that in the mitochondrial genomes of Madagascar house mice, a monophyletic clade forms a basal origin within the species. An analysis of autosomal genomic sequences indicates that the Madagascar house mouse population is genetically a member of M. m. castaneus (CAS). It also contains genetic elements of M. m. domesticus (DOM) resulting from ancient hybridization. The signature of a strong population bottleneck 1000–3000 years ago was observed in the mitochondrial and autosomal genomic data. We also show that the divergence of the Madagascar population from the CAS population occurred approximately 50,000–99,000 years ago. Madagascar house mice show strong genetic affinity to many CAS samples across a wide range of Indian Ocean coastal regions. However, our results suggest that they would not have originated directly from the Indonesian islands, where Austronesian-speaking people in Madagascar originated. Because the ancient hybridization signature with DOM did not appear in the Indonesian and other CAS samples, we propose that Madagascar house mice were not directly brought by Austronesian-speaking people but came from somewhere around the Middle East or South Asia soon after the colonization of initial farmers.
• Demographic history of the brown bear (Ursus arctos) on Hokkaido island, Japan, based on whole-genomic sequence analysis.

  Yu Endo, Naoki Osada, Tsutomu Mano, Ryuichi Masuda

  Genome Biology and Evolution 2021年 [査読有り][通常論文]
   

  Previous studies of the brown bear (Ursus arctos) on Hokkaido Island, Japan, have detected three geographically distinct subpopulations representing different mitochondrial lineages and shown that gene flow between subpopulations has occurred due to male-biased dispersal. In this study, we determined whole-genomic sequences for six Hokkaido brown bears and analyzed these data along with previously published genomic sequences of 17 brown bears from other parts of the world. We found that the Hokkaido population is genetically distinct from the other populations, keeping genetic diversity higher than the endangered populations in Western Europe but lower than most populations on the continents. A reconstruction of historical demography showed no increase in population size for the Hokkaido population during the Eemian interglacial period (130,000–114,000 years ago). In a phylogenetic analysis of the autosomal data, the Hokkaido population formed a clade distinct from North American and European populations, showing that it has maintained genetic diversity independently from continental populations following geographical isolation on the island. This autosomal genetic similarity contrasts with the geographically separate mitochondrial lineages on Hokkaido and indicates the occurrence of male-driven gene flow between subpopulations.
• House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete mitochondrial genome sequences

  Yue Li, Kazumichi Fujiwara, Naoki Osada, Yosuke Kawai, Toyoyuki Takada, Alexey P. Kryukov, Kuniya Abe, Hiromichi Yonekawa, Toshihiko Shiroishi, Kazuo Moriwaki, Naruya Saitou, Hitoshi Suzuki

  Heredity 126 1 132 - 147 2021年01月 [査読有り][通常論文]
   

  The Eurasian house mouse Mus musculus is useful for tracing prehistorical human movement related to the spread of farming. We determined whole mitochondrial DNA (mtDNA) sequences (ca. 16,000 bp) of 98 wild-derived individuals of two subspecies, M. m. musculus (MUS) and M. m. castaneus (CAS). We revealed directional dispersals reaching as far as the Japanese Archipelago from their homelands. Our phylogenetic analysis indicated that the eastward movement of MUS was characterised by five step-wise regional extension events: (1) broad spatial expansion into eastern Europe and the western part of western China, (2) dispersal to the eastern part of western China, (3) dispersal to northern China, (4) dispersal to the Korean Peninsula and (5) colonisation and expansion in the Japanese Archipelago. These events were estimated to have occurred during the last 2000–18,000 years. The dispersal of CAS was characterised by three events: initial divergences (ca. 7000–9000 years ago) of haplogroups in northernmost China and the eastern coast of India, followed by two population expansion events that likely originated from the Yangtze River basin to broad areas of South and Southeast Asia, including Sri Lanka, Bangladesh and Indonesia (ca. 4000–6000 years ago) and to Yunnan, southern China and the Japanese Archipelago (ca. 2000–3500). This study provides a solid framework for the spatiotemporal movement of the human-associated organisms in Holocene Eastern Eurasia using whole mtDNA sequences, reliable evolutionary rates and accurate branching patterns. The information obtained here contributes to the analysis of a variety of animals and plants associated with prehistoric human migration.
• Exploring models of human migration to the Japanese archipelago using genome-wide genetic data

  NAOKI OSADA, YOSUKE KAWAI

  Anthropological Science 129 1 45 - 58 一班社団法人 日本人類学会 2021年 [査読有り][招待有り]
   

  The origins of people in the Japanese archipelago are of long-standing interest among anthropologists, archeologists, linguists, and historians studying the history of Japan. While the 'dual-structure' model proposed by Hanihara in 1991 has been considered the primary working hypothesis for three decades, recent advances in DNA typing and sequencing technologies provide an unprecedented amount of present-day and ancient human nuclear genome data, which enable us to refine or extend the dual-structure model. In this review, we summarize recent genome sequencing efforts of present-day and ancient people in Asia, mostly focusing on East Asia, and we discuss the possible migration routes and admixture patterns of Japanese ancestors. We also report on a meta-analysis we performed by compiling publicly available datasets to clarify the genetic relationships of present-day and ancient Japanese populations with surrounding populations. Because the ancient genetic data from the Japanese archipelago have not yet been fully analyzed, we have to corroborate models of prehistoric human movement using not only new genetic data but also linguistic and archeological data to reconstruct a more comprehensive history of the Japanese people.

• Testing sex-biased admixture origin of macaque species using autosomal and X-chromosomal genomic sequences

  Naoki Osada, Kazunari Matsudaira, Yuzuru Hamada, Suchinda Malaivijitnond

  Genome Biology and Evolution 13 evaa233  2021年 [査読有り][通常論文]
   

  The role of sex-specific demography in hybridization and admixture of genetically diverged species and populations is essential to understand the origins of the genomic diversity of sexually reproducing organisms. In order to infer how sex-linked loci have been differentiated undergoing frequent hybridization and admixture, we examined 17 whole-genome sequences of seven species of the genus Macaca, which shows frequent inter-specific hybridization and predominantly female philopatry. We found that hybridization and admixture were prevalent within these species. For three cases of suggested hybrid origin of species/subspecies, M. arctoides, M. fascicularis ssp. aurea, and Chinese M. mulatta, we examined the level of admixture of X chromosomes, which is less affected by male-biased migration than that of autosomes. In one case, we were able to determine that M. cyclopis and M. fuscata was genetically closer to Chinese M. mulatta than to the Indian M. mulatta, and the admixture level of Chinese M. mulatta and M. fuscata/cyclopis was more pronounced on the X chromosome than on autosomes. Since the mitochondrial genomes of Chinese M. mulatta, M. cyclopis, and M. fuscata were found to cluster together, and the mitochondrial genome of Indian M. mulatta is more distantly related, the observed pattern of genetic differentiation on X-chromosomal loci is consistent with the nuclear swamping hypothesis, in which strong, continuous male-biased introgression from the ancestral Chinese M. mulatta population to a population related to M. fuscata and M. cyclopis generated incongruencies between the genealogies of the mitochondrial and autosomal genomes.
• Identification of Characteristic Genomic Markers in Human Hepatoma HuH-7 and Huh7.5.1-8 Cell Lines

  Masaki Kawamoto, Toshiyuki Yamaji, Kyoko Saito, Yoshitaka Shirasago, Kazuhiro Satomura, Toshinori Endo, Masayoshi Fukasawa, Kentaro Hanada, Naoki Osada

  Frontiers in Genetics 11 2020年10月09日 [査読有り]
  
• Comparative characterization of flavivirus production in two cell lines: Human hepatoma-derived Huh7.5.1-8 and African green monkey kidney-derived Vero.

  Kyoko Saito, Masayoshi Fukasawa, Yoshitaka Shirasago, Ryosuke Suzuki, Naoki Osada, Toshiyuki Yamaji, Takaji Wakita, Eiji Konishi, Kentaro Hanada

  PloS one 15 4 e0232274  2020年 [査読有り][通常論文]
   

  The Flaviviridae is a family of enveloped viruses with a positive-sense single-stranded RNA genome. It contains many viruses that threaten human health, such as Japanese encephalitis virus (JEV) and yellow fever virus (YFV) of the genus Flavivirus as well as hepatitis C virus of the genus Hepacivirus. Cell culture systems highly permissive for the Flaviviridae viruses are very useful for their isolation, propagation, and diagnosis, an understanding of their biology, and the development of vaccines and antiviral agents. Previously, we isolated a human hepatoma HuH-7-derived cell clone, Huh7.5.1-8, which is highly permissive to hepatitis C virus infection. Here, we have characterized flavivirus infection in the Huh7.5.1-8 cell line by comparing with that in the African green monkey kidney-derived Vero cell line, which is permissive for a wide spectrum of viruses. Upon infection with JEV, Huh7.5.1-8 cells produced a higher amount of virus particles early in infection and were more susceptible to virus-induced cell death than Vero cells. Similar outcomes were obtained when the cells were infected with another flavivirus, YFV (17D-204 strain). Quantification of cellular and extracellular viral RNA revealed that high JEV production in Huh7.5.1-8 cells can be attributed to rapid viral replication kinetics and efficient virus release early in infection. In a plaque assay, Huh7.5.1-8 cells developed JEV plaques more rapidly than Vero cells. Although this was not the case with YFV plaques, Huh7.5.1-8 cells developed higher numbers of YFV plaques than Vero cells. Sequence analysis of cDNA encoding an antiviral RNA helicase, RIG-I, showed that Huh7.5.1-8 cells expressed not only a full-length RIG-I mRNA with a known dominant-negative missense mutation but also variants without the mutation. However, the latter mRNAs lacked exon 5/6-12, indicating functional loss of RIG-I in the cells. These characteristics of the Huh7.5.1-8 cell line are helpful for flavivirus detection, titration, and propagation.
• Dysfunctional missense variant of OAT10/SLC22A13 decreases gout risk and serum uric acid levels.

  Toshihide Higashino, Keito Morimoto, Hirofumi Nakaoka, Yu Toyoda, Yusuke Kawamura, Seiko Shimizu, Takahiro Nakamura, Kazuyoshi Hosomichi, Akiyoshi Nakayama, Keiko Ooyama, Hiroshi Ooyama, Toru Shimizu, Miki Ueno, Toshimitsu Ito, Takashi Tamura, Mariko Naito, Hiroshi Nakashima, Makoto Kawaguchi, Mikiya Takao, Yosuke Kawai, Naoki Osada, Kimiyoshi Ichida, Ken Yamamoto, Hiroshi Suzuki, Nariyoshi Shinomiya, Ituro Inoue, Tappei Takada, Hirotaka Matsuo

  Annals of the rheumatic diseases 79 1 164 - 166 2020年01月 [査読有り][通常論文]
  
• Achiasmy and sex chromosome evolution

  Kazuhiro Satomura, Naoki Osada, Toshinori Endo

  Ecological Genetics and Genomics 13 100045  2019年09月 [査読有り][通常論文]
  
• Genetic diversity and population structure of Glossina morsitans morsitans in the active foci of human African trypanosomiasis in Zambia and Malawi

  Yukiko Nakamura, Junya Yamagishi, Kyoko Hayashida, Naoki Osada, Elisha Chatanga, Cornelius Mweempwa, Kalinga Chilongo, John Chisi, Jenelisa Musaya, Ryosuke Omori, Noboru Inoue, Boniface Namangala, Chihiro Sugimoto

  PLoS Negl. Trop. Dis. 13 7 e0007568  2019年07月 [査読有り][通常論文]
  
• Key metabolic gene for recurrent freshwater colonization and radiation in fishes

  Asano Ishikawa, Naoki Kabeya, Koki Ikeya, Ryo Kakioka, Jennifer N. Cech, Naoki Osada, Miguel C. Leal, Jun Inoue, Manabu Kume, Atsushi Toyoda, Ayumi Tezuka, Atsushi J. Nagano, Yo Y. Yamasaki, Yuto Suzuki, Tomoyuki Kokita, Hiroshi Takahashi, Kay Lucek, David Marques, Yusuke Takehana, Kiyoshi Naruse, Seiichi Mori, Oscar Monroig, Nemiah Ladd, Carsten J. Schubert, Blake Matthews, Catherine L. Peichel, Ole Seehausen, Goro Yoshizaki, Jun Kitano

  Science 364 6443 886 - 889 2019年05月 [査読有り][通常論文]
   

  Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and radiated in freshwater habitats, but not in close relatives that failed to colonize. Transgenic manipulation of Fads2 in marine stickleback increased their ability to synthesize DHA and survive on DHA-deficient diets. Multiple freshwater ray-finned fishes also show a convergent increase in Fads2 copies, indicating its key role in freshwater colonization.
• Novel endogenous simian retroviral integrations in Vero cells: Implications for quality control of a human vaccine cell substrate

  Chisato Sakuma, Tsuyoshi Sekizuka, Makoto Kuroda, Fumio Kasai, Kyoko Saito, Masaki Ikeda, Toshiyuki Yamaji, Naoki Osada, Kentaro Hanada

  Scientific Reports 8 1 644  2018年12月01日 [査読有り][通常論文]
   

  African green monkey (AGM)-derived Vero cells have been utilized to produce various human vaccines. The Vero cell genome harbors a variety of simian endogenous type D retrovirus (SERV) sequences. In this study, a transcriptome analysis showed that DNA hypomethylation released the epigenetic repression of SERVs in Vero cells. Moreover, comparative genomic analysis of three Vero cell sublines and an AGM reference revealed that the genomes of the sublines have ~80 SERV integrations. Among them, ~60 integrations are present within all three cell sublines and absent from the reference sequence. At least several of these integrations consist of complete SERV proviruses. These results strongly suggest that SERVs integrated in the genome of Vero cells did not retrotranspose after the establishment of the cell lineage as far as cells were maintained under standard culture and passage conditions, providing a scientific basis for controlling the quality of pharmaceutical cell substrates and their derived biologics.
• Comprehensive phylogenomic analysis reveals a novel cluster of simian endogenous retroviral sequences in Colobinae monkeys

  Masaki Ikeda, Kazuhiro Satomura, Tsuyoshi Sekizuka, Kentaro Hanada, Toshinori Endo, Naoki Osada

  American Journal of Primatology e22882  2018年06月 [査読有り][通常論文]
  
• Development of genotyping method for functionally relevant variants of cytochromes P450 in cynomolgus macaques

  Y. Uno, N. Osada, S. Sakurai, N. Shimozawa, T. Iwata, K. Ikeo, H. Yamazaki

  Journal of Veterinary Pharmacology and Therapeutics 41 1 e30 - e34 2018年02月01日 [査読有り][通常論文]
   

  In cynomolgus macaques (Macaca fascicularis), widely used in drug metabolism studies, CYP2C9, CYP2C76, CYP2D6, CYP3A4, and CYP3A5, important drug-metabolizing enzymes, are abundantly expressed in liver and metabolize cytochrome P450 substrates. CYP2C9 (c.334A> C), CYP2C76 (c.449TG> A), CYP2D6 (c.891A> G), CYP3A4 (IVS3 + 1G> del), and CYP3A5 (c.625A> T) substantially influence metabolic activity of enzymes, and thus are important variants in drug metabolism studies. In this study, a real-time PCR method was developed for genotyping these variants. The validity of the methods was verified by genotyping two wild type, two heterozygous, and two homozygous DNAs and was used to genotype 41 cynomolgus macaques (from Cambodia, Indonesia, the Philippines, or Vietnam) for the five variants, along with another important variant CYP2C19 (c.308C> T). The CYP2C9 and CYP2C19 variants were found only in Cambodian and Vietnamese animals, while the CYP2C76 and CYP2D6 variants were found only in Indonesian and Philippine animals. The CYP3A4 and CYP3A5 variants were not found in any of the animals analyzed. Mauritian animals, genotyped using next-generation sequencing data for comparison, possessed the CYP2C19 and CYP2D6 variants, but not the other variants. These results indicated differences in prevalence of these important variants among animal groups. Therefore, the genotyping tool developed is useful for drug metabolism studies using cynomolgus macaques.
• Ancient hybridization and admixture in macaques (genus Macaca) inferred from whole genome sequences.

  Fan, Zhenxin, Anbo Zhou, Naoki Osada, Jianqiu Yu, Juan Jiang, Peng Li, Lianming Du, Lili Niu, Jiabo Deng, Huailiang Xu, Jinchuan Xing, Bisong Yue, Jing Li

  Molecular Phylogenetics and Evolution 127 376 - 387 2018年 [査読有り][通常論文]
  
• Cis- and Trans-regulatory Effects on Gene Expression in a Natural Population of Drosophila melanogaster

  Naoki Osada, Ryutaro Miyagi, Aya Takahashi

  GENETICS 206 4 2139 - 2148 2017年08月 [査読有り][通常論文]
   

  Cis- and trans-regulatory mutations are important contributors to transcriptome evolution. Quantifying their relative contributions to intraspecific variation in gene expression is essential for understanding the population genetic processes that underlie evolutionary changes in gene expression. Here, we have examined this issue by quantifying genome-wide, allele-specific expression (ASE) variation using a crossing scheme that produces F-1 hybrids between 18 different Drosophila melanogaster strains sampled from the Drosophila Genetic Reference Panel and a reference strain from another population. Head and body samples from F1 adult females were subjected to RNA sequencing and the subsequent ASE quantification. Cis- and trans-regulatory effects on expression variation were estimated from these data. A higher proportion of genes showed significant cis-regulatory variation (similar to 28%) than those that showed significant trans-regulatory variation (similar to 9%). The sizes of cis-regulatory effects on expression variation were 1.98 and 1.88 times larger than trans-regulatory effects in heads and bodies, respectively. A generalized linear model analysis revealed that both cis- and trans-regulated expression variation was strongly associated with nonsynonymous nucleotide diversity and tissue specificity. Interestingly, trans-regulated variation showed a negative correlation with local recombination rate. Also, our analysis on proximal transposable element (TE) insertions suggested that they affect transcription levels of ovary-expressed genes more pronouncedly than genes not expressed in the ovary, possibly due to defense mechanisms against TE mobility in the germline. Collectively, our detailed quantification of ASE variations from a natural population has revealed a number of new relationships between genomic factors and the effects of cis- and trans-regulatory factors on expression variation.
• A Generalized Linear Model for Decomposing Cis-regulatory, Parent-of-Origin, and Maternal Effects on Allele-Specific Gene Expression

  Yasuaki Takada, Ryutaro Miyagi, Aya Takahashi, Toshinori Endo, Naoki Osada

  G3-GENES GENOMES GENETICS 7 7 2227 - 2234 2017年07月 [査読有り][通常論文]
   

  Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles in the developmental process of mammals and flowering plants. However, the influence of these effects on gene expression are difficult to quantify because they act simultaneously with cis-regulatory mutations. Here we propose a simple method to decompose cis-regulatory (i.e., allelic genotype), genomic imprinting [i.e., parent-of-origin (PO)], and maternal [i.e., maternal genotype (MG)] effects on allele-specific gene expression using RNA-seq data obtained from reciprocal crosses. We evaluated the efficiency of method using a simulated dataset and applied the method to whole-body Drosophila and mouse trophoblast stem cell (TSC) and liver RNA-seq data. Consistent with previous studies, we found little evidence of PO and MG effects in adult Drosophila samples. In contrast, we identified dozens and hundreds of mouse genes with significant PO and MG effects, respectively. Interestingly, a similar number of genes with significant PO effect were detect in mouse TSCs and livers, whereas more genes with significant MG effect were observed in livers. Further application of this method will clarify how these three effects influence gene expression levels in different tissues and developmental stages, and provide novel insight into the evolution of gene expression regulation.
• Translational Repression of a Splice Variant of Cynomolgus Macaque CXCL1L by Its C-Terminal Sequence

  Hisayuki Nomiyama, Naoki Osada, Ichiro Takahashi, Keiji Terao, Kazuya Yamagata, Osamu Yoshie

  JOURNAL OF INTERFERON AND CYTOKINE RESEARCH 37 3 129 - 138 2017年03月 [査読有り][通常論文]
   

  We previously isolated a cDNA clone from cynomolgus macaque encoding a novel CXC chemokine that we termed CXCL1L from its close similarity to CXCL1. However, the cDNA consisted of 3 exons instead of 4 exons that were typically seen in other CXC chemokines. Here, we isolated a cDNA encoding the full-length variant of CXCL1L that we termed CXCL1L beta. CXCL1L beta is 50 amino acids longer than the original CXCL1L, which we now term CXCL1L alpha. The CXCL1L beta mRNA is much more abundantly expressed in the cynomolgus macaque tissues than CXCL1L alpha mRNA. However, CXCL1L beta protein was poorly produced by transfected cells compared with that of CXCL1L alpha. When the coding region of the fourth exon was fused to the C-terminus of CXCL1 or even to a nonsecretory protein firefly luciferase, the fused proteins were also barely produced, although the mRNAs were abundantly expressed. The polysome profiling analysis suggested that the inhibition was mainly at the translational level. Furthermore, we demonstrated that the C-terminal 5 amino acids of CXCL1L beta were critical for the translational repression. The present study, thus, reveals a unique translational regulation controlling the production of a splicing variant of CXCL1L. Since the CXCL1L gene is functional only in the Old World monkeys, we also discuss possible reasons for the conservation of the active CXCL1L gene in these monkeys during the primate evolution.
• Compensatory Evolution

  Naoki Osada

  Encyclopedia of Evolutionary Biology 1 329 - 333 2016年05月 [査読有り][招待有り]
  
• 旧世界ザルにおけるサルレトロウイルスの内在化に関する進化系統解析

  池田 昌輝, 遠藤 俊徳, 長田 直樹

  霊長類研究 Supplement 32 59 - 59 日本霊長類学会 2016年 

  旧世界ザルのゲノムには、サルレトロウイルス（SRV）と相同なDNA塩基配列を持つ内在性サルレトロウイルス（SERV）のDNA塩基配列が存在することが知られている。SERVの多くは挿入や欠損などを含んだ不完全な状態でゲノムに存在するが、一部は完全な状態を保っていることが報告されている。また、不完全なSERV配列が組換えを起こすことによって完全な状態になり感染性を再獲得する可能性がある。さらに、旧世界ザルの細胞は細胞製材として使用されているため、SERV感染の可能性は医学的にも非常に重要な問題であるが、SERVが旧世界ザルのゲノム中にどのように分布、進化したかは明らかになっていない。これらの問題に答えるために本研究では、アフリカミドリザル（Chlorocebus sabaeus）、アカゲザル（Macaca mulatta）、アヌビスヒヒ（Papio anubis）、ヒト（Homo sapiens）のゲノム配列に存在するSERV配列を網羅的に探索し、それらの配列を用いて分子系統学的解析を行った。解析は、系統樹作成や同義置換率と非同義置換率の計算を行った。マルチプルアライメントの結果から、旧世界ザルのゲノムに存在する一部のSERVは、全てのタンパク質をコードしている状態でゲノム上に存在していることがわかった。また、得られた系統樹から、SRVとSERVは2つのクラスターに分かれていることもわかった。さらに、探索して得られた塩基配列の非同義置換率と同義置換率を調べて機能的制約の有無を確認したところ、挿入や欠損を含まない塩基配列は機能的制約を受けていることがわかった。解析の結果から、旧世界ザルのゲノム上に完全な状態で存在する内在性サルレトロウイルスは、過去に感染したSRVが機能を失われないままの状態で残っている可能性が示唆された。

• Complex patterns of cis-regulatory polymorphisms in ebony underlie standing pigmentation variation in Drosophila melanogaster

  Ryutaro Miyagi, Noriyoshi Akiyama, Naoki Osada, Aya Takahashi

  MOLECULAR ECOLOGY 24 23 5829 - 5841 2015年12月 [査読有り][通常論文]
   

  Pigmentation traits in adult Drosophila melanogaster were used in this study to investigate how phenotypic variations in continuous ecological traits can be maintained in a natural population. First, pigmentation variation in the adult female was measured at seven different body positions in 20 strains from the Drosophila melanogaster Genetic Reference Panel(DGRP) originating from a natural population in North Carolina. Next, to assess the contributions of cis-regulatory polymorphisms of the genes involved in the melanin biosynthesis pathway, allele-specific expression levels of four genes were quantified by amplicon sequencing using a 454 GS Junior. Among those genes, ebony was significantly associated with pigmentation intensity of the thoracic segment. Detailed sequence analysis of the gene regulatory regions of this gene indicated that many different functional cis-regulatory alleles are segregating in the population and that variations outside the core enhancer element could potentially play important roles in the regulation of gene expression. In addition, a slight enrichment of distantly associated SNP pairs was observed in the similar to 10kb cis-regulatory region of ebony, which suggested the presence of interacting elements scattered across the region. In contrast, sequence analysis in the core cis-regulatory region of tan indicated that SNPs within the region are significantly associated with allele-specific expression level of this gene. Collectively, the data suggest that the underlying genetic differences in the cis-regulatory regions that control intraspecific pigmentation variation can be more complex than those of interspecific pigmentation trait differences, where causal genetic changes are typically confined to modular enhancer elements.
• An Individual-Based Diploid Model Predicts Limited Conditions Under Which Stochastic Gene Expression Becomes Advantageous

  Tomotaka Matsumoto, Katsuhiko Mineta, Naoki Osada, Hitoshi Araki

  FRONTIERS IN GENETICS 6 336  2015年11月 [査読有り][通常論文]
   

  Recent studies suggest the existence of a stochasticity in gene expression (SGE) in many organisms, and its non-negligible effect on their phenotype and fitness. To date, however, how SGE affects the key parameters of population genetics are not well understood. SGE can increase the phenotypic variation and act as a load for individuals, if they are at the adaptive optimum in a stable environment. On the other hand, part of the phenotypic variation caused by SGE might become advantageous if individuals at the adaptive optimum become genetically less adaptive, for example due to an environmental change. Furthermore, SGE of unimportant genes might have little or no fitness consequences. Thus, SGE can be advantageous, disadvantageous, or selectively neutral depending on its context. In addition, there might be a genetic basis that regulates magnitude of SGE, which is often referred to as "modifier genes," but little is known about the conditions under which such an SGE-modifier gene evolves. In the present study, we conducted individual-based computer simulations to examine these conditions in a diploid model. In the simulations, we considered a single locus that determines organismal fitness for simplicity, and that SGE on the locus creates fitness variation in a stochastic manner. We also considered another locus that modifies the magnitude of SGE. Our results suggested that SGE was always deleterious in stable environments and increased the fixation probability of deleterious mutations in this model. Even under frequently changing environmental conditions, only very strong natural selection made SGE adaptive. These results suggest that the evolution of SGE-modifier genes requires strict balance among the strength of natural selection, magnitude of SGE, and frequency of environmental changes. However, the degree of dominance affected the condition under which SGE becomes advantageous, indicating a better opportunity for the evolution of SGE in different genetic models.
• Genetic diversity in humans and non-human primates and its evolutionary consequences

  Naoki Osada

  Genes and Genetic Systems 90 3 133 - 145 2015年10月27日 [査読有り][招待有り]
   

  Genetic diversity is a key parameter in population genetics and is important for understanding the process of evolution and for the development of appropriate conservation strategies. Recent advances in sequencing technology have enabled the measurement of genetic diversity of various organisms at the nucleotide level and on a genome-wide scale, yielding more precise estimates than were previously achievable. In this review, I have compiled and summarized the estimates of genetic diversity in humans and non-human primates based on recent genome-wide studies. Although studies on population genetics demonstrated fluctuations in population sizes over time, general patterns have emerged. As shown previously, genetic diversity in humans is one of the lowest among primates however, certain other primate species exhibit genetic diversity that is comparable to or even lower than that in humans. There exists greater than 10-fold variation in genetic diversity among primate species, and I found weak correlation with species fecundity but not with body or propagule size. I further discuss the potential evolutionary consequences of population size decline on the evolution of primate species. The level of genetic diversity negatively correlates with the ratio of non-synonymous to synonymous polymorphisms in a population, suggesting that proportionally greater numbers of slightly deleterious mutations segregate in small rather than large populations. Although population size decline is likely to promote the fixation of slightly deleterious mutations, there are molecular mechanisms, such as compensatory mutations at various molecular levels, which may prevent fitness decline at the population level. The effects of slightly deleterious mutations from theoretical and empirical studies and their relevance to conservation biology are also discussed in this review.
• CYP2D44 polymorphisms in cynomolgus and rhesus macaques

  Yasuhiro Uno, Shotaro Uehara, Sakae Kohara, Naoki Osada, Norie Murayama, Hiroshi Yamazaki

  MOLECULAR BIOLOGY REPORTS 42 7 1149 - 1155 2015年07月 [査読有り][通常論文]
   

  Macaques, including cynomolgus and rhesus macaques, are important animal species used in drug metabolism studies. CYP2D44 is expressed in cynomolgus macaque liver and encodes a functional drug metabolizing enzyme, metabolizing typical human CYP2D substrates such as bufuralol and dextromethorphan. CYP2D44 is highly homologous to human CYP2D6 that is known to be polymorphic with a large inter-individual variation in metabolic activities, however, genetic polymorphisms have not been investigated in macaque CYP2D44. In the present study, screening of 78 cynomolgus and 40 rhesus macaques found a total of 67 variants, including 64 non-synonymous variants, 1 nonsense mutation, and 2 frameshift mutations, and 1 gene conversion, of which 14, 19, and 15 variants were unique to Indochinese cynomolgus macaques, Indonesian cynomolgus macaques, and Chinese rhesus macaques, respectively. Eleven of the 64 non-synonymous variants were located in substrate recognition sites, the regions important for protein function. By site-directed mutagenesis and metabolic assays, S175N, V185L, A235G, R242G, R245K, and N337D showed substantially decreased activity in bufuralol 1'-hydroxylation as compared with wild-type proteins. Moreover, two null alleles (c.128T > del and c.664G > T) were found in Indonesian cynomolgus macaques, but not in Indochinese cynomolgus macaques or Chinese rhesus macaques. These results suggest that genetic polymorphisms might account for the variability of CYP2D44-dependent metabolism in macaques.
• Model-Based Verification of Hypotheses on the Origin of Modern Japanese Revisited by Bayesian Inference Based on Genome-Wide SNP Data

  Shigeki Nakagome, Takehiro Sato, Hajime Ishida, Tsunehiko Hanihara, Tetsutaro Yamaguchi, Ryosuke Kimura, Shuhei Mano, Hiroki Oota

  MOLECULAR BIOLOGY AND EVOLUTION 32 6 1533 - 1543 2015年06月 [査読有り][通常論文]
   

  Various hypotheses for the peopling of the Japanese archipelago have been proposed, which can be classified into three models: transformation, replacement, and hybridization. In recent years, one of the hybridization models ("dual-structure model") has been widely accepted. According to this model, Neolithic hunter-gatherers known as Jomon, who are assumed to have originated in southeast Asia and lived in the Japanese archipelago greater than 10,000 years ago, admixed with an agricultural people known as Yayoi, whom were migrants from the East Asian continent 2,000-3,000 years ago. Meanwhile, some anthropologists propose that rather, morphological differences between the Jomon and Yayoi people can be explained by microevolution following the lifestyle change. To resolve this controversy, we compared three demographic models by approximate Bayesian computation using genome-wide single nucleotide polymorphism (gwSNP) data from the Ainu people who are thought to be direct descendants of indigenous Jomon. If we assume Chinese people sampled in Beijing from HapMap have the same ancestry as Yayoi, then the hybridization model is predicted to be between 29 and 63 times more likely than the replacement and transformation models, respectively. Furthermore, our data provide strong support for a model in which the Jomon lineages had population structure diversified in local areas before the admixture event. Initial divergence between the Jomon and Yayoi ancestries was dated to late Pleistocene, followed by the divergence of Jomon lineages at early Holocene. These results suggest gwSNP data provides a detailed picture of the complex hybridization model for Japanese population history.
• Population genetics of non-genetic traits: Evolutionary roles of stochasticity in gene expression

  Katsuhiko Mineta, Tomotaka Matsumoto, Naoki Osada, Hitoshi Araki

  GENE 562 1 16 - 21 2015年05月 [査読有り][通常論文]
   

  The role of stochasticity in evolutionary genetics has long been debated. To date, however, the potential roles of non-genetic traits in evolutionary processes have been largely neglected. In molecular biology, growing evidence suggests that stochasticity in gene expression (SGE) is common and that SGE has major impacts on phenotypes and fitness. Here, we provide a general overview of the potential effects of SGE on population genetic parameters, arguing that SGE can indeed have a profound effect on evolutionary processes. Our analyses suggest that SGE potentially alters the fate of mutations by influencing effective population size and fixation probability. In addition, a genetic control of SGE magnitude could evolve under certain conditions, if the fitness of the less-fit individual increases due to SGE and environmental fluctuation. Although empirical evidence for our arguments is yet to come, methodological developments for precisely measuring SGE in living organisms will further advance our understanding of SGE-driven evolution. (C) 2015 Elsevier B.V. All rights reserved.
• Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts

  Chao-Li Huang, Pei-Hua Pu, Hao-Jen Huang, Huang-Mo Sung, Hung-Jiun Liaw, Yi-Min Chen, Chien-Ming Chen, Ming-Ban Huang, Naoki Osada, Takashi Gojobori, Tun-Wen Pai, Yu-Tin Chen, Chi-Chuan Hwang, Tzen-Yuh Chiang

  BMC GENOMICS 16 188  2015年03月 [査読有り][通常論文]
   

  Background: Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in Xanthomonas pathogenic to various plants. Results: Using whole-genome sequences, we examined the genetic divergence in Xanthomonas campestris that infected Brassicaceae, and X. citri, pathogenic to a wider host range. Genetic differentiation between two incipient races of X. citri pv. mangiferaeindicae was attributable to a DNA fragment introduced by phages. In contrast to most portions of the genome that had nearly equivalent levels of genetic divergence between subspecies as a result of the accumulation of point mutations, 10% of the core genome involving with homologous recombination contributed to the diversification in Xanthomonas, as revealed by the correlation between homologous recombination and genomic divergence. Interestingly, 179 genes were under positive selection; 98 (54.7%) of these genes were involved in homologous recombination, indicating that foreign genetic fragments may have caused the adaptive diversification, especially in lineages with nutritional transitions. Homologous recombination may have provided genetic materials for the natural selection, and host shifts likely triggered ecological adaptation in Xanthomonas. To a certain extent, we observed positive selection nevertheless contributed to ecological divergence beyond host shifting. Conclusion: Altogether, mediated with lasting gene flow, species formation in Xanthomonas was likely governed by natural selection that played a key role in helping the deviating populations to explore novel niches (hosts) or respond to environmental cues, subsequently triggering species diversification.
• Whole-Genome Sequencing of Six Mauritian Cynomolgus Macaques (Macaca fascicularis) Reveals a Genome-Wide Pattern of Polymorphisms under Extreme Population Bottleneck

  Naoki Osada, Nilmini Hettiarachchi, Isaac Adeyemi Babarinde, Naruya Saitou, Antoine Blancher

  GENOME BIOLOGY AND EVOLUTION 7 3 821 - 830 2015年03月 [査読有り][通常論文]
   

  Cynomolgus macaques (Macaca fascicularis) were introduced to the island of Mauritius by humans around the 16th century. The unique demographic history of the Mauritian cynomolgus macaques provides the opportunity to not only examine the genetic background of well-established nonhuman primates for biomedical research but also understand the effect of an extreme population bottleneck on the pattern of polymorphisms in genomes. We sequenced the whole genomes of six Mauritian cynomolgus macaques and obtained an average of 20-fold coverage of the genome sequences for each individual. The overall level of nucleotide diversity was23% smaller than that of the Malaysian cynomolgus macaques, and a reduction of low-frequency polymorphisms was observed. In addition, we also confirmed that the Mauritian cynomolgus macaques were genetically closer to a representative of the Malaysian population than to a representative of the Indochinese population. Excess of nonsynonymous polymorphisms in low frequency, which has been observed in many other species, was not very strong in the Mauritian samples, and the proportion of heterozygous nonsynonymous polymorphisms relative to synonymous polymorphisms is higher within individuals in Mauritian than Malaysian cynomolgus macaques. Those patterns indicate that the extreme population bottleneck made purifying selection overwhelmed by the power of genetic drift in the population. Finally, we estimated the number of founding individuals by using the genome-wide site frequency spectrum of the six samples. Assuming a simple demographic scenario with a single bottleneck followed by exponential growth, the estimated number of founders (similar to 20 individuals) is largely consistent with previous estimates.
• モーリシャス島産カニクイザルの全ゲノムシークエンス解析

  長田 直樹, HETTIARACHCHI Nilmini, BABARINDE Isaac Adeyemi, 斎藤 成也, BLANCHER Antoine

  霊長類研究 Supplement 31 58 - 58 日本霊長類学会 2015年 

  カニクイザル（Macaca fascicularis）は東南アジアに広く分布するサルであるが，インド洋に浮かぶモーリシャス島にも16世紀ごろ船乗りたちによって導入されたといわれている．これまでの遺伝学的研究により，モーリシャス島のカニクイザルの遺伝的多様性はおそらく起源となったジャワ島産のものよりも少ないことが知られていたが，ゲノムレベルでの解析は行われていなかった．モーリシャス島に持ち込まれたカニクイザル個体は恐らく非常に少数であったために，この例は，極端なボトルネックがゲノムの遺伝的多様性にどのような影響を与えるかについての興味深いケースとなりうる．われわれは，Illumina社HiSeqを用いて6個体のモーリシャス産カクニイザルのゲノム配列を一個体あたりおよそ20倍の被覆率で決定した．その結果，モーリシャス産カニクイザルの遺伝的多様性は，母集団に近いマレーシア産カニクイザルよりもおよそ2割程度低くなっていた．特に，低頻度の一塩基多型（SNP）が極端に減っており，少数の個体が島に持ち込まれたという事実に一致した．また，タンパク質をコードする遺伝子での同義変異と非同義変異の頻度分布パターンについて，サイズが一定の集団およびサイズが増加した集団で予想されるものとは異なったパターンが観察された．これらのパターンは，モーリシャス集団中での変異の頻度が淘汰よりも遺伝的浮動による強い影響を受けたことを示している．最後に，われわれは集団中の多型頻度スペクトラムを用いて，初期導入個体数の推定を行った．推定モデルによって幅は出るものの，最もシンプルなモデルではおよそ20個体程度と予想され，これまでの推定結果と大きく矛盾はしなかった．
• Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae)

  Chao-Li Huang, Chuan-Wen Ho, Yu-Chung Chiang, Yasumasa Shigemoto, Tsai-Wen Hsu, Chi-Chuan Hwang, Xue-Jun Ge, Charles Chen, Tai-Han Wu, Chang-Hung Chou, Hao-Jen Huang, Takashi Gojobori, Naoki Osada, Tzen-Yuh Chiang

  PLANT JOURNAL 80 5 834 - 847 2014年12月 [査読有り][通常論文]
   

  Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M=3.36x10(-9) to 1.20x10(-6), resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M.sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.
• The Genome Landscape of the African Green Monkey Kidney-Derived Vero Cell Line

  Naoki Osada, Arihiro Kohara, Toshiyuki Yamaji, Noriko Hirayama, Fumio Kasai, Tsuyoshi Sekizuka, Makoto Kuroda, Kentaro Hanada

  DNA RESEARCH 21 6 673 - 683 2014年12月 [査読有り][通常論文]
   

  Continuous cell lines that originate from mammalian tissues serve as not only invaluable tools for life sciences, but also important animal cell substrates for the production of various types of biological pharmaceuticals. Verocells are susceptible to various types of microbes and toxins and have widely contributed to not only microbiology, but also the production of vaccines for human use. We here showed the genome landscape of a Vero cell line, in which 25,877 putative protein-coding genes were identified in the 2.97-Gb genome sequence. A homozygous similar to 9-Mb deletion on chromosome 12 caused the loss of the type I interferon gene cluster and cyclin-dependent kinase inhibitor genes in Vero cells. In addition, an similar to 59-Mb loss of heterozygosity around this deleted region suggested that the homozygosity of the deletion was established by a large-scale conversion. Moreover, a genomic analysis of Vero cells revealed a female Chlorocebus sabaeus origin and proviral variations of the endogenous simian type D retrovirus. These results revealed the genomic basis for the non-tumourigenic permanent Vero cell lineage susceptible to various pathogens and will be useful for generating new sub-lines and developing new tools in the quality control of Vero cells.
• Dopamine Receptor Genes and Evolutionary Differentiation in the Domestication of Fighting Cocks and Long-Crowing Chickens

  Tomoyoshi Komiyama, Hisakazu Iwama, Naoki Osada, Yoji Nakamura, Hiroyuki Kobayashi, Yoshio Tateno, Takashi Gojobori

  PLOS ONE 9 7 e101778  2014年07月 [査読有り][通常論文]
   

  The chicken domestication process represents a typical model of artificial selection, and gives significant insight into the general understanding of the influence of artificial selection on recognizable phenotypes. Two Japanese domesticated chicken varieties, the fighting cock (Shamo) and the long-crowing chicken (Naganakidori), have been selectively bred for dramatically different phenotypes. The former has been selected exclusively for aggressiveness and the latter for long crowing with an obedient sitting posture. To understand the particular mechanism behind these genetic changes during domestication, we investigated the degree of genetic differentiation in the aforementioned chickens, focusing on dopamine receptor D2, D3, and D4 genes. We studied other ornamental chickens such as Chabo chickens as a reference for comparison. When genetic differentiation was measured by an index of nucleotide differentiation (N-ST) newly devised in this study, we found that the N-ST value of DRD4 for Shamo (0.072) was distinctively larger than those of the other genes among the three populations, suggesting that aggressiveness has been selected for in Shamo by collecting a variety of single nucleotide polymorphisms. In addition, we found that in DRD4 in Naganakidori, there is a deletion variant of one proline at the 24th residue in the repeat of nine prolines of exon 1. We thus conclude that artificial selection has operated on these different kinds of genetic variation in the DRD4 genes of Shamo and Naganakidori so strongly that the two domesticated varieties have differentiated to obtain their present opposite features in a relatively short period of time.
• Prdm9 Polymorphism Unveils Mouse Evolutionary Tracks

  Hiromitsu Kono, Masaru Tamura, Naoki Osada, Hitoshi Suzuki, Kuniya Abe, Kazuo Moriwaki, Kunihiro Ohta, Toshihiko Shiroishi

  DNA RESEARCH 21 3 315 - 326 2014年06月 [査読有り][通常論文]
   

  PR/SET domain containing 9 (Prdm9) mediates histone modifications such as H3K4me3 and marks hotspots of meiotic recombination. In many mammalian species, the Prdm9 gene is highly polymorphic. Prdm9 polymorphism is assumed to play two critical roles in evolution: to diversify the spectrum of meiotic recombination hotspots and to cause male hybrid sterility, leading to reproductive isolation and speciation. Nevertheless, information about Prdm9 sequences in natural populations is very limited. In this study, we conducted a comprehensive population survey on Prdm9 polymorphism in the house mouse, Mus musculus. Overall M. musculus Prdm9 displays an extraordinarily high level of polymorphism, particularly in regions encoding zinc finger repeats, which recognize recombination hotspots. Prdm9 alleles specific to various M. musculus subspecies dominate in subspecies territories. Moreover, introgression into other subspecies territories was found for highly divergent Prdm9 alleles associated with t-haplotype. The results of our phylogeographical analysis suggest that the requirement for hotspot diversity depends on geographical range and time span in mouse evolution, and that Prdm9 polymorphism has not been maintained by a simple balanced selection in the population of each subspecies.
• Whole-Genome Sequencing of Tibetan Macaque (Macaca thibetana) Provides New Insight into the Macaque Evolutionary History

  Zhenxin Fan, Guang Zhao, Peng Li, Naoki Osada, Jinchuan Xing, Yong Yi, Lianming Du, Pedro Silva, Hongxing Wang, Ryuichi Sakate, Xiuyue Zhang, Huailiang Xu, Bisong Yue, Jing Li

  MOLECULAR BIOLOGY AND EVOLUTION 31 6 1475 - 1489 2014年06月 [査読有り][通常論文]
   

  Macaques are the most widely distributed nonhuman primates and used as animal models in biomedical research. The availability of full-genome sequences from them would be essential to both biomedical and primate evolutionary studies. Previous studies have reported whole-genome sequences from rhesus macaque (Macaca mulatta) and cynomolgus macaque (M. fascicularis, CE), both of which belong to the fascicularis group. Here, we present a 37-fold coverage genome sequence of the Tibetan macaque (M. thibetana; TM). TM is an endemic species to China belonging to the sinica group. On the basis of mapping to the rhesus macaque genome, we identified approximately 11.9 million single-nucleotide variants), of which 3.9 million were TM specific, as assessed by comparison two Chinese rhesus macaques (CR) and two CE genomes. Some genes carried TM-specific homozygous nonsynonymous variants (TSHNVs), which were scored as deleterious in human by both PolyPhen-2 and SIFT (Sorting Tolerant From Intolerant) and were enriched in the eye disease genes. In total, 273 immune response and disease-related genes carried at least one TSHNV. The heterozygosity rates of two CRs (0.002617 and 0.002612) and two CEs (0.003004 and 0.003179) were approximately three times higher than that of TM (0.000898). Polymerase chain reaction resequencing of 18 TM individuals showed that 29 TSHNVs exhibited high allele frequencies, thus confirming their low heterozygosity. Genome-wide genetic divergence analysis demonstrated that TM was more closely related to CR than to CE. We further detected unusual low divergence regions between TM and CR. In addition, after applying statistical criteria to detect putative introgression regions (PIRs) in the TM genome, up to 239,620 kb PIRs (8.84% of the genome) were identified. Given that TM and CR have overlapping geographical distributions, had the same refuge during the Middle Pleistocene, and show similar mating behaviors, it is highly likely that there was an ancient introgression event between them. Moreover, demographic inferences revealed that TM exhibited a similar demographic history as other macaques until 0.5 Ma, but then it maintained a lower effective population size until present time. Our study has provided new insight into the macaque evolutionary history, confirming hybridization events between macaque species groups based on genome-wide data.
• Extracting population genetics information from a diploid genome sequence

  Naoki Osada

  Frontiers in Ecology and Evolution 2 7  2014年04月 [査読有り][通常論文]
  
• Finding the Factors of Reduced Genetic Diversity on X Chromosomes of Macaca fascicularis: Male-Driven Evolution, Demography, and Natural Selection

  Naoki Osada, Shigeki Nakagome, Shuhei Mano, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao

  GENETICS 195 3 1027 - + 2013年11月 [査読有り][通常論文]
   

  The ratio of genetic diversity on X chromosomes relative to autosomes in organisms with XX/XY sex chromosomes could provide fundamental insight into the process of genome evolution. Here we report this ratio for 24 cynomolgus monkeys (Macaca fascicularis) originating in Indonesia, Malaysia, and the Philippines. The average X/A diversity ratios in these samples was 0.34 and 0.20 in the Indonesian-Malaysian and Philippine populations, respectively, considerably lower than the null expectation of 0.75. A Philippine population supposed to derive from an ancestral population by founding events showed a significantly lower ratio than the parental population, suggesting a demographic effect for the reduction. Taking sex-specific mutation rate bias and demographic effect into account, expected X/A diversity ratios generated by computer simulations roughly agreed with the observed data in the intergenic regions. In contrast, silent sites in genic regions on X chromosomes showed strong reduction in genetic diversity and the observed X/A diversity ratio in the genic regions cannot be explained by mutation rate bias and demography, indicating that natural selection also reduces the level of polymorphism near genes. Whole-genome analysis of a female cynomolgus monkey also supported the notion of stronger reduction of genetic diversity near genes on the X chromosome.
• Systematic classification of vertebrate chemokines based on conserved synteny and evolutionary history

  Hisayuki Nomiyama, Naoki Osada, Osamu Yoshie

  GENES TO CELLS 18 1 1 - 16 2013年01月 [査読有り][通常論文]
   

  The genes involved in host defences are known to undergo rapid evolution. Therefore, it is often difficult to assign orthologs in multigene families among various vertebrate species. Chemokines are a large family of small cytokines that orchestrate cell migration in health and disease. Herein, we have surveyed the genomes of 18 representative vertebrate species for chemokine genes and identified a total of 553 genes. We have determined their orthologous relationships and classified them in accordance with the current systematic chemokine nomenclature system. Our study reveals an interesting evolutionary history that gave origin and diversification to the vertebrate chemokine superfamily.
• Weak Selection and Protein Evolution

  Hiroshi Akashi, Naoki Osada, Tomoko Ohta

  GENETICS 192 1 15 - U43 2012年09月 [査読有り][招待有り]
   

  The "nearly neutral" theory of molecular evolution proposes that many features of genomes arise from the interaction of three weak evolutionary forces: mutation, genetic drift, and natural selection acting at its limit of efficacy. Such forces generally have little impact on allele frequencies within populations from generation to generation but can have substantial effects on long-term evolution. The evolutionary dynamics of weakly selected mutations are highly sensitive to population size, and near neutrality was initially proposed as an adjustment to the neutral theory to account for general patterns in available protein and DNA variation data. Here, we review the motivation for the nearly neutral theory, discuss the structure of the model and its predictions, and evaluate current empirical support for interactions among weak evolutionary forces in protein evolution. Near neutrality may be a prevalent mode of evolution across a range of functional categories of mutations and taxa. However, multiple evolutionary mechanisms (including adaptive evolution, linked selection, changes in fitness-effect distributions, and weak selection) can often explain the same patterns of genome variation. Strong parameter sensitivity remains a limitation of the nearly neutral model, and we discuss concave fitness functions as a plausible underlying basis for weak selection.
• Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome

  Atsunori Higashino, Ryuichi Sakate, Yosuke Kameoka, Ichiro Takahashi, Makoto Hirata, Reiko Tanuma, Tohru Masui, Yasuhiro Yasutomi, Naoki Osada

  Genome Biology 13 7 2012年07月02日 [査読有り][通常論文]
   

  Background: The genetic background of the cynomolgus macaque (Macaca fascicularis) is made complex by the high genetic diversity, population structure, and gene introgression from the closely related rhesus macaque (Macaca mulatta). Herein we report the whole-genome sequence of a Malaysian cynomolgus macaque male with more than 40-fold coverage, which was determined using a resequencing method based on the Indian rhesus macaque genome.Results: We identified approximately 9.7 million single nucleotide variants (SNVs) between the Malaysian cynomolgus and the Indian rhesus macaque genomes. Compared with humans, a smaller nonsynonymous/synonymous SNV ratio in the cynomolgus macaque suggests more effective removal of slightly deleterious mutations. Comparison of two cynomolgus (Malaysian and Vietnamese) and two rhesus (Indian and Chinese) macaque genomes, including previously published macaque genomes, suggests that Indochinese cynomolgus macaques have been more affected by gene introgression from rhesus macaques. We further identified 60 nonsynonymous SNVs that completely differentiated the cynomolgus and rhesus macaque genomes, and that could be important candidate variants for determining species-specific responses to drugs and pathogens. The demographic inference using the genome sequence data revealed that Malaysian cynomolgus macaques have experienced at least three population bottlenecks.Conclusions: This list of whole-genome SNVs will be useful for many future applications, such as an array-based genotyping system for macaque individuals. High-quality whole-genome sequencing of the cynomolgus macaque genome may aid studies on finding genetic differences that are responsible for phenotypic diversity in macaques and may help control genetic backgrounds among individuals. © 2012 Higashino et al. licensee BioMed Central Ltd.
• Footprints of natural and artificial selection for photoperiod pathway genes in Oryza

  Chao-Li Huang, Cheng-Yu Hung, Yu-Chung Chiang, Chi-Chuan Hwang, Tsai-Wen Hsu, Chi-Chun Huang, Kuo-Hsiang Hung, Kun-Chan Tsai, Kuo-Hsiung Wang, Naoki Osada, Barbara Anna Schaal, Tzen-Yuh Chiang

  PLANT JOURNAL 70 5 769 - 782 2012年06月 [査読有り][通常論文]
   

  Asian rice, Oryza sativa, consists of two major subspecies, indica and japonica, which are physiologically differentiated and adapted to different latitudes. Genes for photoperiod sensitivity are likely targets of selection along latitude. We examined the footprints of natural and artificial selections for four major genes of the photoperiod pathway, namely PHYTOCHROME B (PhyB), HEADING DATE 1 (Hd1), HEADING DATE 3a (Hd3a), and EARLY HEADING DATE 1 (Ehd1), by investigation of the patterns of nucleotide polymorphisms in cultivated and wild rice. Geographical subdivision between tropical and subtropical O. rufipogon was found for all of the photoperiod genes in plants divided by the Tropic of Cancer (TOC). All of these genes, except for PhyB, were characterized by the existence of clades that split a long time ago and that corresponded to latitudinal subdivisions, and revealed a likely diversifying selection. Ssp. indica showed close affinity to tropical O. rufipogon for all genes, while ssp. japonica, which has a much wider range of distribution, displayed complex patterns of differentiation from O. rufipogon, which reflected various agricultural needs in relation to crop yield. In japonica, all genes, except Hd3a, were genetically differentiated at the TOC, while geographical subdivision occurred at 31 degrees N in Hd3a, probably the result of varying photoperiods. Many other features of the photoperiod genes revealed domestication signatures, which included high linkage disequilibrium (LD) within genes, the occurrence of frequent and recurrent non-functional Hd1 mutants in cultivated rice, crossovers between subtropical and tropical alleles of Hd1, and significant LD between Hd1 and Hd3a in japonica and indica.
• Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae)

  Chi-Chun Huang, Kuo-Hsiang Hung, Wei-Kuang Wang, Chuan-Wen Ho, Chao-Li Huang, Tsai-Wen Hsu, Naoki Osada, Chi-Chuan Hwang, Tzen-Yuh Chiang

  GENE 499 1 194 - 201 2012年05月 [査読有り][通常論文]
   

  Recovering the genetic divergence between species is one of the major interests in the evolutionary biology. It requires accurate estimation of the neutral substitution rates. Arabidopsis thaliana, the first whole-genome sequenced plant, and its out-crossing relatives provide an ideal model for examining the split between sister species. In the study, rates of molecular evolution at markers frequently used for systematics and population genetics, including 14 nuclear genes spanning most chromosomes, three noncoding regions of chloroplast genome, and one intron of mitochondrial genome. between A. thaliana and four relatives were estimated. No deviation from neutrality was detected in the genes examined. Based on the known divergence between A. thaliana and its sisters about 8.0-17.6 MYA, evolutionary rates of the eighteen genes were estimated. Accordingly, the ratio of rates of synonymous substitutions among mitochondrial, chloroplast and nuclear genes was calculated with an average and 95% confidence interval of 1 (0.25-1.75): 15.77 (7.48-114.09): 74.79 (36.27-534.61). Molecular evolutionary rates of nuclear genes varied, with a range of 0.383-0.856 x 10(-8) for synonymous substitutions per site per year and 0.036-0.081 x 10(-9) for nonsynonymous substitutions per site per year. Compared with orthologs in Populus, a long life-span tree, genes in Arabidopsis evolved faster in an order of magnitude at the gene level, agreeing with a generation time hypothesis. The estimated substitution rates of these genes can be used as a reference for molecular dating. (C) 2012 Elsevier B.V. All rights reserved.
• Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome

  Atsunori Higashino, Ryuichi Sakate, Yosuke Kameoka, Ichiro Takahashi, Makoto Hirata, Reiko Tanuma, Tohru Masui, Yasuhiro Yasutomi, Naoki Osada

  GENOME BIOLOGY 13 7 R58  2012年 [査読有り][通常論文]
   

  Background: The genetic background of the cynomolgus macaque (Macaca fascicularis) is made complex by the high genetic diversity, population structure, and gene introgression from the closely related rhesus macaque (Macaca mulatta). Herein we report the whole-genome sequence of a Malaysian cynomolgus macaque male with more than 40-fold coverage, which was determined using a resequencing method based on the Indian rhesus macaque genome. Results: We identified approximately 9.7 million single nucleotide variants (SNVs) between the Malaysian cynomolgus and the Indian rhesus macaque genomes. Compared with humans, a smaller nonsynonymous/synonymous SNV ratio in the cynomolgus macaque suggests more effective removal of slightly deleterious mutations. Comparison of two cynomolgus (Malaysian and Vietnamese) and two rhesus (Indian and Chinese) macaque genomes, including previously published macaque genomes, suggests that Indochinese cynomolgus macaques have been more affected by gene introgression from rhesus macaques. We further identified 60 nonsynonymous SNVs that completely differentiated the cynomolgus and rhesus macaque genomes, and that could be important candidate variants for determining species-specific responses to drugs and pathogens. The demographic inference using the genome sequence data revealed that Malaysian cynomolgus macaques have experienced at least three population bottlenecks. Conclusions: This list of whole-genome SNVs will be useful for many future applications, such as an array-based genotyping system for macaque individuals. High-quality whole-genome sequencing of the cynomolgus macaque genome may aid studies on finding genetic differences that are responsible for phenotypic diversity in macaques and may help control genetic backgrounds among individuals.
• Mitochondrial-Nuclear Interactions and Accelerated Compensatory Evolution: Evidence from the Primate Cytochrome c Oxidase Complex

  Naoki Osada, Hiroshi Akashi

  MOLECULAR BIOLOGY AND EVOLUTION 29 1 337 - 346 2012年01月 [査読有り][通常論文]
   

  Accelerated rates of mitochondrial protein evolution have been proposed to reflect Darwinian coadaptation for efficient energy production for mammalian flight and brain activity. However, several features of mammalian mtDNA (absence of recombination, small effective population size, and high mutation rate) promote genome degradation through the accumulation of weakly deleterious mutations. Here, we present evidence for "compensatory" adaptive substitutions in nuclear DNA- (nDNA) encoded mitochondrial proteins to prevent fitness decline in primate mitochondrial protein complexes. We show that high mutation rate and small effective population size, key features of primate mitochondrial genomes, can accelerate compensatory adaptive evolution in nDNA-encoded genes. We combine phylogenetic information and the 3D structure of the cytochrome c oxidase (COX) complex to test for accelerated compensatory changes among interacting sites. Physical interactions among mtDNA- and nDNA-encoded components are critical in COX evolution; amino acids in close physical proximity in the 3D structure show a strong tendency for correlated evolution among lineages. Only nuclear-encoded components of COX show evidence for positive selection and adaptive nDNA-encoded changes tend to follow mtDNA-encoded amino acid changes at nearby sites in the 3D structure. This bias in the temporal order of substitutions supports compensatory weak selection as a major factor in accelerated primate COX evolution.
• Characterization of MHC class I transcripts of a Malaysian cynomolgus macaque by high-throughput pyrosequencing and EST libraries

  Alice Aarnink, Pol-Andre Apoil, Ichiro Takahashi, Naoki Osada, Antoine Blancher

  IMMUNOGENETICS 63 11 703 - 713 2011年11月 [査読有り][通常論文]
   

  We characterized the repertoire of MHC class I transcripts of a Malaysian cynomolgus macaque by the study of EST libraries derived from the mRNA extracted from six tissues (thymus, spleen, bone marrow, liver, heart and pancreas). The MHC class I transcripts present in a lymph node of the same animal were characterized by pyrosequencing of amplified cDNA fragments (515 bp from exon 2 to the beginning of exon 4). All pyrosequence consensus sequences, but three corresponding to rare transcripts, were identical to those obtained from EST libraries. In total, we characterized 19 classical class I transcripts in the Malaysian macaque studied here. By means of high- throughput sequencing of exon 2 amplified from the genomic DNA (190 bp), we characterized 38 classical class I genes in the genome of this animal. By comparison, using the same method, we found 23 classical class I genes in the genome of a MHC homozygous Mauritian animal (H2/H2). All these results suggested that the Malaysian animal was most probably heterozygous. This study reveals that the high- throughput pyrosequencing allows not only to characterize the MHC class I transcripts but also to estimate the number of MHC class I genes in the genome of cynomolgus macaque.
• CpG site degeneration triggered by the loss of functional constraint created a highly polymorphic macaque drug-metabolizing gene, CYP1A2

  Yasuhiro Uno, Naoki Osada

  BMC EVOLUTIONARY BIOLOGY 11 283 - 283 2011年10月 [査読有り][通常論文]
   

  Background: Elucidating the pattern of evolutionary changes in drug-metabolizing genes is an important subject not only for evolutionary but for biomedical research. We investigated the pattern of divergence and polymorphisms of macaque CYP1A1 and CYP1A2 genes, which are major drug-metabolizing genes in humans. In humans, CYP1A2 is specifically expressed in livers while CYP1A1 has a wider gene expression pattern in extrahepatic tissues. In contrast, macaque CYP1A2 is expressed at a much lower level than CYP1A1 in livers. Interestingly, a previous study has shown that Macaca fascicularis CYP1A2 harbored unusually high genetic diversity within species. Genomic regions showing high genetic diversity within species is occasionally interpreted as a result of balancing selection, where natural selection maintains highly diverged alleles with different functions. Nevertheless many other forces could create such signatures. Results: We found that the CYP1A1/2 gene copy number and orientation has been highly conserved among mammalian genomes. The signature of gene conversion between CYP1A1 and CYP1A2 was detected, but the last gene conversion event in the simian primate lineage occurred before the Catarrhini-Platyrrhini divergence. The high genetic diversity of macaque CYP1A2 therefore cannot be explained by gene conversion between CYP1A1 and CYP1A2. By surveying CYP1A2 polymorphisms in total 91 M. fascicularis and M. mulatta, we found several null alleles segregating in these species, indicating functional constraint on CYP1A2 in macaques may have weakened after the divergence between humans and macaques. We propose that the high genetic diversity in macaque CYP1A2 is partly due to the degeneration of CpG sites, which had been maintained at a high level by purifying selection, and the rapid degeneration process was initiated by the loss of functional constraint on macaque CYP1A2. Conclusions: Our findings show that the highly polymorphic CYP1A2 gene in macaques has not been created by balancing selection but by the burst of CpG site degeneration after loss of functional constraint. Because the functional importance of CYP1A1/2 genes is different between humans and macaques, we have to be cautious in extrapolating a drug-testing data using substrates metabolized by CYP1A genes from macaques to humans, despite of their somewhat overlapping substrate specificity.
• Novel DNA sequence isolated from blood donors with high transaminase levels

  Koei Satoh, Akiko Iwata-Takakura, Naoki Osada, Akira Yoshikawa, Yuji Hoshi, Keiko Miyakawa, Yuko Gotanda, Masahiro Satake, Kenji Tadokoro, Hideaki Mizoguchi

  HEPATOLOGY RESEARCH 41 10 971 - 981 2011年10月 [査読有り][通常論文]
   

  Aim: In Japan, the etiology of 10-20% of cases of acute hepatitis remains unclarified. This study was conducted to verify the agent causing non-A-E hepatitis. Methods: Serum samples from 500 blood donors with elevated alanine aminotransferase (ALT) levels were screened by polymerase chain reaction using primers constructed from conserved areas of RNA virus helicase. The sequence obtained was investigated for viral properties. Results: Four blood samples were found to contain a novel DNA sequence of 9496 bp, which was designated KIs-V. KIs-V was sensitive to the restriction enzyme SalI and BstXI. Rolling-circle amplification produced an excessive amount of KIs-V DNA. In sucrose density gradient ultracentrifugation, KIs-V banded at a 1.158-g/cm(3) density. Detergent treatment increased the density of KIs-V. There was no KIs-V DNA amplification from human leukocyte DNA. Serial filtration suggested that KIs-V was included in a 30-50-nm size particle. In silico analysis revealed that KIs-V contained 13 potential genes, none of which showed homology to any viral proteins reported. One gene showed similarity to a DNA polymerase domain. Strong signals for transcription initiation and a CpG island were identified. The nucleotide composition of KIs-V showed a characteristic feature of circular DNA genomes that contain a replication origin and a terminus. In a preliminary study, KIs-V was frequently identified among hepatitis E virus antibody positive individuals with elevated ALT levels. Conclusion: A new sequence KIs-V was isolated from blood donors with elevated ALT levels. It was suggested that KIs-V is a double-stranded circular DNA genome derived from a novel category of enveloped viruses.
• Population Genetics in Nonmodel Organisms: II. Natural Selection in Marginal Habitats Revealed by Deep Sequencing on Dual Platforms

  Renchao Zhou, Shaoping Ling, Wenming Zhao, Naoki Osada, Sufang Chen, Meng Zhang, Ziwen He, Hua Bao, Cairong Zhong, Bing Zhang, Xuemei Lu, David Turissini, Norman C. Duke, Jian Lu, Suhua Shi, Chung-I Wu

  MOLECULAR BIOLOGY AND EVOLUTION 28 10 2833 - 2842 2011年10月 [査読有り][通常論文]
   

  Population genetics of species living in marginal habitats could be particularly informative about the genetics of adaptation, but such analyses have not been readily feasible until recently. Sonneratia alba, a mangrove species widely distributed in the Indo-West Pacific, provides a very suitable system for the study of local adaptation. In this study, we analyzed DNA variation by pooling 71 genes from 85-100 individuals for DNA sequencing. For each of the two nearby S. alba populations, we obtained similar to 2,500 x coverage on the Illumina GA platform and for the Sanya population, an additional 5,400 x coverage on the AB SOLiD platform. For the Sanya sample, although each sequencing method called many putative single nucleotide polymorphisms, the two sets of calls did not overlap, suggesting platform-dependent errors. Conventional sequencing corroborated that each population is monomorphic. The two populations differ by 54 bp of 79,000 sites, but 90% of the variants are found in 10% of the genes. Strong local adaptation and high migration may help to explain the extensive monomorphism shared by the two populations in the presence of a small number of highly differentiated loci.
• Phylogenetic Inconsistency Caused by Ancient Sex-Biased Gene Migration

  Naoki Osada

  PLOS ONE 6 9 e25549 - e25549 2011年09月 [査読有り][通常論文]
   

  Inferences of ancient sex-biased migration patterns using sex-linked genetic markers are usually difficult because of a stochastic process of allele fixation. Nevertheless, incongruent phylogenetic trees between different sex-linked markers and between sex-linked and autosomal markers are frequently interpreted as a signature of sex-biased migration without further statistical evaluation. I investigated the types of incongruent phylogenetic trees from which past sex-biased migration events can be statistically supported under the coalescent model. In the case of mammals, detecting a sex-biased migration pattern is not guaranteed by comparing the phylogenetic pattern of mitochondrial and Y-chromosomal loci Likewise, evidence of introgression at a mitochondrial locus, but not at autosomal loci, does not support the hypothesis of an ancient female-biased migration pattern with statistical significance. In contrast, evidence of introgression at >= 5 unlinked autosomal loci, but not at a Y-chromosomal locus, would reject the null hypothesis of a sexually equal migration ate with statistical significance. A similar argument can be made to infer a male-biased migration pattern. Furthermore, the Investigation of many recombining sex-biased markers such as X-chromosomal loci in mammals has the potential to efficiently detect ancient sex-biased demographic patterns.
• A family tree of vertebrate chemokine receptors for a unified nomenclature

  Hisayuki Nomiyama, Naoki Osada, Osamu Yoshie

  DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 35 7 705 - 715 2011年07月 [査読有り][通常論文]
   

  Chemokines receptors are involved in the recruitment of various cell types in inflammatory and physiological conditions. There are 23 known chemokine receptor genes in the human genome. However, it is still unclear how many chemokine receptors exist in the genomes of various vertebrate species other than human and mouse. Moreover, the orthologous relationships are often obscure between the genes of higher and lower vertebrates. In order to provide a basis for a unified nomenclature system of the vertebrate chemokine receptor gene family, we have analysed the chemokine receptor genes from the genomes of 16 vertebrate species, and classify them into 29 orthologous groups using phylogenetic and comparative genomic analyses. The results reveal a continuous gene birth and death process during the vertebrate evolution and an interesting evolutionary history of the chemokine receptor genes after the emergence in agnathans. (C) 2011 Elsevier Ltd. All rights reserved.
• The evolution of mammalian chemokine genes

  Hisayuki Nomiyama, Naoki Osada, Osamu Yoshie

  CYTOKINE & GROWTH FACTOR REVIEWS 21 4 253 - 262 2010年08月 [査読有り][通常論文]
   

  Chemokines play an important role in orchestrating cell recruitment and localization in both physiological and pathological conditions. More than 44 ligands have been identified in the human genome. A significantly different set of chemokines, however, is found in the mouse genome, suggesting a rapid evolution of the chemokine system in mammalian genomes. Thus, there are lineage and even individual-specific differences in chemokine genes in mammals. Differences in the expression and function between even recently duplicated genes are also evident. In this review, we discuss how evolutionary events such as gene duplication and gene conversion have shaped the diverse arrays of chemokines in mammalian genomes. (C) 2010 Elsevier Ltd. All rights reserved.
• Ancient genome-wide admixture extends beyond the current hybrid zone between Macaca fascicularis and M-mulatta

  Naoki Osada, Yasuhiro Uno, Katsuhiko Mineta, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao

  MOLECULAR ECOLOGY 19 14 2884 - 2895 2010年07月 [査読有り][通常論文]
   

  Macaca fascicularis and Macaca mulatta are two of the most commonly used laboratory macaques, yet their genetic differences at a genome-wide level remain unclear. We analysed the multilocus DNA sequence data of 54 autosomal loci obtained from M. fascicularis samples from three different geographic origins and M. mulatta samples of Burmese origin. M. fascicularis shows high nucleotide diversity, four to five times higher than humans, and a strong geographic population structure between Indonesian-Malaysian and Philippine macaques. The pattern of divergence and polymorphism between M. fascicularis and M. mulatta shows a footprint of genetic exchange not only within their current hybrid zone but also across a wider range for more than 1 million years. However, genetic admixture may not be a random event in the genome. Whereas randomly selected genic and intergenic regions have the same evolutionary dynamics between the species, some cytochrome oxidase P450 (CYP) genes (major chemical metabolizing genes and potential target genes for local adaptation) have a significantly larger species divergence than other genes. By surveying CYP3A5 gene sequences of more than a hundred macaques, we identified three nonsynonymous single nucleotide polymorphisms that were highly differentiated between the macaques. The mosaic pattern of species divergence in the genomes may be a consequence of genetic differentiation under ecological adaptation and may be a salient feature in the genomes of nascent species under parapatry.
• Genetic Variants of CYP3A4 and CYP3A5 in Cynomolgus and Rhesus Macaques

  Yasuhiro Uno, Akinori Matsushita, Naoki Osada, Shotaro Uehara, Sakae Kohara, Ryoichi Nagata, Koichiro Fukuzaki, Masahiro Utoh, Norie Murayama, Hiroshi Yamazaki

  DRUG METABOLISM AND DISPOSITION 38 2 209 - 214 2010年02月 [査読有り][通常論文]
   

  Cynomolgus and rhesus macaques are frequently used in preclinical trials due to their close evolutionary relationships to humans. We conducted an initial screening for genetic variants in cynomolgus and rhesus macaque genes orthologous to human CYP3A4 and CYP3A5. Genetic screening of 78 Indochinese and Indonesian cynomolgus macaques and 34 Chinese rhesus macaques revealed a combined total of 42 CYP3A4 genetic variants, including 12 nonsynonymous variants, and 34 CYP3A5 genetic variants, including nine nonsynonymous variants. Four of these nonsynonymous variants were located at substrate recognition sites or the heme-binding region, domains essential for protein function, including c. 886G>A (V296M) and c. 1310G>A (S437N) in CYP3A4 and c. 1437C>G (N479K) and c.1310G>C (T437S) in CYP3A5. The mutant proteins of these genetic variants were expressed in Escherichia coli and purified. Metabolic activity of these proteins measured using midazolam and nifedipine as substrates showed that none of these protein variants substantially influences the drug-metabolizing capacity of CYP3A4 or CYP3A5 protein. In Indonesian cynomolgus macaques, we also found IVS3+1delG in CYP3A4 and c.625A>T in CYP3A5, with which an intact protein cannot be produced due to a frameshift generated. Screening additional genomes revealed that two of 239 animals and three of 258 animals were heterozygous for IVS3+1delG of CYP3A4 and c.625A>T of CYP3A5, respectively. Some genetic variants were unevenly distributed between Indochinese and Indonesian cynomolgus macaques and between cynomolgus and rhesus macaques. Information on genetic diversity of macaque CYP3A4 and CYP3A5 presented here could be useful for successful drug metabolism studies conducted in macaques.
• Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture

  Wei-Kuang Wang, Chuan-Wen Ho, Kuo-Hsiang Hung, Kuo-Hsiung Wang, Chi-Chun Huang, Hitoshi Araki, Chi-Chuan Hwang, Tsai-Wen Hsu, Naoki Osada, Tzen-Yuh Chiang

  NEW PHYTOLOGIST 188 2 488 - 500 2010年 [査読有り][通常論文]
   

  P>Outcrossing Arabidopsis species that diverged from their inbreeding relative Arabidopsis thaliana 5 million yr ago and display a biogeographical pattern of interspecific sympatry vs intraspecific allopatry provides an ideal model for studying impacts of gene introgression and polyploidization on species diversification. Flow cytometry analyses detected ploidy polymorphisms of 2x and 4x in Arabidopsis lyrata ssp. kamchatica of Taiwan. Genomic divergence between species/subspecies was estimated based on 98 randomly chosen nuclear genes. Multilocus analyses revealed a mosaic genome in diploid A. l. kamchatica composed of Arabidopsis halleri-like and A. lyrata-like alleles. Coalescent analyses suggest that the segregation of ancestral polymorphisms alone cannot explain the high inconsistency between gene trees across loci, and that gene introgression via diploid A. l. kamchatica likely distorts the molecular phylogenies of Arabidopsis species. However, not all genes migrated across species freely. Gene ontology analyses suggested that some nonmigrating genes were constrained by natural selection. High levels of estimated ancestral polymorphisms between A. halleri and A. lyrata suggest that gene flow between these species has not completely ceased since their initial isolation. Polymorphism data of extant populations also imply recent gene flow between the species. Our study reveals that interspecific gene flow affects the genome evolution in Arabidopsis.
• Collection of Macaca fascicularis cDNAs derived from bone marrow, kidney, liver, pancreas, spleen, and thymus.

  Naoki Osada, Makoto Hirata, Reiko Tanuma, Yutaka Suzuki, Sumio Sugano, Keiji Terao, Jun Kusuda, Yosuke Kameoka, Katsuyuki Hashimoto, Ichiro Takahashi

  BMC research notes 2 199 - 199 2009年09月29日 [査読有り][通常論文]
   

  BACKGROUND: Consolidating transcriptome data of non-human primates is essential to annotate primate genome sequences, and will facilitate research using non-human primates in the genomic era. Macaca fascicularis is a macaque monkey that is commonly used for biomedical and ecological research. FINDINGS: We constructed cDNA libraries of Macaca fascicularis, derived from tissues obtained from bone marrow, liver, pancreas, spleen, and thymus of a young male, and kidney of a young female. In total, 5'-end sequences of 56,856 clones were determined. Including the previously established cDNA libraries from brain and testis, we have isolated 112,587 cDNAs of Macaca fascicularis, which correspond to 56% of the curated human reference genes. CONCLUSION: These sequences were deposited in the public sequence database as well as in-house macaque genome database http://genebank.nibio.go.jp/qfbase/. These data will become valuable resources for identifying functional parts of the genome of macaque monkeys in future studies.
• IL-10 is a negative regulatory factor of CAWS-vasculitis in CBA/J mice as assessed by comparison with Bruton's tyrosine kinase-deficient CBA/N mice.

  Noriko N Miura, Motohiko Komai, Yoshiyuki Adachi, Naoki Osada, Yosuke Kameoka, Kazuo Suzuki, Naohito Ohno

  Journal of immunology (Baltimore, Md. : 1950) 183 5 3417 - 24 2009年09月01日 [査読有り][通常論文]
   

  Candida albicans water-soluble fraction (CAWS), a mannoprotein-beta-glucan complex obtained from the culture supernatant of C. albicans NBRC1385, exhibits vasculitis-inducing activity (CAWS-vasculitis) in mice. The sensitivity to CAWS-vasculitis varies greatly among mouse strains. This study examined the factors contributing to or inhibiting CAWS-vasculitis using CAWS-vasculitis-resistant CBA/J mice and Bruton's tyrosine kinase-deficient CBA/N mice, which is a CAWS-vasculitis-sensitive strain that has the same origin as CBA/J mice. After stimulation with various kinds of pathogen-associated molecular patterns, the production of inflammatory cytokines IL-6 and IFN-gamma was induced in CBA/N mice, whereas that of immunosuppressive IL-10 was induced in CAWS-vasculitis-resistant CBA/J mice. Furthermore, the production of tissue inhibitor of metalloproteinase 1, an endogenous matrix metalloproteinase inhibitor, was observed in CBA/J mice. The results strongly suggest that the difference in the production of these cytokines is closely linked to the development of CAWS-vasculitis.
• Development of an integrative database with 499 novel microsatellite markers for Macaca fascicularis

  Atsunori Higashino, Naoki Osada, Yumiko Suto, Makoto Hirata, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao

  BMC GENETICS 10 24  2009年06月 [査読有り][通常論文]
   

  Background: Cynomolgus macaques (Macaca fascicularis) are a valuable resource for linkage studies of genetic disorders, but their microsatellite markers are not sufficient. In genetic studies, a prerequisite for mapping genes is development of a genome-wide set of microsatellite markers in target organisms. A whole genome sequence and its annotation also facilitate identification of markers for causative mutations. The aim of this study is to establish hundreds of microsatellite markers and to develop an integrative cynomolgus macaque genome database with a variety of datasets including marker and gene information that will be useful for further genetic analyses in this species. Results: We investigated the level of polymorphisms in cynomolgus monkeys for 671 microsatellite markers that are covered by our established Bacterial Artificial Chromosome (BAC) clones. Four hundred and ninety-nine (74.4%) of the markers were found to be polymorphic using standard PCR analysis. The average number of alleles and average expected heterozygosity at these polymorphic loci in ten cynomolgus macaques were 8.20 and 0.75, respectively. Conclusion: BAC clones and novel microsatellite markers were assigned to the rhesus genome sequence and linked with our cynomolgus macaque cDNA database (QFbase). Our novel microsatellite marker set and genomic database will be valuable integrative resources in analyzing genetic disorders in cynomolgus macaques.
• Multiple duplication of the bucentaur gene family, which recruits the APE-like domain of retrotransposon: Identification of a novel homolog and distinct cellular expression

  Shintaro Iwashita, Kentaro Nakashima, Motoki Sasaki, Naoki Osada, Si-Young Song

  GENE 435 1-2 88 - 95 2009年04月 [査読有り][通常論文]
   

  The p97bcnt/cfdp2 is a ruminant-specific gene created by a combination of gene duplication of ancestral bcnt (bucentaur) or cfdp1 (craniofacial developmental protein 1), bcnt/cfdp1, and the insertion of a retro-transposable element-1 (RTE). As a result, p97Bcnt recruits the whole apurinic/apyrimidinic endonuclease (APE)-like domain of RTE in the middle of the molecule (RTE domain) as a region encoded by an exon. In addition, p97Bcnt contains two intramolecular repeats (IRs) of 40 amino acids each in the C-terminal region, whereas Bcnt/Cfdp1 contains one IR. We have identified an additional bovine homolog with a structure highly similar to p97Bcnt, designated p97Bcnt2, which contains three IRs. p97bcnt2 is located in tandem with bcnt/cfdp1 and p97bcnt within a 177-kb range on bovine chromosome 18, a syntenic region of human The gene product is expressed as a protein with an apparent molecular mass of 102 kDa. The chromosome 16. phylogenetic tree strongly Suggests that p97bcnt-2 forms a third clade of the bcnt family and that the first duplication of the IR unit occurred prior to the divergence of p97bcnt and p97bcnt-2. To address the question of whether these bcnt members have distinct functions, we first examined the expression and localization of the p97Bcnt family members. p97Bcnt is substantially expressed in many tissues involved in responses to external and internal Stress. In the testis, p97Bcnt localizes preferentially in the nuclei of spermatozoa, while Bcnt/Cfdp1 localizes predominantly in the cytosol of Leydig cells and some spermatogenic cells, implying that at least these two molecules of the Bcnt family play different functional roles. These results provide evidence for the direct contribution of RTE to gene diversity to form gene families that may support cellular function. (C) 2009 Elsevier B.V. All rights reserved.
• Quantifying dominance and deleterious effect on human disease genes

  Naoki Osada, Shuhei Mano, Jun Gojobori

  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 106 3 841 - 846 2009年01月 [査読有り][通常論文]
   

  Human genes responsible for inherited diseases are important for the understanding of human disease. We investigated the degree of polymorphism and divergence in the human disease genes to elucidate the effect of natural selection on human disease genes. In particular, the effect of disease dominance was incorporated into the analysis. Both dominant disease genes (DDG) and recessive disease genes (RDG) had a higher mutation rate per site and encoded longer proteins than the nondisease genes, which exposed the disease genes to a faster flux of new mutations. Using an unbiased polymorphism dataset, we found that, proportionally, RDG harbor more nonsynonymous polymorphisms compared with DDG. We estimated the selection intensity on the disease genes using polymorphism and divergence data and determined whether the different patterns of polymorphism and divergence between DDG and RDG could be explained by the difference in only dominance. Even after the dominance effect was considered, the selection intensity on RDG was significantly different from DDG, suggesting that the deleterious effect of the dominant and recessive disease mutations are fundamentally different.
• Duplication and Gene Conversion in the Drosophila melanogaster Genome

  Naoki Osada, Hideki Innan

  PLOS GENETICS 4 12 e1000305  2008年12月 [査読有り][通常論文]
   

  Using the genomic sequences of Drosophila melanogaster subgroup, the pattern of gene duplications was investigated with special attention to interlocus gene conversion. Our fine-scale analysis with careful visual inspections enabled accurate identification of a number of duplicated blocks (genomic regions). The orthologous parts of those duplicated blocks were also identified in the D. simulans and D. sechellia genomes, by which we were able to clearly classify the duplicated blocks into post- and pre-speciation blocks. We found 31 post-speciation duplicated genes, from which the rate of gene duplication (from one copy to two copies) is estimated to be 1.0 x 10(-9) per single-copy gene per year. The role of interlocus gene conversion was observed in several respects in our data: (1) synonymous divergence between a duplicated pair is overall very low. Consequently, the gene duplication rate would be seriously overestimated by counting duplicated genes with low divergence; (2) the sizes of young duplicated blocks are generally large. We postulate that the degeneration of gene conversion around the edges could explain the shrinkage of "identifiable'' duplicated regions; and (3) elevated paralogous divergence is observed around the edges in many duplicated blocks, supporting our gene conversion degeneration model. Our analysis demonstrated that gene conversion between duplicated regions is a common and genome-wide phenomenon in the Drosophila genomes, and that its role should be especially significant in the early stages of duplicated genes. Based on a population genetic prediction, we applied a new genome-scan method to test for signatures of selection for neofunctionalization and found a strong signature in a pair of transporter genes.
• Extensive expansion and diversification of the chemokine gene family in zebrafish: Identification of a novel chemokine subfamily CX

  Hisayuki Nomiyama, Kunio Hieshima, Naoki Osada, Yoko Kato-Unoki, Kaori Otsuka-Ono, Sumio Takegawa, Toshiaki Izawa, Akio Yoshizawa, Yutaka Kikuchi, Sumio Tanase, Retsu Miura, Jun Kusuda, Miki Nakao, Osamu Yoshie

  BMC GENOMICS 9 222  2008年05月 [査読有り][通常論文]
   

  Background: The chemokine family plays important roles in cell migration and activation. In humans, at least 44 members are known. Based on the arrangement of the four conserved cysteine residues, chemokines are now classified into four subfamilies, CXC, CC, XC and CX3C. Given that zebrafish is an important experimental model and teleost fishes constitute an evolutionarily diverse group that forms half the vertebrate species, it would be useful to compare the zebrafish chemokine system with those of mammals. Prior to this study, however, only incomplete lists of the zebrafish chemokine genes were reported. Results: We systematically searched chemokine genes in the zebrafish genome and EST databases, and identified more than 100 chemokine genes. These genes were CXC, CC and XC subfamily members, while no CX3C gene was identified. We also searched chemokine genes in pufferfish fugu and Tetraodon, and found only 18 chemokine genes in each species. The majority of the identified chemokine genes are unique to zebrafish or teleost fishes. However, several groups of chemokines are moderately similar to human chemokines, and some chemokines are orthologous to human homeostatic chemokines CXCL12 and CXCL14. Zebrafish also possesses a novel species-specific subfamily consisting of five members, which we term the CX subfamily. The CX chemokines lack one of the two N-terminus conserved cysteine residues but retain the third and the fourth ones. (Note that the XC subfamily only retains the second and fourth of the signature cysteines residues.) Phylogenetic analysis and genome organization of the chemokine genes showed that successive tandem duplication events generated the CX genes from the CC subfamily. Recombinant CXL-chr24a, one of the CX subfamily members on chromosome 24, showed marked chemotactic activity for carp leukocytes. The mRNA was expressed mainly during a certain period of the embryogenesis, suggesting its role in the zebrafish development. Conclusion: The phylogenic and genomic organization analyses suggest that a substantial number of chemokine genes in zebrafish were generated by zebrafish-specific tandem duplication events. During such duplications, a novel chemokine subfamily termed CX was generated in zebrafish. Only two human chemokines CXCL12 and CXCL14 have the orthologous chemokines in zebrafish. The diversification observed in the numbers and sequences of chemokines in the fish may reflect the adaptation of the individual species to their respective biological environment.
• Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M-fascicularis and M-mulatta

  Naoki Osada, Katsuyuki Hashimoto, Yosuke Kameoka, Makoto Hirata, Reiko Tanuma, Yasuhiro Uno, Itsuro Inoue, Munetomo Hida, Yutaka Suzuki, Sumio Sugano, Keiji Terao, Jun Kusuda, Ichiro Takahashi

  BMC GENOMICS 9 90  2008年02月 [査読有り][通常論文]
   

  Background: Cynomolgus macaques (Macaca fascicularis) are widely used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as rhesus macaques (M. mulatta). We isolated 85,721 clones and determined 9407 full-insert sequences from cynomolgus monkey brain, testis, and liver. These sequences were annotated based on homology to human genes and stored in a database, QFbase http://genebank.nibio.go.jp/qfbase/. Results: We found that 1024 transcripts did not represent any public human cDNA sequence and examined their expression using M. fascicularis oligonucleotide microarrays. Significant expression was detected for 544 (51%) of the unidentified transcripts. Moreover, we identified 226 genes containing exon alterations in the untranslated regions of the macaque transcripts, despite the highly conserved structure of the coding regions. Considering the polymorphism in the common ancestor of cynomolgus and rhesus macaques and the rate of PCR errors, the divergence time between the two species was estimated to be around 0.9 million years ago. Conclusion: Transcript data from Old World monkeys provide a means not only to determine the evolutionary difference between human and non-human primates but also to unveil hidden transcripts in the human genome. Increasing the genomic resources and information of macaque monkeys will greatly contribute to the development of evolutionary biology and biomedical sciences.
• Expressed sequence tags from cynomolgus monkey (Macaca fascicularis) liver: A systematic identification of drug-metabolizing enzymes

  Yasuhiro Uno, Yutaka Suzuki, Hiroyuki Wakaguri, Yoshiko Sakamoto, Hitomi Sano, Naoki Osada, Katsuyuki Hashimoto, Sumio Sugano, Ituro Inoue

  FEBS LETTERS 582 2 351 - 358 2008年01月 [査読有り][通常論文]
   

  The liver, a major organ for drug metabolism, is physiologically similar between monkeys and humans. However, the paucity of identified genes has hampered a deep understanding of drug metabolism in monkeys. To provide such a genetic resource, 28 655 expressed sequence tags (ESTs) were generated from a cynomolgus monkey liver full-length enriched cDNA library, which contained 23 unique ESTs homologous to human drug-metabolizing enzymes. Our comparative genomics approach identified nine lineage-specific candidate ESTs, including three drug-metabolizing enzymes, which could be important for understanding the physiological differences between monkeys and humans. (C) 2007 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
• Inference of expression-dependent negative selection based on polymorphism and divergence in the human genome

  Naoki Osada

  MOLECULAR BIOLOGY AND EVOLUTION 24 8 1622 - 1626 2007年08月 [査読有り][通常論文]
   

  There is a mounting evidence for the correlation between the gene expression pattern and sequence divergence. However, little is known about the relationship between the gene expression pattern and polymorphism. We compiled the gene expression, polymorphism, and divergence data from the public databases of the human genome. The ratios of nonsynonymous (A) to synonymous (S) substitutions in polymorphism and divergence in the human genome were strongly influenced by the expression pattern and breadth of genes and showed strong correlations. Among the tissues we analyzed, the brain-expressed genes have the smallest and the liver-expressed genes have the largest proportion of amino acid changes both in polymorphism and divergence. The analysis implies that negative selection is the primary factor affecting expression-dependent gene evolution and the prevalent but nonuniform distribution of slightly deleterious mutations in the genome. Although the genes under relaxed negative selection evolved faster than the other genes, these genes are even more liable to slightly deleterious mutations in the population. On the other hand, nonneutral mutations in the highly conservative genes, such as brain-expressed and housekeeping genes, are largely deleterious and eliminated before they enter the population.
• Positive and negative regulation of adenovirus infection by CAR-like soluble protein, CLSP

  K. Kawabata, K. Tashiro, F. Sakurai, N. Osada, J. Kusuda, T. Hayakawa, K. Yamanishi, H. Mizuguchi

  GENE THERAPY 14 16 1199 - 1207 2007年08月 [査読有り][通常論文]
   

  Coxsackievirus and adenovirus receptor (CAR) is a member of the immunoglobulin (lg) superfamily and a component of epithelial tight junction. CAR also functions as a primary receptor for coxsackievirus B and adenovirus (Ad) infection. In this study, we report the identification of a novel protein, CAR-like soluble protein (CLSP), which is closely related to CAR. Mouse CLSP (mCLSP) was composed of 390 amino acids, including three lg domains, and showed strong homology to the lgV domain of CAR. Interestingly, mCLSP lacks a transmembrane domain, indicating that this is a soluble protein. mCLSP mRNA was detected primarily in the brain and ovary. When mCLSP cDNA was introduced into SK HEP-1 cells, which were known to be CAR positive and easily infected with Ad vector, the infection with Ad vector was severely inhibited. On the other hand, mCLSP promoted the infection with Ad vector in CAR-negative NIH3T3 cells. Furthermore, recombinant CLSP directly bound to Ad and inhibited the Ad vector-mediated transduction in SK HEP-1 cells. Computational analysis for a genome database showed that the CLSP gene is rodent-specific, and that human and bovine lack this gene. These results suggest that CLSP may play a role in the antiviral defense of the host in rodent animals.
• Aberrant termination of reproduction-related TMEM30C transcripts in the hominoids

  Naoki Osada, Katsuyuki Hashimoto, Momoki Hirai, Jun Kusuda

  GENE 392 1-2 151 - 156 2007年05月 [査読有り][通常論文]
   

  Finding genetic novelties that may contribute to human-specific physiology and diseases is a key issue of current biomedical studies. TMEM30C is a gene containing two transmembrane (TM) domains and homologous to the yeast CDC50 family, which is related to polarized cell division. It is conserved among mammals along with two other paralogs, TMEM30A and TMEM30B. We found that TMEM30C is expressed specifically in the testis of mammals, in contrast to the relatively wide expression distributions of the other paralogs. While macaques expressed two alternative splicing isoforms which include one or two TM domains, humans and chimpanzees predominantly expressed truncated transcripts because of the mutations in the splicing and/or poly(A) signal sites. The major transcript in humans harbored non-stop ORF (open reading frame) while the chimpanzee counterpart encoded a protein with one TM domain. The difference was due to the 1-bp indel upstream of the poly(A) signal site. In addition, both the hominoids expressed minor transcripts encoding short proteins with one TM domain. Phylogenetic analysis has showed the acceleration of amino acid substitution after the human and chimpanzee divergence, which may have been caused by a recent relaxation in functional constraints or positive selection on TMEM30C. Elucidating the precise reproductive function of TMEM30C in mammals will be important to the foundation of divergence in higher primates at a molecular level. (c) 2006 Elsevier B.V. All rights reserved.
• Rate of evolution in brain-expressed genes in humans and other primates

  Hurng-Yi Wang, Huan-Chieh Chien, Naoki Osada, Katsuyuki Hashimoto, Sumio Sugano, Takashi Gojobori, Chen-Kung Chou, Shih-Feng Tsai, Chung-I Wu, C. -K. James Shen

  PLOS BIOLOGY 5 2 335 - 342 2007年02月 [査読有り][通常論文]
   

  Brain-expressed genes are known to evolve slowly in mammals. Nevertheless, since brains of higher primates have evolved rapidly, one might expect acceleration in DNA sequence evolution in their brain-expressed genes. In this study, we carried out full-length cDNA sequencing on the brain transcriptome of an Old World monkey (OWM) and then conducted three-way comparisons among (i) mouse, OWM, and human, and (ii) OWM, chimpanzee, and human. Although brain-expressed genes indeed appear to evolve more rapidly in species with more advanced brains (apes. OWM. mouse), a similar lineage effect is observable for most other genes. The broad inclusion of genes in the reference set to represent the genomic average is therefore critical to this type of analysis. Calibrated against the genomic average, the rate of evolution among brain-expressed genes is probably lower (or at most equal) in humans than in chimpanzee and OWM. Interestingly, the trend of slow evolution in coding sequence is no less pronounced among brain-specific genes, vis-a-vis brain-expressed genes in general. The human brain may thus differ from those of our close relatives in two opposite directions: (i) faster evolution in gene expression, and (ii) a likely slowdown in the evolution of protein sequences. Possible explanations and hypotheses are discussed.
• Identification of a novel CXCL1-like chernokine gene in macaques and its inactivation in hominids

  Hisayuki Nomiyama, Kaori Otsuka-Ono, Retsu Miura, Naoki Osada, Keiji Terao, Osamu Yoshie, Jun Kusuda

  JOURNAL OF INTERFERON AND CYTOKINE RESEARCH 27 1 32 - 37 2007年01月 [査読有り][通常論文]
   

  Chemokines are a rapidly evolving cytokine gene family. Because of various genome rearrangements after divergence of primates and rodents, humans and mice have different sets of chemokine genes, with humans having members outnumbering those of mice. Here, we report the occurrence of lineage-specific chemokine gene generation or inactivation events within primates. By using human chemokine sequences as queries, we isolated a novel cynomolgus macaque CXC chemokine cDNA. The encoded chemokine, termed CXCL1L (from CXCL1-like) showed the highest similarity to human CXCL1. A highly homologous gene was also found in the rhesus macaque genome. By comparing the genome organization of the major CXC chemokine clusters among the primates, we found that one copy of the duplicated CXCL1 genes turned into a pseudogene in the hominids, whereas the gene in macaques has been maintained as a functionally active CXCL1L. In addition, cynomolgus macaque was found to contain an additional CXC chemokine highly homologous to CXCL3, termed CXCL3L (from CXCL3-like). These results demonstrate the birth-and-death process of a new gene in association with gene duplication within the primates.
• Genomic inferences of the cis-regulatory nucleotide polymorphisms underlying gene expression differences between Drosophila melanogaster mating races

  Naoki Osada, Michael H. Kohn, Chung-I Wu

  MOLECULAR BIOLOGY AND EVOLUTION 23 8 1585 - 1591 2006年08月 [査読有り][通常論文]
   

  Nucleotide sequence polymorphisms affecting gene expression occur in the regulatory region of genes (in cis) and elsewhere in the genome (in trans). Further study is required to weigh the relative importance of cis- and trans-acting mutations in mediating gene expression differences within and between species. Here, microarray hybridization experiments were used to isolate 363 gene expression differences between the female fly head transcriptomes of 2 Drosophila melanogaster strains. One strain (French) represented the cosmopolitan M mating race and the other strain (ZS30) represented the Z mating race derived from Zimbabwe, Africa. From chromosomal substitution strains engineered from the 2 strains, we inferred that the expression differences between M and Z alleles largely could be attributed to the genotype of the chromosomes where the differentially expressed genes were located, that is, cis-regulatory polymorphisms prominently influence gene expression differences between M and Z. The effects of trans-regulatory polymorphisms were apparent yet difficult to quantity. Results have implications for models of gene regulatory evolution as well as experimental studies trying to identify the nucleotide sequence polymorphisms underlying gene expression differences between Drosophila strains.
• A tandem gene duplication followed by recruitment of a Retrotransposon created the paralogous bucentaur gene (bcnt(p97)) in the ancestral ruminant

  S Iwashita, S Ueno, K Nakashima, SY Song, K Ohshima, K Tanaka, H Endo, J Kimura, M Kurohmaru, K Fukuta, L David, N Osada

  MOLECULAR BIOLOGY AND EVOLUTION 23 4 798 - 806 2006年04月 [査読有り][通常論文]
   

  Retrotransposable element-1 (RTE-1) is a class of long interspersed nucleotide elements that contain in its open reading frame an apurinic/apyrimidinic endonuclease domain (AP-END) and a reverse transcriptase domain. Ruminants have a clade-specific RTE-1 (BovB/RTE). The bovine bcnt gene (bucentaur or craniofacial developmental protein 1) has a duplicated paralog (bcnt(p97)) in tandem that recruited an AP-END of BovB/RTE as a coding exon (RTE exon). We obtained sequence of the bcnt region from several animals and showed that other ruminants also have the bcnt(p97) with a conserved RTE exon while camels and pigs do not. Genomic Southern analysis showed that camels and pigs have multiple bcnt-related sequences but not BovB/RTE which bovines and lesser mouse deer have abundantly. These results indicate that the bcnt gene duplication followed by the creation of bcnt(p97) including recruitment of the RTE exon occurred in the ancestral ruminant about 55 MYA. The indication of time frame is supported by a phylogenetic analysis. Taken together with a result of differential tissue expression of the two bcnt paralogs, we conclude that bcnt(p97) was created concurrently with the early radiation of BovB/RTE in an ancestral ruminant and then acquired a novel function.
• Substitution rate and structural divergence of 5'UTR evolution: Comparative analysis between human and cynomolgus monkey cDNAs

  N Osada, M Hirata, R Tanuma, J Kusuda, M Hida, Y Suzuki, S Sugano, T Gojobori, CKJ Shen, CI Wu, K Hashimoto

  MOLECULAR BIOLOGY AND EVOLUTION 22 10 1976 - 1982 2005年10月 [査読有り][通常論文]
   

  The substitution rate and structural divergence in the 5'- untranslated region ( UTR) were investigated by using human and cynomolgus monkey cDNA sequences. Due to the weaker functional constraint in the UTR than in the coding sequence, the divergence between humans and macaques would provide a good estimate of the nucleotide substitution rate and structural divergence in the 5' UTR. We found that the substitution rate in the 5' UTR ( K-5UTR) averaged approximate to 10% - 20% lower than the synonymous substitution rate ( K-s). However, both the K-5UTR and nonsynonymous substitution rate ( K-a) were significantly higher in the testicular cDNAs than in the brain cDNAs, whereas the Ks did not differ. Further, an in silico analysis revealed that 27% ( 169/ 622) of macaque testicular cDNAs had an altered exon- intron structure in the 5' UTR compared with the human cDNAs. The fraction of cDNAs with an exon alteration was significantly higher in the testicular cDNAs than in the brain cDNAs. We confirmed by using reverse transcriptase - polymerase chain reaction that about one- third ( 6/ 16) of in silico `` macaque - specific'' exons in the 5' UTR were actually macaque specific in the testis. The results imply that positive selection increased K5UTR and structural alteration rate of a certain fraction of genes as well as Ka. We found that both positive and negative selection can act on the 5' UTR sequences.
• Evolution of sexual isolation during secondary contact: Genotypic versus phenotypic changes in laboratory populations

  JA Alipaz, S Fang, N Osada, CI Wu

  AMERICAN NATURALIST 165 4 420 - 428 2005年04月 [査読有り][通常論文]
   

  We monitored the phenotypic and genotypic changes that occur when two behavioral races come into contact in laboratory populations. Drosophila melanogaster from Zimbabwe and nearby regions (Z type) show strong but asymmetric sexual isolation from their cosmopolitan counterparts ( M type). Crosses of Z females and M males do not take place readily when other choices are available. At least 15 loci are known to control Z-type mating preferences and performance. By thoroughly mixing the genomes of the two types in laboratory populations, we artificially created maximum secondary contact. Despite the strength of sexual selection favoring Z-type male characters, Z-type behavior is eliminated or greatly diminished in all 12 hybrid populations after only 60 generations. This trend is consistent with the spread of the M-type behavior throughout the world as well as a detailed analysis of fitness components. Surprisingly, in contrast with the phenotypic convergence toward the M-type, genotypic samples broadly covering the genomic regions of mapped behavioral loci show no such trend. The genome appears to be "fine grained," with adjacent loci having different evolutionary dynamics and genealogical histories.
• Inferring the mode of speciation from genomic data: A study of the great apes

  N Osada, CI Wu

  GENETICS 169 1 259 - 264 2005年01月 [査読有り][通常論文]
   

  The strictly allopatric model of speciation makes definable predictions on the pattern of divergence, one of which is the uniformity in the divergence time across genomic regions. Using 345 coding and 143 intergenic sequences from the African great apes, we were able to reject the mill hypothesis that the divergence time in the coding sequences (CDSs) and intergenic sequences (IGSs) is the same between human and chimpanzee. The conclusion is further supported by the analysis of whole-genome sequences between these species. The difference suggests a prolonged period of genetic exchange during the formation of these two species. Because the analysis should be generally applicable, collecting DNA sequence data from many genomic regions between closely related species should help to settle the debate over the prevalence of the allopatric mode of speciation.
• A transposable element-mediated gene divergence that directly produces a novel type bovine Bcnt protein including the endonuclease domain of RTE-1

  S Iwashita, N Osada, T Itoh, M Sezaki, K Oshima, E Hashimoto, Y Kitagawa-Arita, Takahashi, I, T Masui, K Hashimoto, W Makalowski

  MOLECULAR BIOLOGY AND EVOLUTION 20 9 1556 - 1563 2003年09月 [査読有り][通常論文]
   

  Ruminant Bent protein with a molecular mass of 97 kDa (designated p97Bcnt) includes a region derived from the endonuclease domain of a retrotransposable element RTE-1. Human and mouse Bcnt proteins lack the corresponding region but have a highly conserved 82-amino acid region at the C-terminus that is not present in p97Bcnt. By screening a bovine BAC library, we found two more bcnt-related genes: human-type bent (h-type bent) and its processed pseudogene. Whereas the pseudogene is localized on chromosome 26, both bcnt(p97) and the h-type bent genes are found on bovine chromosome 18, a synteny region of human chromosome 16 on which human BCNT is localized. Complete nucleotide sequencing of the BAC clone reveals that the bcnt(p97) and h-type bent genes are located just 6 kb apart in a tandem manner. The two h-type bent and bcnt(p97) genes are active at both the transcriptional level and the protein level. H-type bovine Bent is more like human BCNT than p97Bcnt, when compared at their N-terminal regions. However, phylogenetic analysis using the N-terminal region of the bent gene family revealed that the duplication of bovine genes occurred within the bovine lineage with significantly accelerated substitution in bcnt(p97). This acceleration was not ascribed definitely to positive selection. After duplication, one of the bovine bent genes recruited the endonuclease domain of an intronic RTE-1 repeat accompanied by the accelerated substitution at the 5'-ORF, resulting in creation of a novel type of Bcnt protein in bovine.
• Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116(Clone2_XRR) and macaque testis

  FM Mesak, N Osada, K Hashimoto, QY Liu, CE Ng

  BMC GENOMICS 4 32  2003年08月 [査読有り][通常論文]
   

  Background: As part of our investigation into the genetic basis of tumor cell radioresponse, we have isolated several clones with a wide range of responses to X-radiation (XR) from an unirradiated human colorectal tumor cell line, HCT116. Using human cDNA microarrays, we recently identified a novel gene that was down-regulated by two-fold in an XR-resistant cell clone, HCT116(Clone2_ XRR). We have named this gene as X-ray radiation resistance associated 1 (XRRA1) ( GenBank BK000541). Here, we present the first report on the molecular cloning, genomic characterization and over-expression of the XRRA1 gene. Results: We found that XRRA1 was expressed predominantly in testis of both human and macaque. cDNA microarray analysis showed three-fold higher expression of XRRA1 in macaque testis relative to other tissues. We further cloned the macaque XRRA1 cDNA ( GenBank AB072776) and a human XRRA1 splice variant from HCT116(Clone2_ XRR) (GenBank AY163836). In silico analysis revealed the full-length human XRRA1, mouse, rat and bovine Xrra1 cDNAs. The XRRA1 gene comprises 11 exons and spans 64 kb on chromosome 11q13.3. Human and macaque cDNAs share 96% homology. Human XRRA1 cDNA is 1987 nt long and encodes a protein of 559 aa. XRRA1 protein is highly conserved in human, macaque, mouse, rat, pig, and bovine. GFP-XRRA1 fusion protein was detected in both the nucleus and cytoplasm of HCT116 clones and COS-7 cells. Interestingly, we found evidence that COS-7 cells which over-expressed XRRA1 lacked Ku86 (Ku80, XRCC5), a non-homologous end joining (NHEJ) DNA repair molecule, in the nucleus. RT-PCR analysis showed differential expression of XRRA1 after XR in HCT116 clones manifesting significantly different XR responses. Further, we found that XRRA1 was expressed in most tumor cell types. Surprisingly, mouse Xrra1 was detected in mouse embryonic stem cells R1. Conclusions: Both XRRA1 cDNA and protein are highly conserved among mammals, suggesting that XRRA1 may have similar functions. Our results also suggest that the genetic modulation of XRRA1 may affect the XR responses of HCT116 clones and that XRRA1 may have a role in the response of human tumor and normal cells to XR. XRRA1 might be correlated with cancer development and might also be an early expressed gene.
• Analysis of 5 '-end sequences of chimpanzee cDNAs

  R Sakate, N Osada, M Hida, S Sugano, Hayasaka, I, N Shimohira, S Yanagi, Y Suto, K Hashimoto, M Hirai

  GENOME RESEARCH 13 5 1022 - 1026 2003年05月 [査読有り][通常論文]
   

  We constructed full-length enriched cDNA libraries from chimpanzee brain, skin, and liver tissues by the oligo-capping method to establish a database of sequences of chimpanzee genes. Randomly selected clones from the libraries were subjected to one-pass sequencing from their 5'-ends. As a result, we collected 6813 chimpanzee cDNA sequences longer than 400 bp. Homology search against human mRNA sequences (RefSeq mRNAs) revealed that our collection included sequences of 1652 putative chimpanzee genes. In order to calculate the sequence identity between human and chimpanzee homologs, we constructed 5'-end consensus sequences of 226 chimpanzee genes by aligning at least three sequences for individual genes. Sequence identity was estimated by comparing these consensus sequences and the corresponding sequences of their human homologs. The average sequence identity of the 5'-end cDNAs was 99.30%. Those of the 5'-UTRs and CDSs were 98.79% and 99.42%, respectively. The results confirmed that human and chimpanzee genes are highly conserved at the nucleotide level. As for amino acids, the average sequence identity was 99.44%. The average synonymous (K(S)) and nonsynonymous (K(A)) divergences were estimated to be 1.33% and 0.28%, respectively.
• Search for genes positively selected during primate evolution by 5 '-end-sequence screening of cynomolgus monkey cDNAs

  N Osada, J Kusuda, M Hirata, R Tanuma, M Hida, S Sugano, M Hirai, K Hashimoto

  GENOMICS 79 5 657 - 662 2002年05月 [査読有り][通常論文]
   

  It is possible to assess positive selection by using the ratio of K-a (nonsynonymous substitutions per plausible nonsynonymous sites) to K-s (synonymous substitutions per plausible synonymous sites). We have searched candidate genes positively selected during primate evolution by using 5'-end sequences of 21,302 clones derived from cynomolgus monkey (Macaca fascicularis) brain cDNA libraries. Among these candidates, 10 genes that had not been shown by previous studies to undergo positive selection exhibited a K-a/K-s ratio > 1. Of the 10 candidate genes we found, 5 were included in the mitochondrial respiratory enzyme complexes, suggesting that these nuclear-encoded genes coevolved with mitochondrial-encoded genes, which have high mutation rates. The products of other candidate genes consisted of a cell-surface protein, a member of the lipocalin family, a nuclear transcription factor, and hypothetical proteins.
• Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain.

  Osada N, Hida M, Kusuda J, Tanuma R, Hirata M, Hirai M, Terao K, Suzuki Y, Sugano S, Hashimoto K

  Genome biology 3 RESEARCH0006  1 2002年 [査読有り][通常論文]
  
• Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence

  N Osada, M Hida, J Kusuda, R Tanuma, M Hirata, Y Suto, M Hirai, K Terao, S Sugano, K Hashimoto

  BMC GENOMICS 3 36  2002年 [査読有り][通常論文]
   

  Background: In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcripts for identification of their human homologues. Result: The full-insert sequences of 512 cDNA clones were determined. Ultimately we found 302 non-redundant cDNAs carrying open reading frames of 300 bp-length or longer. Among them, 89 cDNAs were found not to be annotated previously in the Ensembl human database. After searching against the Ensembl mouse database, we also found 69 putative coding sequences have no homologous cDNAs in the annotated human and mouse genome sequences in Ensembl. We subsequently designed a DNA microarray including 396 non-redundant cDNAs (with and without open reading frames) to examine the expression of the full-sequenced genes. With the testicular probe and a mixture of probes of 10 other tissues, 316 of 332 effective spots showed intense hybridized signals and 75 cDNAs were shown to be expressed very highly in the cynomolgus monkey testis, but not ubiquitously. Conclusions: In this report, we determined 302 full-insert sequences of cynomolgus monkey cDNAs with enough length of open reading frames to discover novel transcripts as human homologues. Among 302 cDNA sequences, human homologues of 89 cDNAs have not been predicted in the annotated human genome sequence in the Ensembl. Additionally, we identified 75 dominantly expressed genes in testis among the full-sequenced clones by using a DNA microarray. Our cDNA clones and analytical results will be valuable resources for future functional genomic studies.
• Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain

  Naoki Osada, Munetomo Hida, Jun Kusuda, Reiko Tanuma, Makoto Hirata, Momoki Hirai, Keiji Terao, Yutaka Suzuki, Sumio Sugano, Katsuyuki Hashimoto

  GENOME BIOLOGY 3 1 2002年 [査読有り][通常論文]
   

  Background: The complete assignment of the protein-coding regions of the human genonne is a major challenge for genonne biology today. We have already isolated many hitherto unknown full-length cDNAs as orthologs of unidentified human genes from cDNA libraries of the cynomolgus monkey (Macaca fascicularis) brain (parietal lobe and cerebellum). In this study, we used cDNA libraries of three other parts of the brain (frontal lobe, temporal lobe and medulla oblongata) to isolate novel full-length cDNAs. Results: The entire sequences of novel cDNAs of the cynomolgus monkey were determined, and the orthologous human cDNA sequences were predicted from the human genonne sequence. We predicted 29 novel human genes with putative coding regions sharing an open reading frame with the cynomolgus monkey, and we confirmed the expression of 21 pairs of genes by the reverse transcription-coupled polymerase chain reaction method. The hypothetical proteins were also functionally annotated by computer analysis. Conclusions: The 29 new genes had not been discovered in recent explorations for novel genes in humans, and the ab initio method failed to predict all exons. Thus, monkey cDNA is a valuable resource for the preparation of a complete human gene catalog, which will facilitate post-genomic studies.
• Assignment of 118 novel cDNAs of cynomolgus monkey brain to human chromosomes

  N Osada, M Hida, J Kususda, R Tanuma, K Iseki, M Hirata, Y Suto, M Hirai, K Terao, Y Suzuki, S Sugano, K Hashimoto

  GENE 275 1 31 - 37 2001年09月 [査読有り][通常論文]
   

  In order to isolate genes that may not be represented in current human brain cDNA libraries, we have sequenced about 20,000 sequence tags of cDNA clones derived from cerebellum and parietal lobe of cynomolgus monkeys (Macaca fascicularis). We determined the entire cDNA sequence of approximately 700 clones whose 5'-terminal sequences showed no homology to annotated putative genes or expressed sequence tags in current databases of genetic information. From this, 118 clones with sequences encoding novel open reading frames of more than 100 amino acid residues were selected for further analysis. To localize the genes corresponding to these 118 newly identified cDNA clones on human chromosomes, we performed a homology search using the human genome sequence and fluorescent in situ hybridization. In total, 108 of 118 clones were successfully assigned to specific regions of human chromosomes. This result demonstrates that genes expressed in cynomolgus monkey are highly conserved throughout primate evolution, and that virtually all had human homologs. Furthermore, we will be able to discover novel human genes in the human genome using monkey homologs as probes. (C) 2001 Elsevier Science B.V. All rights reserved.
• Identification and characterization of the potential promoter regions of 1031 kinds of human genes

  Y Suzuki, T Tsunoda, J Sese, H Taira, J Mizushima-Sugano, H Hata, T Ota, T Isogai, T Tanaka, Y Nakamura, A Suyama, Y Sakaki, S Morishita, K Okubo, S Sugano

  GENOME RESEARCH 11 5 677 - 684 2001年05月 [査読有り][通常論文]
   

  To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumes of genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA libraries constructed by the "oligo-capping" method. We aligned the mRNA start sites with the genomic sequences and retrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences were searched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) contained TATA boxes, 872 (85%) contained initiators, 999 (97%) contained CC box, and 663 (64%) contained CAAT box. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced in TATA(+)/lnr(+) PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRA gene, and the TM30pl genes, which showed highly colon specific expression patterns, the consensus sequences of E boxes were commonly observed. The PPRs were also useful For exploring promoter SNPs.
• Sequence analysis, gene expression, and chromosomal assignment of mouse Borg4 gene and its human orthologue

  N Osada, J Kusuda, Y Suzuki, S Sugano, K Hashimoto

  JOURNAL OF HUMAN GENETICS 45 6 374 - 377 2000年 [査読有り][通常論文]
   

  The Borg (binder of Rho GTPases) family proteins interact with CDC42 and TC10 in a guanosine triphosphate (GTP)-dependent manner. We have isolated a full-length cDNA of the mouse Borg4 gene, which is a member of this family. Sequence analysis revealed that this gene encoded a putative 349-amino acid protein. By reverse transcription - coupled polymerase chain reaction (RT-PCR) analysis, we observed that Borg4 was er;pressed ubiquitously in adult tissues. Additionally, we determined the entire cDNA sequence of the putative human Borg4 orthologue, By fluorescence in situ hybridization, mouse Borg4 and the putative human orthologue have been assigned to mouse chromosome 11E and human chromosome 17q24-25, which has been described as syntenic to the mouse region.

書籍

• 霊長類学の百科事典 = The encyclopedia of primatology

  日本霊長類学会 (担当:分担執筆範囲:pp10-11,44-45)
  丸善出版 2023年07月 (ISBN: 9784621308042) xxii, 716p, 図版 [8] p
• 遺伝学の百科事典 : 継承と多様性の源

  日本遺伝学会 (担当:分担執筆範囲:pp42-43, 418-419)
  丸善出版 2022年01月 (ISBN: 9784621306604) xvii, 668p
• 進化で読み解く バイオインフォマティクス入門

  長田直樹 (担当:単著)
  森北出版 2019年06月 (ISBN: 4627261411) 232
• ヒトは病気とともに進化した (シリーズ認知と文化)

  太田博樹, 長谷川真理子 (担当:単著範囲:第二章)
  勁草書房 2013年12月 (ISBN: 4326199458) 212

  
• 遺伝子図鑑

  明石裕, 長田直樹 (担当:分担執筆範囲:第7章1,2,11節)
  悠書館 2013年10月 (ISBN: 4903487792)
• Post-Genome Biology of Primates (Primatology Monographs)

  Hirohisa Hirai, Hiroo Imai, Yasuhiro Go 
  Springer 2012年03月 (ISBN: 4431540105) 280

  
• Handbook of human molecular evolution : [set]

  Cooper David, N. Dr, Kehrer-Sawatzki Hildegard, Dawkins Richard 
  John Wiley & Sons 2008年 (ISBN: 9780470517468)

講演・口頭発表等

• ゲノム多様性のバイオインフォマティクス解析：野生ハツカネズミの歴史とゲノム進化

  長田直樹

  第一回北海道バイオ”Mix up” 2023年08月 口頭発表（招待・特別）
• Genomic Insights into the Hybridization of House Mouse Subspecies in East Asia

  Naoki Osada

  SMBE2023 2023年07月 ポスター発表
• Hybrids meet in Japan: pattern and mode of genomic admixture between subspecies of wild house mice (Mus musculus) in East Asia  [通常講演]

  Kazumichi Fujiwara, Shunpei Kubo, Tomoki Yano, Toshinori Endo, Toyoyuki Takada, Toshihiko Shiroishi, Hitoshi Suzuki, Naoki Osada

  IMGC2023 2023年03月 口頭発表（一般）
• 日本産野生ハツカネズミの混合過程における選択について

  久保俊平, 藤原一道, 長田直樹

  第4回ヤポネシアくにうみミーティング 2023年03月 ポスター発表
• 時をかけるゲノム～膨大な遺伝情報からたどるヤポネシア人の起源  [招待講演]

  長田直樹

  サイエンスカフェ 2022年10月 公開講演，セミナー，チュートリアル，講習，講義等
• ゲノムから探る人類と野生ハツカネズミの歴史

  長田直樹

  第94回日本遺伝学会大会 2022年10月 口頭発表（招待・特別）
• 人類の多様性と歴史を解明するバイオインフォマティクス  [招待講演]

  長田直樹

  第二回名古屋産学官・医連携研究会（NJK） 2022年08月 公開講演，セミナー，チュートリアル，講習，講義等
• くにうみやわらか講座：ゲノム解析の基礎と考え方  [招待講演]

  長田直樹

  第3回ヤポネシアゲノムくにうみミーティング 2022年03月 公開講演，セミナー，チュートリアル，講習，講義等
• 東アジア人の分化と歴史

  長田直樹

  第3回ヤポネシアゲノムくにうみミーティング 2022年03月 公開講演，セミナー，チュートリアル，講習，講義等
• 東アジアから俯瞰する二重構造説  [招待講演]

  長田直樹

  埴原和郎二重構造モデル論文発表30周年記念公開シンポジウム 2021年11月 公開講演，セミナー，チュートリアル，講習，講義等
• 現代・古代人ゲノム情報を用いた日本列島への移住経路と混合様式の推定  [招待講演]

  長田直樹

  日本人類遺伝学会第67回大会 2021年10月 シンポジウム・ワークショップパネル（指名）
• 古代・現代人ゲノムデータをもとにしたヤポネシアへの人類移住経路の考察  [招待講演]

  長田直樹

  第75回日本人類学会 2021年10月 シンポジウム・ワークショップパネル（指名）
• 現代・古代東アジア人の遺伝的構造について  [招待講演]

  長田直樹

  第2回ヤポネシアゲノムくにうみミーティング 2021年03月 シンポジウム・ワークショップパネル（指名）
• Genome-wide genetic diversity of wild house mice across Eurasia  [招待講演]

  Naoki Osada

  Genome Concept Centennial Symposium 2021年02月 公開講演，セミナー，チュートリアル，講習，講義等
• マカク属7種のゲノム解析による進化モデルの構築  [通常講演]

  長田直樹, 松平一成, 濱田穣, Malaivijitnond Suchinda

  第36回日本霊長類学会 2020年12月 口頭発表（一般）
• Inference of East and Northeast Asian Population Histories using Present-day and Ancient Genome Sequence Data  [招待講演]

  Naoki Osada

  The First Meeting of the Academic Year 2020 Joint Research Project on “Studies in Asian and African Geolinguistics”, ILCAA 2020年10月 シンポジウム・ワークショップパネル（指名）
• ゲノム配列データからヤポネシア人の起源について考える  [招待講演]

  長田直樹

  第22回日本進化学会オンライン大会 2020年09月 シンポジウム・ワークショップパネル（指名）
• Big data in biology: perspectives of genomic diversity studies  [招待講演]

  Naoki Osada

  2019 Winter International Symposium on Big-Data, Cybersecurity and IoT 2019年12月 口頭発表（招待・特別）
• ソフトウェア講習  [招待講演]

  長田直樹

  第3回木村資生記念進化学セミナー 2019年08月 公開講演，セミナー，チュートリアル，講習，講義等
• 霊長類種間における遺伝子浸透様式の解析  [通常講演]

  長田直樹

  ヤポネシアゲノム若手研究集会 2019年01月 口頭発表（一般）
• 移住率の性による偏りをゲノムデータから探る  [通常講演]

  長田直樹

  ヤポネシアゲノムB02班班会議 2019年01月 公開講演，セミナー，チュートリアル，講習，講義等
• ゲノムからたどる人類進化の歴史  [招待講演]

  長田直樹

  名古屋大学遺伝子実験施設公開セミナー「ゲノム解析が見える化する生命の成り立ち」 2018年12月 公開講演，セミナー，チュートリアル，講習，講義等
• 性による移住率の偏りをゲノムデータから推定する  [招待講演]

  長田直樹

  日本人類学会大会公開シンポジウム：DNAからみたヒトの進化 2018年10月 口頭発表（招待・特別） 静岡県三島市
• 旧世界ザルゲノムに存在する内在性サルレトロウィルス（SERV）配列の探索と分子系統解析  [通常講演]

  池田昌輝, 里村和浩, 関塚剛史, 花田賢太郎, 遠藤俊徳, 長田直樹

  第90回日本遺伝学会 2018年09月 口頭発表（一般）
• Dissecting genetic and epigenetic gene expression regulatory variations in diploid organisms  [招待講演]

  長田直樹

  14th Japanese-German Frontiers of Science Symposium 2018年09月 ポスター発表
• ゲノム進化解析ソフトウェアの使い方  [通常講演]

  長田直樹

  第2回木村資生記念進化学セミナー 2018年09月 公開講演，セミナー，チュートリアル，講習，講義等
• 集団遺伝学とゲノム進化学  [招待講演]

  長田直樹

  第11回生物学基礎論研究会特別講演 2017年09月 口頭発表（招待・特別）
• 環境変動と集団サイズ変動の関係を考える  [通常講演]

  長田直樹

  日本列島（ヤポネシア）人のゲノム歴史学 2017年08月 口頭発表（一般）
• Quantifying genetic and epigenetic control of gene expression in Drosophila and mice  [招待講演]

  長田直樹

  The 5th international symposium “Frontier Science in Ecology, Genetics and Genomics” 2017年03月 口頭発表（招待・特別）
• 集団遺伝学データ解析  [招待講演]

  長田直樹

  ゲノム多様性データの統計解析ワークショップ 2016年12月 公開講演，セミナー，チュートリアル，講習，講義等
• Genomics of non-human primates: application to biomedical studies  [招待講演]

  Naoki Osada

  2016 HU/SNU joint symposium 2016年11月 口頭発表（招待・特別）
• Population genomics of non-human primates: a case of Mauritian cynomolgus macaques (Macaca fascicularis)  [通常講演]

  Naoki Osada, Soichi Sakurai

  5th Asian Primate Symposium 2016年10月 口頭発表（一般）
• An impact of population bottleneck on genomes: a case of Mauritian cynomolgus macaques (Macaca fascicularis)  [招待講演]

  Naoki Osada

  13th Japanese-German Frontiers of Science Symposium 2016年10月 ポスター発表
• 集団遺伝学データ解析  [通常講演]

  長田直樹

  ゲノム多様性データの統計解析ワークショップ 2015年12月 公開講演，セミナー，チュートリアル，講習，講義等 総合研究大学院大学葉山キャンパス
• Genetic architecture of gene expression variation in fruit flies  [通常講演]

  Naoki Osada

  12th Japanese-German Frontiers of Science Symposium 2015年10月 ポスター発表
• モーリシャス島産カニクイザルの全ゲノムシークエンス解析  [通常講演]

  長田直樹, Hettiarachchi Nilmini, Babarinde Isaac Adeyemi, 斎藤成也, Blancher Antoine

  第31回日本霊長類学会大会 2015年07月 口頭発表（一般）
• ボトルネックがゲノムに与える現象の解析：モーリシャス産カニクイザルを例に  [通常講演]

  長田直樹

  遺伝研研究集会「ビッグデータ時代の分子進化」 2015年06月 口頭発表（招待・特別）
• 集団遺伝学データ解析：ABCのABC  [通常講演]

  長田直樹

  ゲノム多様性データの統計解析ワークショップ 2014年12月 公開講演，セミナー，チュートリアル，講習，講義等
• Challenge of population genomics in non-model organisms  [通常講演]

  長田直樹

  Frontiers in Genomic Research 2014年12月 口頭発表（基調）
• 木村先生の研究に関連した、私の二つの研究トピック: 優性度による選択圧の違いと補完的進化  [通常講演]

  長田直樹

  木村資生博士生誕90周年記念シンポジウム 2014年11月 シンポジウム・ワークショップパネル（指名）
• Compensatory Evolution  [通常講演]

  長田直樹

  EvoDevo・PopGenの融合アプローチから明らかになる適応進化の新局面 2014年10月 シンポジウム・ワークショップパネル（指名）
• 日本遺伝学会奨励賞受賞講演「ゲノム情報と進化理論の統合による進化機構の解明」  [通常講演]

  長田直樹

  第86回日本遺伝学会大会 2014年09月 口頭発表（招待・特別）
• Allele-specific gene expression among Drosophila melanogaster hybrid lines revealed abundant cis-regulatory mutations  [通常講演]

  長田直樹

  国立遺伝学研究所研究会：ゲノム進化分野におけるビッグデータ情報解析の新展開 2014年03月 口頭発表（一般）
• Finding evidence for weak compensatory evolution  [通常講演]

  Naoki Osada, Hiroshi Akashi

  SMBE Satellite Meeting/NIG International Workshop: The Causes of Genome Evolution 2014年03月 口頭発表（招待・特別）
• 帰無モデルとしての中立説と歴史推定  [通常講演]

  長田直樹

  統計数理研究所研究集会：ゲノム多様性のデータ解析 2013年12月 口頭発表（招待・特別）
• Dissecting regulatory mechanisms of transcriptome variation in Drosophila melanogaster  [通常講演]

  Naoki Osada

  Seminar at Academia Sinica 2013年11月 口頭発表（招待・特別）
• Dissecting regulatory mechanisms of transcriptome variation in Drosophila melanogaster  [通常講演]

  Naoki Osada

  ISEGB2013 2013年11月 口頭発表（招待・特別）
• 霊長類のゲノム進化  [通常講演]

  長田直樹

  日本人類学会大会 2013年11月 口頭発表（一般）
• キイロショウジョウバエにおける集団内でのcisおよびtrans遺伝子発現変異の定量  [通常講演]

  長田直樹, 宮城竜太郎, 高橋文

  日本遺伝学会大会 2013年09月 口頭発表（一般）
• Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis  [通常講演]

  Naoki Osada, Shigeki Nakagome, Shuhei Mano, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao

  SMBE2013 2013年07月 ポスター発表
• Finding evidence for weak compensatory evolution  [通常講演]

  長田直樹

  NIG Collaborative Workshop: Evolution of Junk DNAs 2013年06月 口頭発表（一般）
• ヒトゲノムの進化における自然選択と遺伝的浮動の役割  [通常講演]

  長田直樹

  インシリコ・メガバンク研究会 2013年05月 口頭発表（招待・特別）
• Evolution of rice photoperiod genes  [通常講演]

  長田直樹

  NIG collaborative research meeting: Evolutionary Genetics and Proteomics of Natural Resources in Asia 2013年02月 口頭発表（一般）
• Ecological and Evolutionary Genomics of non-model organisms in Asia  [通常講演]

  長田直樹

  CKJ meeting: Genomics, Proteomics, and Bioinformatics with the Asian Perspective 2012年12月 口頭発表（一般）
• 実験用霊長類のゲノムとその多様性  [通常講演]

  長田直樹

  霊長類医科学研究フォーラム 2012年11月 口頭発表（招待・特別）
• 霊長類でのX染色体と常染色体との遺伝的多様性の比について  [通常講演]

  長田直樹

  日本人類学会大会 2012年11月 口頭発表（一般）
• ゲノムの分岐パターンから探る-歴史，種分化，適応  [通常講演]

  長田直樹

  みちのく進化生物セミナー 2012年10月 口頭発表（招待・特別）
• Genetic diversity of humans and nonhuman primates and its evolutionary implications  [通常講演]

  Naoki Osada

  Seminar at Academia Sinica 2012年09月 口頭発表（招待・特別）
• Inference of population history from genomic data  [通常講演]

  Naoki Osada

  Arabidopsis symposium 2012年09月 口頭発表（招待・特別）
• ゲノム情報を用いた集団の歴史の推定：霊長類や植物の例  [通常講演]

  長田直樹

  統計数理研究所研究集会：生物集団に関する遺伝データと集団遺伝学 2012年08月 口頭発表（一般）
• Compensatory Evolution between Mitochondrial and Nuclear Genomes  [通常講演]

  Naoki Osada

  Okazaki Biological Conference 8 (OBC8) 2012年03月 口頭発表（招待・特別）
• Inference of natural selection by stratifying individual genome sequences  [通常講演]

  長田直樹

  国立遺伝学研究所研究会：ゲノム多様性研究における革新的な知的発見のための戦略～次世代シーケンサーを用いたゲノム多様性研究における今後の課題～ 2012年03月 口頭発表（一般）
• Genetic diversity and population history of macaque monkeys  [通常講演]

  Naoki Osada

  Genomic Conservation and Diversity of Organisms: Beyond the NGS time of Life Science 2011年12月 口頭発表（招待・特別）
• Inference of population history using a single genome data  [通常講演]

  長田直樹

  日本分子生物学会年会 2011年12月 口頭発表（一般）
• 多座位データを用いたゲノムヒストリーの推定  [通常講演]

  長田直樹

  統計数理研究所共同利用重点型研究による研究集会：ゲノムの多様性，進化，疾患に関わる話題についての講演 2011年12月 口頭発表（招待・特別）
• メタゲノム解析とその応用  [通常講演]

  長田直樹

  メタゲノム解析を利用した下水道情報網基盤構築に関する研究集会 2011年11月 口頭発表（一般）
• 機能喪失とCpGサイトの崩壊による旧世界ザルCYP1A2遺伝子の高い遺伝的多様性  [通常講演]

  長田直樹, 宇野泰広

  日本遺伝学会大会 2011年09月 口頭発表（一般）
• Compensatory evolution between mitochondrial and nuclear genomes: evidence from primate respiratory chain complex genes  [通常講演]

  Naoki Osada

  SMBE2011 2011年07月 口頭発表（招待・特別）
• Compensatory Evolution between Mitochondrial and Nuclear Genomes: Evidence from Primate Respiratory Chain Complex Genes  [通常講演]

  Naoki Osada

  Seminar at National Taiwan University 2011年07月 口頭発表（招待・特別）
• 霊長類の中のヒト:ゲノム多様性の種間比較  [通常講演]

  長田直樹

  遺伝研共同研究集会：ヒト形質のゲノム発掘による新しい進化人類学の創成 2011年07月 口頭発表（一般）
• ヒトの遺伝的多様性―進化生物学的視点から  [通常講演]

  長田直樹

  日本赤十字第6回学術講演会 2011年06月 口頭発表（招待・特別）
• Compensatory Evolution between Mitochondrial and Nuclear Genomes: Evidence from Primate Respiratory Chain Complex Genes  [通常講演]

  Naoki Osada

  Seminar at National Cheng-Kung University 2011年03月 口頭発表（招待・特別）
• 人類集団における自然淘汰  [通常講演]

  長田直樹

  現生人類の拡散による遺伝子と文化の多様性創出に関する総合的研究 2011年03月 口頭発表（一般）
• Genetic analysis using multi-locus DNA sequence data for ecology and evolution research  [通常講演]

  長田直樹

  NIG Collaborative Research Meeting: Toward Next Generation Studies of Biodiversity and Bioresources 2010年11月 口頭発表（一般）
• ヒトの遺伝的多様性とゲノムにかかる自然選択について  [通常講演]

  長田直樹

  遺伝研共同研究集会：個人ゲノム時代におけるヒトゲノムDNA多型研究 2010年11月 口頭発表（一般）
• ミトコンドリア・核遺伝子間の弱有害補完モデル：霊長類COX遺伝子群の進化を例に  [通常講演]

  長田直樹, 明石裕

  日本遺伝学会大会 2010年08月 口頭発表（一般）
• マルチローカスデータを用いた進化生態学研究について  [通常講演]

  長田直樹

  日本進化学会大会 2010年08月 口頭発表（一般）
• Polymorphism, Divergence, and Speciation: Genomic Perspective  [通常講演]

  Naoki Osada

  Seminar at National Cheng-Kung University 2010年03月 口頭発表（招待・特別）
• 実験用霊長類の種差・個体差について：ゲノム解析の視点から  [通常講演]

  長田直樹

  日本薬学会大会融合型シンポジウム 2010年03月 口頭発表（招待・特別）
• カニクイザルのトランスクリプトーム解析  [通常講演]

  長田直樹

  国際生物多様性会議：霊長類のゲノム多様性研究 2010年03月 口頭発表（一般）
• 進化生物学への次世代シークエンサーの応用について  [通常講演]

  長田直樹

  国立遺伝学研究所研究集会：次世代シーケンサーを活用したゲノム多様性の研究 2010年01月 口頭発表（一般）
• カニクイザルcDNAライブラリーの解析とゲノム統合データベースの開発  [通常講演]

  長田直樹, 平田誠, 田沼玲子, 亀岡洋祐, 高橋一朗, 東濃篤範, 鈴木穣, 菅野純夫, 寺尾恵治, 楠田潤, 橋本雄之

  日本分子生物学会年会 2009年12月 ポスター発表
• 有害な突然変異とその優性度の推定について：ヒト疾患遺伝子の解析  [通常講演]

  長田直樹

  日本遺伝学会大会 2009年09月 口頭発表（一般）
• Ecological adaptation and speciation: genomic perspective  [通常講演]

  Naoki Osada

  Eawag CEEB joint workshop: Beyond the gaps among ecology, evolution and biogeochemistry 2009年08月 口頭発表（招待・特別）
• Analysis of gene duplication and conversion in the Drosophila melanogaster genome.  [通常講演]

  Naoki Osada, Hideki Innan

  JSPS Japan-Germany International Colloquium 2009年03月 口頭発表（招待・特別）
• Polymorphism, Divergence, and Speciation: Genomic Perspective  [通常講演]

  長田直樹

  国立遺伝学研究所 Biological symposium 2009年03月 口頭発表（招待・特別）
• カニクイザル骨髄・脾臓・膵臓由来cDNAライブラリーの解析  [通常講演]

  長田直樹, 亀岡洋祐, 平田誠, 田沼玲子, 鈴木穣, 菅野純夫, 高橋一朗

  日本分子生物学会年会 2008年12月 ポスター発表
• ヒトゲノム中の塩基置換多型と疾患関連遺伝子について  [通常講演]

  長田直樹

  日本人類学会大会 2008年11月 口頭発表（一般）
• Deleterious Mutations and Human Diseases: Genomic Perspective  [通常講演]

  長田直樹

  日本進化学会大会 2008年08月 口頭発表（一般）
• ヒト疾患とほぼ中立説  [通常講演]

  長田直樹

  国立遺伝学研究所研究集会：中立進化論の現在 2008年07月 口頭発表（招待・特別）
• 実験用マカク間における遺伝的分化と交雑についてのゲノム解析  [通常講演]

  長田直樹, 亀岡洋祐, 高橋一朗, 寺尾恵治

  日本霊長類学会大会 2008年07月 口頭発表（一般）
• Pattern of genetic admixture and differentiation between Macaca fascicularis and M. mulatta genome  [通常講演]

  Naoki Osada, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao

  SMBE2008 2008年06月 口頭発表（一般）
• Primate speciation: genes and genome  [通常講演]

  Naoki Osada

  Seminar at National Taiwan University 2008年05月 口頭発表（招待・特別）
• Primate speciation: genes and genome  [通常講演]

  長田直樹

  Seminar at National Cheng-Kung University 2008年05月 口頭発表（招待・特別）
• カニクイザルcDNAライブラリーコレクションの拡充とその解析  [通常講演]

  長田直樹, 橋本雄之, 楠田潤, 亀岡洋祐, 田沼玲子, 平田誠, 高橋一朗

  日本分子生物学会年会 2007年12月 ポスター発表
• 突然変異にかかる淘汰圧と遺伝子発現の関係について  [通常講演]

  長田直樹

  北海道大学バイオインフォマティクスセミナー 2007年10月 口頭発表（招待・特別）
• ヒトゲノム中での遺伝子発現パターンと淘汰圧との関係について  [通常講演]

  長田直樹

  日本遺伝学会大会 2007年09月 口頭発表（一般）
• 遺伝子配列と発現パターンから見た霊長類進化  [通常講演]

  長田直樹

  京都大学霊長類研究所共同利用プログラム/京都大学グローバルCOEプログラム：霊長類ゲノムと脳・感覚研究の最前線 2007年07月 口頭発表（招待・特別）
• カニクイザル由来cDNAデータベースの構築，アカゲザルとの比較解析  [通常講演]

  長田直樹, 橋本雄之, 平田誠, 田沼玲子, 亀岡洋祐, 楠田潤, 寺尾恵治, 高橋一朗

  日本霊長類学会大会 2007年07月 口頭発表（一般）
• 高等霊長類でのTMEM30C遺伝子転写の進化  [通常講演]

  長田直樹

  日本進化学会大会 2006年08月 ポスター発表
• Collection and analysis of primate disease-related homologs  [通常講演]

  Naoki Osada, Reiko Tanuma, Makoto Hirata, Ichirou Takahashi, Yousuke Kameoka, Katsuyuki Hashimoto, Jun Kusuda

  20th International congress of biochemistry and molecular biology and 11th FAOBMB congress 2006年06月 ポスター発表
• Divergence between human and macaque beyond the protein evolution  [通常講演]

  Naoki Osada, Katsuyuki Hashimoto, Reiko Tanuma, Makoto Hirata, Jun Kusuda

  Human Genome Meeting 2006 2006年05月 口頭発表（一般）
• カニクイザルcDNAの解析とデータベース構築  [通常講演]

  長田直樹, 平田誠, 田沼玲子, 高橋一朗, 亀岡洋祐, 橋本雄之, 楠田潤

  日本分子生物学会年会 2005年12月 ポスター発表
• カニクイザルcDNAデータベースの紹介と応用: ミトコンドリア蛋白で起こった正の淘汰  [通常講演]

  長田直樹

  日本遺伝学会大会 2005年09月 口頭発表（一般）
• ゲノムレベルでわかる霊長類進化  [通常講演]

  長田直樹

  遺伝研生命情報センターCIBセミナー 2005年06月 口頭発表（招待・特別）
• Cynomolgus monkey cDNA libraries: Rate and Pattern of 5’UTR evolution in primates  [通常講演]

  Naoki Osada, Makoto Hirata, Reiko Tanuma, Jun Kusuda, Katsuyuki Hashimoto

  Human Genome Meeting 2005 2005年04月 ポスター発表
• Rate and pattern of 5’ UTR evolution: comparative analysis between human and cynomolgus monkey  [通常講演]

  Naoki Osada, Makoto Hirata, Jun Kusuda, Reiko Tanuma, Katsuyuki Hashimoto

  International Workshop on Encoding Information in DNA Sequences 2005年02月 ポスター発表
• Gene expression of Drosophila melanogaster head with sexual isolation - cis-associated difference and pattern of sex, virginity and genotype  [通常講演]

  長田直樹, Kohn Michael, Greenberg Anthony, Shapiro Joshua, Wu Chung-I

  日本分子生物学会年会 2004年12月 ポスター発表
• Testing the mode of speciation with genomic data  [通常講演]

  Naoki Osada, Chung-I Wu

  Keystone symposia, Natural variation and quantitative genetics in model organism 2004年03月 ポスター発表
• カニクイザル脳cDNAを利用したヒトゲノム配列からのヒト新規遺伝子予測  [通常講演]

  長田直樹長田直樹, 肥田宗友, 楠田潤, 田沼玲子, 平田誠, 平井百樹, 橋本雄之

  2002年12月 口頭発表（一般）
• Identification of human homologs for novel cynomolgus monkey cDNAs  [通常講演]

  Naoki Osada

  Gordon Research Conference: GENOMICS & STRUCTURAL/EVOLUTIONARY BIOINFORMATICS 2002年08月 ポスター発表
• カニクイザル完全長cDNAの分離ーヒトゲノム配列での新規ヒト遺伝子同定および既知ヒト遺伝子との配列比較  [通常講演]

  長田直樹

  哺乳動物遺伝学研究会 2002年06月 口頭発表（一般）
• カニクイザル脳由来完全長cDNAライブラリーからの新規遺伝子の探索及び解析  [通常講演]

  長田直樹, 肥田宗友, 楠田潤, 田沼玲子, 伊関可奈子, 平田誠, 平井百樹, 数藤由美子, 橋本雄之

  日本人類学会大会 2001年08月 口頭発表（一般）
• カニクイザル脳由来完全長cDNAライブラリーの解析と新規遺伝子の探索  [通常講演]

  長田直樹, 肥田宗友, 楠田潤, 田沼玲子, 伊関可奈子, 平田誠, 平井百樹, 数藤由美子, 橋本雄之

  日本分子生物学会年会 2000年11月 ポスター発表
• CpGアイランドを指標にしたマウス脳由来新規完全長cDNAクローンの分離  [通常講演]

  田直樹, 楠田潤, 田沼玲子, 伊藤亜紀子, 平田誠, 平井百樹, 橋本雄之

  日本分子生物学会年会 1999年11月 ポスター発表
• ヒト第11番染色体末端領域におけるDNA複製タイミングの解析  [通常講演]

  長田直樹, 笠井文生, 伊関可奈子, 楠田潤, 橋本雄之

  日本分子生物学会年会 1998年11月 ポスター発表
• 染色体DNA複製タイミングのヒトと近縁霊長類における比較－FISH法による解析  [通常講演]

  長田直樹, 笠井文生, 寺尾恵治, 森祐介, 早坂郁夫

  日本人類学会大会 1998年09月 ポスター発表
• FISH法を利用したDNA複製タイミングの解析  [通常講演]

  長田直樹, 平井百樹

  日本人類学会大会 1997年11月 ポスター発表
• Population Genetics of Non-human Primates: How Are We Diverse?  [通常講演]

  Naoki Osada

  International Primatological Society Congress 口頭発表（一般）
• 進化生物学への次世代シークエンサーの応用について  [通常講演]

  長田直樹

  国立遺伝学研究所研究集会：次世代シーケンサーを活用したゲノム多様性の研究 口頭発表（一般）

その他活動・業績

• ソフトウェア紹介13：SLiM－前向きシミュレーターについて

  長田直樹 Yaponesian 4 (はる) 12 -13 2022年06月 [査読無し][招待有り]
  
• 最先端医療の今 ヤポネシア人の人口・歴史推定

  長田 直樹 Medical Science Digest 47 (9) 476 -478 2021年08月 

  日本という国家が成立するはるか以前、およそ4万年前から日本列島にはさまざまなひとびとが居住していた。これらの日本列島人を、われわれは「ヤポネシア人」と総称し、その成り立ちや歴史をゲノム科学・言語学・考古学との協業によって明らかにするために、2018年度より文部科学省科研費・新学術領域「ヤポネシアゲノム」プロジェクトを進めてきた。このような研究は、日本列島人のルーツを明らかにするということ以外にも、集団構造を考慮に入れた疾患原因遺伝子の探索や、地域差のある疾患原因変異の解明など、医学分野に対して貢献することも期待できる。研究計画班「ヤポネシア人の人口推定を中心とした巨大データ解析」では、多数のヒトゲノムから得られる一塩基多型(SNP)を含むさまざまな情報を用いて、ヤポネシア人がたどった歴史の推定などを行っている。(著者抄録)
• 東アジアから俯瞰する二重構造説

  Yaponesian 3 (ふゆ) 2021年 [査読無し][招待有り]
  
• ソフトウェア紹介9：TreeMixとqpGraph

  長田直樹 Yaponesian 3 (はる) 37 -39 2021年 [査読無し][通常論文]
  
• 論文紹介4：ゲノム規模の遺伝子データを用いた日本列島への人類の移動モデルの探索

  長田直樹 Yaponesian 3 (はる) 17 -21 2021年 [査読無し][招待有り]
  
• ソフトウェア紹介6：PLINK

  長田直樹 Yaponesian 2 (なつ) 9 -10 2020年09月 [査読無し][招待有り]
  
• ソフトウェア紹介1：FastQC

  長田直樹 Yaponesian 1 (はる) 20 -21 2019年05月 [査読無し][招待有り]
  
• ヤポネシア人の歴史の解明が医学にもたらすもの

  長田直樹 実験医学 37 926 -936 2019年04月 [査読無し][通常論文]
  
• ソフトウェア紹介はじまります

  長田直樹 Yaponesian 0 (0) 27 -28 2019年03月 [査読無し][通常論文]
  
• 研究計画B03班の紹介

  長田直樹 Yaponesian 0 (0) 16 -17 2019年03月 [査読無し][通常論文]
  
• Genome-wide analysis of cis- and trans-regulatory effects on gene expression using allele samples from a natural population of Drosophila melanogaster

  Naoki Osada, Ryutaro Miyagi, Aya Takahashi GENES & GENETIC SYSTEMS 91 (6) 372 -372 2016年12月 [査読無し][通常論文]
  
• Revisiting the Relationship between Evolutionary Conservation and Disease Causality: A Case Study of Beta Globin Gene

  Sangeetha Udani Ratnayake, Toshinori Endo, Naoki Osada GENES & GENETIC SYSTEMS 91 (6) 345 -345 2016年12月 [査読無し][通常論文]
  
• The cause of gene expression changes in reciprocal crosses of Drosophila melanogaster by measuring allele-specific gene expression

  Yasuaki Takada, Aya Takahashi, Ryutaro Miyagi, Toshinori Endo, Naoki Osada GENES & GENETIC SYSTEMS 91 (6) 372 -372 2016年12月 [査読無し][通常論文]
  
• 古代ゲノムの解析手法（情報編）

  長田直樹 細胞工学 34 1092 -1095 2015年11月 [査読無し][招待有り]
  
• Genome-scale approaches for studying human and non-human primate evolution

  Naoki Osada Genes and Genetic Systems 90 (3) 121 -122 2015年10月27日 [査読無し][通常論文]
  
• ポスドクからの留学先の選び方

  長田直樹 実験医学Webコラム 2015年08月 [査読無し][招待有り]
  
• ゲノム情報から生物進化の過程に迫る

  長田直樹 北海道大学大学院情報科学研究科ネットジャーナル 40 2015年06月 [査読無し][通常論文]
  
• Lineage-specific genome evolution in the Drosophila melanogaster subgroup

  Neha Mishra, Tomotaka Matsumoto, Naoki Osada, Hiroshi Akashi GENES & GENETIC SYSTEMS 89 (6) 277 -277 2014年12月 [査読無し][通常論文]
  
• 大規模全ゲノムシーケンシングによるニホンザルの種特異的ゲノム情報の探索

  福多 賢太郎, 野口 英樹, 豊田 敦, 長田 直樹, 郷 康弘, 石田 貴文, 伊佐 正, 藤山 秋佐夫 霊長類研究 Supplement 30 (0) 49 -49 2014年 

  ニホンザルは他のマカク属サルには見られない形態的特徴・社会的特徴を有しているとされ，運動学的，生理学的，認知学的，あるいは病理学的な様々な研究が進められている．
  マカク属の比較ゲノム解析には，2007年に公開されたインド産アカゲザルの全ゲノム配列（rheMac2）が参照配列として広く使われてきたが，ニホンザルを対象にした地域間ないし個体間の比較を行うためには，高精度かつ大規模な配列情報を元にしたニホンザル固有の参照配列を用いることが望ましい．そのため，我々はゲノムの200倍以上の被覆度を持つ配列（Illumina Hiseq2000による大阪府箕面産の個体の配列）を用いて参照配列の作成を進めているが，これと並行して，青森県下北半島産・長野県北部産・宮崎県幸島産の3個体のニホンザル，タイワンザル1個体*，タイ産カニクイザル1個体，中国産アカゲザル1個体*について，それぞれ約50倍の被覆度の配列データを用意し，rheMac2を参照配列とした比較ゲノム解析を実施した（*京大霊長類研究所共同利用研究）．
  ニホンザルは比較した他の個体に比べてホモ接合性が極めて高く，他のマカク属サルではヘテロ接合で有しているSNVs（single nucleotide variants）の多くがニホンザルではホモ接合となっていることが明らかとなった．分子系統学的解析の結果から，ニホンザルのゲノムの分岐年代（約144万年前）や有効集団サイズの歴史が推定され，これによって，ニホンザルが大陸から渡ってきた年代（約60万年前）や，ニホンザルに普遍的と思われる共通の強いボトルネックが約10万年前に存在することが推定できた．さらにSNVsの詳細な解析から，ニホンザルに特有なSNVsやニホンザルで有意に進化速度が速いと思われる遺伝子候補を見出した．本会では，全ゲノムレベルの大規模解析によって得られたニホンザルゲノムの特性について報告する．
• 進化学者に聞く！学生からの10の質問

  長田直樹 日本進化学会ニュース 15 (2) 6 -7 2014年 [査読無し][通常論文]
  
• Expression variation analyses of the dopamine biosynthesis pathway genes within Drosophila melanogaster wild population using PCR and 454 GS Junior

  Ryutaro Miyagi, Naoki Osada, Aya Takahashi GENES & GENETIC SYSTEMS 88 (6) 367 -367 2013年12月 [査読無し][通常論文]
  
• t-haplotype and molecular evolution of mouse Prdm9 gene

  Hiromitsu Kono, Masaru Tamura, Naoki Osada, Kunihiro Ohta, Toshihiko Shiroishi GENES & GENETIC SYSTEMS 88 (6) 368 -368 2013年12月 [査読無し][通常論文]
  
• 有害な変異と偶然の効果―中立説とほぼ中立説

  長田直樹 遺伝 (5) 322 -326 2013年05月 [査読無し][招待有り]
  
• Polymorphism analysis of mouse speciation / recombination hotspots activator gene Prdm9

  Hiromitsu Kono, Masaru Tamura, Naoki Osada, Hitoshi Suzuki, Kazuo Moriwaki, Kunihiro Ohta, Toshihiko Shiroishi GENES & GENETIC SYSTEMS 87 (6) 401 -401 2012年12月 [査読無し][通常論文]
  
• Genome-wide expression analyses using allelic samples from a natural population of Drosophila melanogaster

  Aya Takahashi, Naoki Osada GENES & GENETIC SYSTEMS 87 (6) 416 -416 2012年12月 [査読無し][通常論文]
  
• マレーシア産カニクイザルのゲノム解析

  東濃 篤徳, 坂手 龍一, 亀岡 洋祐, 高橋 一朗, 平田 誠, 田沼 玲子, 増井 徹, 保富 康宏, 長田 直樹 霊長類研究 Supplement 28 (0) 61 -61 2012年 [査読無し][通常論文]
   

  目的，カニクイザルは主要な実験動物の一種であるが種内での遺伝的差異が大きい上に，交配可能なアカゲザルとの遺伝子交流の頻度は産地ごとに異なると予想される．我々は産地による遺伝的差異を解明し，実験動物としてのカニクイザルの利用価値を高めるために，今回はマレーシア産カニクイザルの全ゲノム配列の決定を行った．
  方法，独立行政法人医薬基盤研究所・霊長類医科学研究センターで飼育管理されているマレーシア産カニクイザル（F1，オス）末梢血から抽出したゲノミックDNAをサンプルとした．カニクイザル全ゲノム配列にはSOLiD 3 Plusシステムを用いて約4.9 × 109リードを得た．ゲノムマッピングにはBioScopeを用い，リファレンス配列としてインド産アカゲザルゲノムを用いた．
  結果，インド産アカゲザルゲノムへのマッピングの結果，マッピング率は69.8％，合計1.1 × 1011 bpがマッピングされ，平均41.5倍のカバレージを持つマレーシア産カニクイザルゲノムデータを得た．インド産アカゲザルに対する1塩基多型（SNP）解析はSamtoolsを用いて行った．その結果およそ960万のSNPが検出された．更に，得られたゲノム配列をこれまでに決定されたベトナム産カニクイザル，中国産アカゲザル，インド産アカゲザルと比較することにより，カニクイザル-アカゲザル間で完全に分離しているSNPを同定した．免疫関連遺伝子群，薬剤代謝遺伝子群にかかわる遺伝子の中では60個の非同義置換が種特異的変異の候補として見つかった．全SNPデータはcDNAライブラリ，BACクローン，マイクロサテライトデータとともにデータベースを構築して公開している．
  考察，非同義置換SNPはカニクイザルとアカゲザルにおける薬剤や病原体に対する種特異的な反応を規定する候補因子を探索する際に有用なデータとなる．高カバレージのカニクイザル全ゲノム配列はマカク種内での遺伝的差異の解明のための基礎データとして，さらに実験動物リソースとしての価値を高めると考えられる．
• 遺伝子発現の確率的な挙動が生物集団へ与える影響

  峯田克彦, 松本知高, 長田直樹, 荒木仁志 日本分子生物学会年会プログラム・要旨集(Web) 35th 1P-0013 (WEB ONLY) 2012年 [査読無し][通常論文]
  
• Gene expression and protein evolution in Drosophila

  Hiroshi Akashi, Naoki Osada GENES & GENETIC SYSTEMS 86 (6) 388 -388 2011年12月 [査読無し][通常論文]
  
• Functional loss and CpG site degeneration created a high genetic diversity of macaque CYP1A2

  Naoki Osada, Yasuhiro Uno GENES & GENETIC SYSTEMS 86 (6) 443 -443 2011年12月 [査読無し][通常論文]
  
• Compensatory mutation model between mitochondrial and nuclear genomes: an example of COX evolution in primates

  Naoki Osada, Hiroshi Akashi GENES & GENETIC SYSTEMS 85 (6) 439 -439 2010年12月 [査読無し][通常論文]
  
• 次世代シークエンサーを用いたカニクイザルにおける遺伝子発現解析

  東濃篤徳, 長田直樹, 坂手龍一, 平田誠, 亀岡洋祐, 保富康弘, 高橋一朗 生化学 ROMBUNNO.1P-0709 2010年 [査読無し][通常論文]
  
• Genetic admixture and differentiation between laboratory macaques

  Naoki Osada, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao GENES & GENETIC SYSTEMS 83 (6) 523 -523 2008年12月 [査読無し][通常論文]
  
• 系統特異的重複および欠失によるケモカイン遺伝子ファミリーの急速な進化

  野見山 尚之, 長田 直樹, 楠田 潤, 義江 修 日本生化学会大会・日本分子生物学会年会合同大会講演要旨集 81回・31回 1T2 -11 2008年11月 [査読無し][通常論文]
  
• JCRB遺伝子バンク： 疾患研究と創薬にむけた遺伝子バンク

  長田直樹, 高橋一朗 細胞工学 26 1307 -1308 2007年 [査読無し][招待有り]
  
• Mitochondrial DNA diversity of the Philippine Negrito populations.

  Y Suto, N Osada, M Hirai, S Misawa, K Omoto ANTHROPOLOGICAL SCIENCE 111 (1) 74 -74 2003年01月 [査読無し][通常論文]
  
• Isolation and sequence analysis of newly identified clones from full-length cynomolgus monkey brain cDNA library

  N Osada, Y Suto, M Hida, M Hirai, J Kusuda, R Tanuma, K Iseki, M Hirata, K Hashimoto ANTHROPOLOGICAL SCIENCE 110 (1) 81 -81 2002年01月 [査読無し][通常論文]
  
• Assignment of 118 novel cDNAs of cynomolgus monkey brain to human chromosomes (vol 275, pg 31, 2001)

  N Osada, M Hida, J Kusuda, R Tanuma, K Iseki, M Hirata, Y Suto, M Hirai, K Terao, Y Suzuki, S Sugano, K Hashimoto GENE 278 (1-2) 267 -267 2001年10月 [査読無し][通常論文]
  
• 第24回日本分子生物学会年会 The 24th Annual Meeting of the Molecular Biology Society of Japan

  長田直樹, 山下順範, 川崎勝己 バイオサイエンスとインダストリー = Bioscience & industry 60 41 -42 2001年 [査読無し][通常論文]
  
• 第23回日本分子生物学会年会 The 23th Annual Meeting of the Molecular Biology Society of Japan

  和地正明, 長田直樹, 山下康治 バイオサイエンスとインダストリー = Bioscience & industry 59 40 -41 2000年 [査読無し][通常論文]
  
• Analysis of DNA replication timing using FISH: A comparative study in primates

  N Osada, F Kasai, K Terao, Y Mori, Hayasaka, I, M Hirai ANTHROPOLOGICAL SCIENCE 107 (1) 56 -56 1999年01月 [査読無し][通常論文]
  
• ヒト第11番染色体末端領域におけるDNA複製タイミングの解析

  長田 直樹, 笠井 文生, 伊関 可奈子, 楠田 潤, 橋本 雄之, 平井 百樹 日本分子生物学会年会プログラム・講演要旨集 21 363 -363 1998年12月01日
• Analysis of replication timing of chromosomal DNA by FISH-based assay

  N Osada, M Hirai ANTHROPOLOGICAL SCIENCE 106 (2) 166 -166 1998年04月 [査読無し][通常論文]
  

受賞

• 2019年07月 日本学術振興会 特別研究員等審査会専門委員（書面担当）の表彰
   

  受賞者: 長田直樹
• 2014年09月 日本遺伝学会 日本遺伝学会奨励賞
   ゲノム情報と進化理論の統合による進化機構の解明 

  受賞者: 長田直樹
• 2007年10月 日本遺伝学会 ベストペーパー賞
   On the correlation between gene expression pattern and selection intensity in the human genome 

  受賞者: 長田直樹

共同研究・競争的資金等の研究課題

• 先史人類による人為的環境形成（動物相）に関する研究

  日本学術振興会：科学研究費助成事業 学術変革領域研究(A)

  研究期間 : 2023年04月 -2028年03月 

  代表者 : 長田 直樹
• 日本列島域における先史人類史の総合的復元方法の研究

  日本学術振興会：科学研究費助成事業 学術変革領域研究(A)

  研究期間 : 2023年04月 -2028年03月 

  代表者 : 山田 康弘
• ヒトゲノム中に多型的に存在するウイルス様配列の大規模探索と集団ゲノム解析

  日本学術振興会：科学研究費助成事業 基盤研究(B)

  研究期間 : 2022年04月 -2026年03月 

  代表者 : 長田 直樹, 河合 洋介
• 種内数千ゲノム比較によるピンポイント適応変異数千の検出

  日本学術振興会：科学研究費助成事業

  研究期間 : 2023年04月 -2026年03月 

  代表者 : 小林 一三, 長田 直樹, 内山 郁夫, 大崎 敬子, 印南 秀樹
• 血中exosome内circRNA発現解析による膵癌の診断・予後関連マーカー探索

  日本学術振興会：科学研究費助成事業 基盤研究(C)

  研究期間 : 2022年04月 -2025年03月 

  代表者 : 柿坂 達彦, 蒲池 浩文, 長田 直樹, 神山 俊哉, 折茂 達也
• ヤポネシア人の人口推定を中心とした巨大データ解析

  日本学術振興会：科学研究費助成事業

  研究期間 : 2018年06月 -2023年03月 

  代表者 : 長田 直樹, 五條堀 淳, 河合 洋介, 藤本 明洋

   

  当初の計画に沿って研究を進行したが，その他の関連する研究も行った．ヤポネシア人ゲノムの解析については，東アジア人におけるアミラーゼ遺伝子のコピー数推定を行った．その際，コピー数推定のバラツキが少なくなるような手法を開発し，従来手法よりもよい精度で東アジア人集団のアミラーゼ遺伝子コピー数推定を行った．その結果，縄文人が現代東アジア人で典型的な8コピーのAMY1遺伝子をもっていることが示された．また，ハプロタイプ情報を用いてヤポネシア人と他の人類集団との分岐年代を推定した．その他，新規手法に基づいて同定されたマイクロサテライト配列の多型を用いて人類集団の解析を行い，従来手法よりもSNP解析に近い結果を得ることができた．さらに，9850人のヤポネシア人全ゲノムシークエンスデータの解析を行い，日本列島内での現代人の遺伝的構造を高解像度で示すことに成功した．他に，希少変異解析を用いて複数の縄文人個体ゲノムや弥生人ゲノムを解析し，別の手法を用いて解析を行った結果と比較した． その他，マダガスカル産ハツカネズミの全ゲノム解析による渡来経路の推定，北海道産ヒグマの全ゲノム解析による集団動態の解析，日本列島におけるハツカネズミの亜種間交雑過程の全ゲノム規模での解析，ハイイロオオカミ，ニホンオオカミ，イヌなどのゲノム解析に関する研究など，ヤポネシア人に関する研究だけでなく，動植物のゲノム解析などについての解析を他研究班と共同で進めた．
• ゲノム配列を核としたヤポネシア人の起源と成立の解明

  日本学術振興会：科学研究費助成事業

  研究期間 : 2018年06月 -2023年03月 

  代表者 : 斎藤 成也, 藤尾 慎一郎, 木部 暢子, 篠田 謙一, 遠藤 光暁, 鈴木 仁, 長田 直樹

   

  リースしているサーバー(すさのを)および国立遺伝学研究所のスーパーコンピュータを用いて、現代人ゲノムの解析環境をととのえた。2019年度に購入したサーバー2台(うみさちとやまさち)を用いて、古代人や公開されている現代人ゲノムや動植物ゲノムデータの格納をおこない、それらデータの解析環境を整えた。季刊誌Yaponesianの2021年はる号、なつ号、あき号、2022年ふゆ号を編集刊行した。新学術領域研究ヤポネシアゲノムのウェブサイトを運営した。2021年6月12-13日に、オンラインにて総括班会議と全体会議を開催した。2021年11月28日に、国際日本文化研究センターと共催で「埴原和郎の二重構造モデル論文発表３０周年記念公開シンポジウム」をハイブリッド方式で開催した。2022年2月12-13日に、オンラインにて全体会議と総括班会議をハイブリッド方式で開催した。2022年3月15-17日に、 「第3回くにうみミーティング」(若手研究者育成の一環)を開催した。
• 補完的分子進化に関する理論的・実験的研究

  日本学術振興会：科学研究費助成事業

  研究期間 : 2014年04月 -2017年03月 

  代表者 : 長田 直樹

   

  DNA塩基配列やタンパク質アミノ酸配列において，二つ以上の突然変異が互いに補い合って適応度を保つように進化することを補完的分子進化と呼ぶ．本研究計画では，まず弱有害な効果が集団中に固定し，その後それを補完する適応的変異が固定するという弱有害補完的分子進化について，どのような分子メカニズムが存在するか，また，現実に存在する分子データから存在の大きさが確かめられるかについて様々な分子メカニズムを対象として検証を行った．
• 霊長類ゲノムをモデルとした塩基配列進化の総合的研究

  日本学術振興会：科学研究費助成事業

  研究期間 : 2014年04月 -2017年03月 

  代表者 : 斎藤 成也, 池尾 一穂, 太田 聡史, 長田 直樹, 古賀 章彦, 北野 誉

   

  斎藤成也を中心に、進化的に保存されている非コード領域（ＣＮＳ）について、全真核生物、羊膜類、ヒト上科、ヒト科といったさまざまな生物群のゲノムを比較して一連の解析をおこない、ＣＮＳのさまざまな新規特徴があきらかになった。古賀章彦を中心に、新世界ザルの反復配列進化を解析した。北野誉を中心に、チンパンジーのＲｈ式血液型遺伝子の構造を詳細に解析した。長田直樹を中心に、モーリシャス島のカニクイザルゲノム配列を解析した。またチベットマカクのゲノム解析もおこなった。太田聡史を中心に、マウスのENU誘発突然変異のパターンを解析した。池尾一穂を中心に、カニクイザルゲノムのアノテーションを行なった。
• 体色の多様化が生む脳遺伝子の発現変化と性行動不適合性の解析

  日本学術振興会：科学研究費助成事業

  研究期間 : 2011年04月 -2016年03月 

  代表者 : 高橋 文, 長田 直樹

   

  本研究では、環境適応が引き金となって新たな生殖的隔離が生じるという種分化機構のモデルケースとしてショウジョウバエの体色と行動の両方に関与するドーパミン生合成系の遺伝子群の種内発現変異を研究材料とし、新たなシス制御領域の存在やの体色と行動の両方に影響を与える遺伝的な変異の存在が明らかとなった。また、新たな実験デザインによるゲノムワイドなトランスクリプトーム解析を行い、遺伝子発現制御に関わるゲノム因子の間の様々な相関関係が浮き彫りになった。
• 次世代シークエンサーを用いた人工・自然雑種の遺伝子発現ネットワーク解析

  日本学術振興会：科学研究費助成事業

  研究期間 : 2010年04月 -2014年03月 

  代表者 : 長田 直樹

   

  異なった二種のゲノムが一つになった時には，様々な遺伝的な相互作用が起こると考えられている．本研究は特に，モデル生物であるシロイヌナズナの近縁種に注目して，次世代シークエンサーを用いたトランスクリプトーム解析を行った．これらの二種には自然に発生したと考えられる異質倍数体が存在することが知られている．これらの異質倍数体と親種の遺伝子発現様式をゲノムレベルで比較した．本研究で新たに解読された親種のゲノム配列をもとに各染色体由来の転写産物が偏りなく推定できるような方法を開発し，それをもとに転写産物の発現量を推定した．
• 動物資源の安定供給に向けた繁殖および品質管理技術の高度化に関する研究

  厚生労働省：生物資源研究事業

  研究期間 : 2007年05月 -2010年03月 

  代表者 : 寺尾恵治
• ケモカインファミリー遺伝子の「生と死」と新規機能獲得に関する研究

  文部科学省：科学研究費補助金(基盤研究(C))

  研究期間 : 2007年 -2008年 

  代表者 : 野見山尚之, 瀬戸山千秋, 長田直樹

   

  ケモカインファミリー遺伝子は進化速度が特に早い. そのメンバーであるカニクイザル特異的CXCL1L遺伝子は, mRNAは発現するにもかかわらず, タンパク質はほとんど合成しない. その翻訳抑制機構を解析し, ケモカイン遺伝子進化との関係において考察した.
• 実験用霊長類(マカク属)における種内および種間の遺伝的多様性に関する研究

  文部科学省：科学研究費補助金(若手研究(B))

  研究期間 : 2007年 -2008年 

  代表者 : 長田直樹

   

  感染症などの医学研究、創薬などの薬学研究において、哺乳類実験動物、特に霊長類はヒトと遺伝的に非常に近く、重要な位置を占める.ところが、医薬学の実験にサル類の遺伝的多様性がどのような影響を及ぼすかは全くの未知数である.また、これらの実験用霊長類のなかにどれだけの種間・種内の遺伝的多様性があるのかもはっきりとはわかっていないのが現状である.これらを明らかにするため、マカク属の中でも実験用霊長類としてメジャーなアカゲザルとカニクイザルの個体より得られたDNAの多型解析を行った.その結果、1)カニクイザルの遺伝的多様性は現生人類よりも4-5倍高い値を示す、2)カニクイザルとアカゲザルでは、種がわかれた後に遺伝子交流があったかもしれない、3)薬剤代謝にかかわる遺伝子のいくつかは種間の遺伝子での分化度が非常に高い、ということが示された.

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