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Last Updated :2024/07/25

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Master

Affiliation (Master)

  • Faculty of Information Science and Technology　Bioengineering and Bioinformatics　Bioinformatics

Affiliation (Master)

  • Faculty of Information Science and Technology　Bioengineering and Bioinformatics　Bioinformatics

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Profile and Settings

Profile and Settings

  • Name (Japanese)

    Osada

  • Name (Kana)

    Naoki

  • Name

    200901034194227400

Alternate Names

Achievement

Research Interests

  • 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   

Research Areas

  • Life sciences / Systems genomics
  • Life sciences / Genomics
  • Life sciences / Biodiversity and systematics
  • Life sciences / Evolutionary biology

Research Experience

  • 2019/04 - Today Hokkaido University
  • 2012/05 - Today 放射線医科学総合研究所 客員研究員
  • 2017/09 - 2021/03 Hokkaido University
  • 2015/04 - 2019/03 Hokkaido University Graduate School of Information Science and Technology
  • 2010/01 - 2015/03 National Institute of Genetics, SOKENDAI 助教
  • 2011/12 - 2011/12 台湾国立成功大学 客員助理教授
  • 2009/01 - 2009/12 台湾国立成功大学 兼任助理教授
  • 2005/04 - 2009/12 独立行政法人医薬基盤研究所 研究員
  • 2004/10 - 2005/03 国立感染症研究所 研究官
  • 2003/03 - 2004/10 シカゴ大学 リサーチアソシエイト
  • 2002/04 - 2002/12 東京大学 特別研究員

Education

  • 1997/04 - 2002/03  東京大学大学院
  • 1993/04 - 1997/03  University of Tokyo

Awards

  • 2019/07 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
  • 2014/09 Genetic Society of Japan The GSJ Award for Young Scientists
     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: Naoki Osada
  • 2007/10 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

Published Papers

  • Zhenxin Fan, Rusong Zhang, Anbo Zhou, Jody Hey, Yang Song, Naoki Osada, Yuzuru Hamada, Bisong Yue, Jinchuan Xing, Jing Li
    Journal of Molecular Evolution 0022-2844 2024/04/18 [Refereed]
  • Kazumichi Fujiwara, Shunpei Kubo, Toshinori Endo, Toyoyuki Takada, Toshihiko Shiroishi, Hitoshi Suzuki, Naoki Osada
    Genome Research 1088-9051 2024/03/20 [Refereed]
     
    The house mouse (Mus musculus), which is commensal to humans, has spread globally via human activities, leading to secondary contact between genetically divergent subspecies. This pattern of genetic admixture can provide insights into the selective forces at play in this well-studied model organism. Our analysis of 163 house mouse genomes, with a particular focus on East Asia, revealed substantial admixture between the subspeciescastaneusandmusculus, particularly in Japan and southern China. We revealed, despite the different level of autosomal admixture among regions, that all Y Chromosomes in the East Asian samples belonged to themusculus-type haplogroup, potentially explained by genomic conflict under sex-ratio distortion owing to varying copy numbers of ampliconic genes on sex chromosomes,SlxandSly. Our computer simulations, designed to replicate the observed scenario, show that the preferential fixation ofmusculus-type Y Chromosomes can be achieved with a slight increase in the male-to-female birth ratio. We also investigated the influence of selection on the posthybridization of the subspeciescastaneusandmusculusin Japan. Even though the genetic background of most Japanese samples closely resembles the subspeciesmusculus, certain genomic regions overrepresented thecastaneus-like genetic components, particularly in immune-related genes. Furthermore, a large genomic block (∼2 Mbp) containing a vomeronasal/olfactory receptor gene cluster predominantly harboredcastaneus-type haplotypes in the Japanese samples, highlighting the crucial role of olfaction-based recognition in shaping hybrid genomes.
  • Sangeetha Ratnayake, Axel Martinelli, Toshinori Endo, Naoki Osada
    IPSJ Transactions on Bioinformatics 17 10 - 17 2024/02 [Refereed][Not invited]
  • Satoshi D. Ohdachi, Kazumichi Fujiwara, Chandra Shekhar, Nguyn Trưng Sơn, Hitoshi Suzuki, Naoki Osada
    Zoological Science 41 (2) 0289-0003 2024/01/30 [Refereed][Not invited]
  • Sangeetha Ratnayake, Axel Martinelli, Toshinori Endo, Naoki Osada
    IPSJ Transactions on Bioinformatics 17 40 - 47 2024 [Refereed][Not invited]
  • Kaisa Thorell, Zilia Y. Muñoz-Ramírez, Difei Wang, Santiago Sandoval-Motta, Rajiv Boscolo Agostini, Silvia Ghirotto, Roberto C. Torres, Judith Romero-Gallo, Uma Krishna, Richard M. Peek, M. Blanca Piazuelo, Naïma Raaf, Federico Bentolila, Hafeza Aftab, Junko Akada, Takashi Matsumoto, Freddy Haesebrouck, Rony P. Colanzi, Thais F. Bartelli, Diana Noronha Nunes, Adriane Pelosof, Claudia Zitron Sztokfisz, Emmanuel Dias-Neto, Paulo Pimentel Assumpção, Ivan Tishkov, Laure Brigitte Kouitcheu Mabeku, Karen J. Goodman, Janis Geary, Taylor J. Cromarty, Nancy L. Price, Douglas Quilty, Alejandro H. Corvalan, Carolina A. Serrano, Robinson Gonzalez, Arnoldo Riquelme, Apolinaria García-Cancino, Cristian Parra-Sepúlveda, Giuliano Bernal, Francisco Castillo, Alisa M. Goldstein, Nan Hu, Philip R. Taylor, Maria Mercedes Bravo, Alvaro Pazos, Luis E. Bravo, Keith T. Wilson, James G. Fox, Vanessa Ramírez-Mayorga, Silvia Molina-Castro, Sundry Durán-Bermúdez, Christian Campos-Núñez, Manuel Chaves-Cervantes, Evariste Tshibangu-Kabamba, Ghislain Disashi Tumba, Antoine Tshimpi-Wola, Patrick de Jesus Ngoma-Kisoko, Dieudonné Mumba Ngoyi, Modesto Cruz, Celso Hosking, José Jiménez Abreu, Christine Varon, Lucie Benejat, Ousman Secka, Alexander Link, Peter Malfertheiner, Michael Buenor Adinortey, Ansumana Sandy Bockarie, Cynthia Ayefoumi Adinortey, Eric Gyamerah Ofori, Dionyssios N. Sgouras, Beatriz Martinez-Gonzalez, Spyridon Michopoulos, Sotirios Georgopoulos, Elisa Hernandez, Braulio Volga Tacatic, Mynor Aguilar, Ricardo L. Dominguez, Douglas R. Morgan, Hjördís Harðardóttir, Anna Ingibjörg Gunnarsdóttir, Hallgrímur Guðjónsson, Jón Gunnlaugur Jónasson, Einar S. Björnsson, Mamatha Ballal, Vignesh Shetty, Muhammad Miftahussurur, Titong Sugihartono, Ricky Indra Alfaray, Langgeng Agung Waskito, Kartika Afrida Fauzia, Ari Fahrial Syam, Hasan Maulahela, Reza Malekzadeh, Masoud Sotoudeh, Avi Peretz, Maya Azrad, Avi On, Valli De Re, Stefania Zanussi, Renato Cannizzaro, Vincenzo Canzonieri, Takaya Shimura, Kengo Tokunaga, Takako Osaki, Shigeru Kamiya, Khaled Jadallah, Ismail Matalka, Nurbek Igissinov, Mariia Satarovna Moldobaeva, Attokurova Rakhat, Il Ju Choi, Jae Gyu Kim, Nayoung Kim, Minkyo Song, Mārcis Leja, Reinis Vangravs, Ģirts Šķenders, Dace Rudzīte, Aiga Rūdule, Aigars Vanags, Ilze Kikuste, Juozas Kupcinskas, Jurgita Skieceviciene, Laimas Jonaitis, Gediminas Kiudelis, Paulius Jonaitis, Vytautas Kiudelis, Greta Varkalaite, Jamuna Vadivelu, Mun Fai Loke, Kumutha Malar Vellasamy, Roberto Herrera-Goepfert, Juan Octavio Alonso-Larraga, Than Than Yee, Kyaw Htet, Takeshi Matsuhisa, Pradeep Krishna Shrestha, Shamshul Ansari, Olumide Abiodun, Christopher Jemilohun, Kolawole Oluseyi Akande, Oluwatosin Olu-Abiodun, Francis Ajang Magaji, Ayodele Omotoso, Chukwuemeka Chukwunwendu Osuagwu, Uchenna Okonkwo, Opeyemi O. Owoseni, Carlos Castaneda, Miluska Castillo, Billie Velapatino, Robert H. Gilman, Paweł Krzyżek, Grażyna Gościniak, Dorota Pawełka, Izabela Korona-Glowniak, Halina Cichoz-Lach, Monica Oleastro, Ceu Figueiredo, Jose C. Machado, Rui M. Ferreira, Dmitry S. Bordin, Maria A. Livzan, Vladislav V. Tsukanov, Patrick Tan, Khay Guan Yeoh, Feng Zhu, Reid Ally, Rainer Haas, Milagrosa Montes, María Fernández-Reyes, Esther Tamayo, Jacobo Lizasoain, Luis Bujanda, Sergio Lario, María José Ramírez-Lázaro, Xavier Calvet, Eduard Brunet-Mas, María José Domper-Arnal, Sandra García-Mateo, Daniel Abad-Baroja, Pedro Delgado-Guillena, Leticia Moreira, Josep Botargues, Isabel Pérez-Martínez, Eva Barreiro-Alonso, Virginia Flores, Javier P. Gisbert, Edurne Amorena Muro, Pedro Linares, Vicente Martin, Laura Alcoba, Tania Fleitas-Kanonnikoff, Hisham N. Altayeb, Lars Engstrand, Helena Enroth, Peter M. Keller, Karoline Wagner, Daniel Pohl, Yi-Chia Lee, Jyh-Ming Liou, Ming-Shiang Wu, Bekir Kocazeybek, Suat Sarıbas, İhsan Tasçı, Süleyman Demiryas, Nuray Kepil, Luis Quiel, Miguel Villagra, Morgan Norton, Deborah Johnson, Robert J. Huang, Joo Ha Hwang, Wendy Szymczak, Saranathan Rajagopalan, Emmanuel Asare, William R. Jacobs, Haejin In, Roni Bollag, Aileen Lopez, Edward J. Kruse, Joseph White, David Y. Graham, Charlotte Lane, Yang Gao, Patricia I. Fields, Benjamin D. Gold, Marcia Cruz-Correa, María González-Pons, Luz M. Rodriguez, Vo Phuoc Tuan, Ho Dang Quy Dung, Tran Thanh Binh, Tran Thi Huyen Trang, Vu Van Khien, Xiongfong Chen, Castle Raley, Bailey Kessing, Yongmei Zhao, Bao Tran, Andrés J. Gutiérrez-Escobar, Yunhu Wan, Belynda Hicks, Bin Zhu, Kai Yu, Bin Zhu, Meredith Yeager, Amy Hutchinson, Kedest Teshome, Kristie Jones, Wen Luo, Quentin Jehanne, Yukako Katsura, Patricio Gonzalez-Hormazabal, Xavier Didelot, Sam Sheppard, Eduardo Tarazona-Santos, Leonardo Mariño-Ramírez, John T. Loh, Steffen Backert, Michael Naumann, Christian C. Abnet, Annemieke Smet, Douglas E. Berg, Álvaro Chiner-Oms, Iñaki Comas, Francisco José Martínez-Martínez, Roxana Zamudio, Philippe Lehours, Francis Megraud, Koji Yahara, Martin J. Blaser, Tamas Vincze, Richard D. Morgan, Richard J. Roberts, Stephen J. Chanock, John P. Dekker, Javier Torres, Timothy L. Cover, Mehwish Noureen, Wolfgang Fischer, Filipa F. Vale, Joshua L. Cherry, Naoki Osada, Masaki Fukuyo, Masanori Arita, Yoshio Yamaoka, Ichizo Kobayashi, Ikuo Uchiyama, Daniel Falush, M. Constanza Camargo, Charles S. Rabkin
    Nature Communications 14 (1) 2023/12/11 [Refereed][Not invited]
     
    Abstract Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics.
  • Kazuhiro Zakoh, Kazumichi Fujiwara, Toyoyuki Takada, Naoki Osada, Hitoshi Suzuki
    Genes & Genetic Systems 1341-7568 2023 [Refereed][Not invited]
  • Kazumichi Fujiwara, Marie C. Ranorosoa, Satoshi D. Ohdachi, Satoru Arai, Yuki Sakuma, Hitoshi Suzuki, Naoki Osada
    Genes & Genetic Systems 97 (4) 193 - 207 1341-7568 2022/08/01 [Refereed][Not invited]
  • Yi Cong, Misaki Shintani, Fuga Imanari, Naoki Osada, Toshinori Endo
    OMICS: A Journal of Integrative Biology 26 (6) 339 - 347 2022/06/01 [Refereed][Not invited]
  • Kazumichi Fujiwara, Yosuke Kawai, Toyoyuki Takada, Toshihiko Shiroishi, Naruya Saitou, Hitoshi Suzuki, Naoki Osada
    Genome Biology and Evolution 14 (5) 2022/05/03 [Refereed][Not invited]
     
    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.
  • Kazuhiro Konishi, Toshiyuki Yamaji, Chisato Sakuma, Fumio Kasai, Toshinori Endo, Arihiro Kohara, Kentaro Hanada, Naoki Osada
    Frontiers in Genetics 13 1 - 9 2022/03/22 [Refereed][Not invited]
     
    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.
  • Takahiro Nakamura, Toshinori Endo, Naoki Osada
    IPSJ Transactions on Bioinformatics 15 9 - 16 2022/03 [Refereed][Not invited]
  • Toki Takeishi, Kazumichi Fujiwara, Naoki Osada, Akihiko Mita, Toyoyuki Takada, Toshihiko Shiroishi, Hitoshi Suzuki
    Genes & Genetic Systems 96 1 - 14 1341-7568 2022/03 [Refereed][Not invited]
  • Kazumichi Fujiwara, Marie C Ranorosoa, Satoshi D Ohdachi, Satoru Arai, Yuki Sakuma, Hitoshi Suzuki, Naoki Osada
    2021/09/10 [Not refereed]
     
    AbstractIn 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.
  • Yu Endo, Naoki Osada, Tsutomu Mano, Ryuichi Masuda
    Genome Biology and Evolution 2021 [Refereed][Not invited]
     
    Abstract 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.
  • 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 0018-067X 2021/01 [Refereed][Not invited]
     
    AbstractThe 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.
  • NAOKI OSADA, YOSUKE KAWAI
    Anthropological Science 一班社団法人 日本人類学会 129 (1) 45 - 58 0918-7960 2021 [Refereed][Invited]
     

    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.

  • Naoki Osada, Kazunari Matsudaira, Yuzuru Hamada, Suchinda Malaivijitnond
    Genome Biology and Evolution 13 evaa233  2021 [Refereed][Not invited]
     
    Abstract 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.
  • Masaki Kawamoto, Toshiyuki Yamaji, Kyoko Saito, Yoshitaka Shirasago, Kazuhiro Satomura, Toshinori Endo, Masayoshi Fukasawa, Kentaro Hanada, Naoki Osada
    Frontiers in Genetics 11 2020/10/09 [Refereed]
  • Kyoko Saito, Masayoshi Fukasawa, Yoshitaka Shirasago, Ryosuke Suzuki, Naoki Osada, Toshiyuki Yamaji, Takaji Wakita, Eiji Konishi, Kentaro Hanada
    PloS one 15 (4) e0232274  2020 [Refereed][Not invited]
     
    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.
  • 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 2020/01 [Refereed][Not invited]
  • Kazuhiro Satomura, Naoki Osada, Toshinori Endo
    Ecological Genetics and Genomics 13 100045  2019/09 [Refereed][Not invited]
  • 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  2019/07 [Refereed][Not invited]
  • 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 2019/05 [Refereed][Not invited]
     
    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.
  • Chisato Sakuma, Tsuyoshi Sekizuka, Makoto Kuroda, Fumio Kasai, Kyoko Saito, Masaki Ikeda, Toshiyuki Yamaji, Naoki Osada, Kentaro Hanada
    Scientific Reports 8 (1) 644  2045-2322 2018/12/01 [Refereed][Not invited]
     
    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.
  • Masaki Ikeda, Kazuhiro Satomura, Tsuyoshi Sekizuka, Kentaro Hanada, Toshinori Endo, Naoki Osada
    American Journal of Primatology e22882  2018/06 [Refereed][Not invited]
  • Y. Uno, N. Osada, S. Sakurai, N. Shimozawa, T. Iwata, K. Ikeo, H. Yamazaki
    Journal of Veterinary Pharmacology and Therapeutics 41 (1) e30 - e34 1365-2885 2018/02/01 [Refereed][Not invited]
     
    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.
  • 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 [Refereed][Not invited]
  • Naoki Osada, Ryutaro Miyagi, Aya Takahashi
    GENETICS 206 (4) 2139 - 2148 0016-6731 2017/08 [Refereed][Not invited]
     
    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.
  • Yasuaki Takada, Ryutaro Miyagi, Aya Takahashi, Toshinori Endo, Naoki Osada
    G3-GENES GENOMES GENETICS 7 (7) 2227 - 2234 2160-1836 2017/07 [Refereed][Not invited]
     
    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.
  • Hisayuki Nomiyama, Naoki Osada, Ichiro Takahashi, Keiji Terao, Kazuya Yamagata, Osamu Yoshie
    JOURNAL OF INTERFERON AND CYTOKINE RESEARCH 37 (3) 129 - 138 1079-9907 2017/03 [Refereed][Not invited]
     
    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.
  • Naoki Osada
    Encyclopedia of Evolutionary Biology 1 329 - 333 2016/05 [Refereed][Invited]
  • Ryutaro Miyagi, Noriyoshi Akiyama, Naoki Osada, Aya Takahashi
    MOLECULAR ECOLOGY 24 (23) 5829 - 5841 0962-1083 2015/12 [Refereed][Not invited]
     
    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.
  • Tomotaka Matsumoto, Katsuhiko Mineta, Naoki Osada, Hitoshi Araki
    FRONTIERS IN GENETICS 6 336  1664-8021 2015/11 [Refereed][Not invited]
     
    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.
  • Naoki Osada
    Genes and Genetic Systems 90 (3) 133 - 145 1880-5779 2015/10/27 [Refereed][Invited]
     
    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.
  • Yasuhiro Uno, Shotaro Uehara, Sakae Kohara, Naoki Osada, Norie Murayama, Hiroshi Yamazaki
    MOLECULAR BIOLOGY REPORTS 42 (7) 1149 - 1155 0301-4851 2015/07 [Refereed][Not invited]
     
    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.
  • Shigeki Nakagome, Takehiro Sato, Hajime Ishida, Tsunehiko Hanihara, Tetsutaro Yamaguchi, Ryosuke Kimura, Shuhei Mano, Hiroki Oota
    MOLECULAR BIOLOGY AND EVOLUTION 32 (6) 1533 - 1543 0737-4038 2015/06 [Refereed][Not invited]
     
    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.
  • Katsuhiko Mineta, Tomotaka Matsumoto, Naoki Osada, Hitoshi Araki
    GENE 562 (1) 16 - 21 0378-1119 2015/05 [Refereed][Not invited]
     
    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.
  • 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  1471-2164 2015/03 [Refereed][Not invited]
     
    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.
  • Naoki Osada, Nilmini Hettiarachchi, Isaac Adeyemi Babarinde, Naruya Saitou, Antoine Blancher
    GENOME BIOLOGY AND EVOLUTION 7 (3) 821 - 830 1759-6653 2015/03 [Refereed][Not invited]
     
    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.
  • 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 0960-7412 2014/12 [Refereed][Not invited]
     
    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.
  • Naoki Osada, Arihiro Kohara, Toshiyuki Yamaji, Noriko Hirayama, Fumio Kasai, Tsuyoshi Sekizuka, Makoto Kuroda, Kentaro Hanada
    DNA RESEARCH 21 (6) 673 - 683 1340-2838 2014/12 [Refereed][Not invited]
     
    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.
  • Tomoyoshi Komiyama, Hisakazu Iwama, Naoki Osada, Yoji Nakamura, Hiroyuki Kobayashi, Yoshio Tateno, Takashi Gojobori
    PLOS ONE 9 (7) e101778  1932-6203 2014/07 [Refereed][Not invited]
     
    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.
  • Hiromitsu Kono, Masaru Tamura, Naoki Osada, Hitoshi Suzuki, Kuniya Abe, Kazuo Moriwaki, Kunihiro Ohta, Toshihiko Shiroishi
    DNA RESEARCH 21 (3) 315 - 326 1340-2838 2014/06 [Refereed][Not invited]
     
    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.
  • 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 0737-4038 2014/06 [Refereed][Not invited]
     
    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.
  • Naoki Osada
    Frontiers in Ecology and Evolution 2 7  2014/04 [Refereed][Not invited]
  • Naoki Osada, Shigeki Nakagome, Shuhei Mano, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao
    GENETICS 195 (3) 1027 - + 1943-2631 2013/11 [Refereed][Not invited]
     
    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.
  • Hisayuki Nomiyama, Naoki Osada, Osamu Yoshie
    GENES TO CELLS 18 (1) 1 - 16 1356-9597 2013/01 [Refereed][Not invited]
     
    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.
  • Hiroshi Akashi, Naoki Osada, Tomoko Ohta
    GENETICS 192 (1) 15 - U43 0016-6731 2012/09 [Refereed][Invited]
     
    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.
  • Atsunori Higashino, Ryuichi Sakate, Yosuke Kameoka, Ichiro Takahashi, Makoto Hirata, Reiko Tanuma, Tohru Masui, Yasuhiro Yasutomi, Naoki Osada
    Genome Biology 13 (7) R58  1474-760X 2012/07/02 [Refereed][Not invited]
     
    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.
  • 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 0960-7412 2012/06 [Refereed][Not invited]
     
    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.
  • 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 0378-1119 2012/05 [Refereed][Not invited]
     
    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.
  • Naoki Osada, Hiroshi Akashi
    MOLECULAR BIOLOGY AND EVOLUTION 29 (1) 337 - 346 0737-4038 2012/01 [Refereed][Not invited]
     
    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.
  • Alice Aarnink, Pol-Andre Apoil, Ichiro Takahashi, Naoki Osada, Antoine Blancher
    IMMUNOGENETICS 63 (11) 703 - 713 0093-7711 2011/11 [Refereed][Not invited]
     
    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.
  • Yasuhiro Uno, Naoki Osada
    BMC EVOLUTIONARY BIOLOGY 11 283 - 283 1471-2148 2011/10 [Refereed][Not invited]
     
    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.
  • 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 1386-6346 2011/10 [Refereed][Not invited]
     
    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.
  • 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 0737-4038 2011/10 [Refereed][Not invited]
     
    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.
  • Naoki Osada
    PLOS ONE 6 (9) e25549 - e25549 1932-6203 2011/09 [Refereed][Not invited]
     
    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.
  • Hisayuki Nomiyama, Naoki Osada, Osamu Yoshie
    DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 35 (7) 705 - 715 0145-305X 2011/07 [Refereed][Not invited]
     
    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.
  • Hisayuki Nomiyama, Naoki Osada, Osamu Yoshie
    CYTOKINE & GROWTH FACTOR REVIEWS 21 (4) 253 - 262 1359-6101 2010/08 [Refereed][Not invited]
     
    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.
  • Naoki Osada, Yasuhiro Uno, Katsuhiko Mineta, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao
    MOLECULAR ECOLOGY 19 (14) 2884 - 2895 0962-1083 2010/07 [Refereed][Not invited]
     
    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.
  • 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 0090-9556 2010/02 [Refereed][Not invited]
     
    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.
  • 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 0028-646X 2010 [Refereed][Not invited]
     
    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.
  • 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 2009/09/29 [Refereed][Not invited]
     
    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.
  • 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 0022-1767 2009/09/01 [Refereed][Not invited]
     
    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.
  • Atsunori Higashino, Naoki Osada, Yumiko Suto, Makoto Hirata, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao
    BMC GENETICS 10 24  1471-2156 2009/06 [Refereed][Not invited]
     
    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.
  • Shintaro Iwashita, Kentaro Nakashima, Motoki Sasaki, Naoki Osada, Si-Young Song
    GENE 435 (1-2) 88 - 95 0378-1119 2009/04 [Refereed][Not invited]
     
    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.
  • Naoki Osada, Shuhei Mano, Jun Gojobori
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 106 (3) 841 - 846 0027-8424 2009/01 [Refereed][Not invited]
     
    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.
  • Naoki Osada, Hideki Innan
    PLOS GENETICS 4 (12) e1000305  1553-7390 2008/12 [Refereed][Not invited]
     
    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.
  • 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  1471-2164 2008/05 [Refereed][Not invited]
     
    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.
  • 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  1471-2164 2008/02 [Refereed][Not invited]
     
    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.
  • Yasuhiro Uno, Yutaka Suzuki, Hiroyuki Wakaguri, Yoshiko Sakamoto, Hitomi Sano, Naoki Osada, Katsuyuki Hashimoto, Sumio Sugano, Ituro Inoue
    FEBS LETTERS 582 (2) 351 - 358 0014-5793 2008/01 [Refereed][Not invited]
     
    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.
  • Naoki Osada
    MOLECULAR BIOLOGY AND EVOLUTION 24 (8) 1622 - 1626 0737-4038 2007/08 [Refereed][Not invited]
     
    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.
  • K. Kawabata, K. Tashiro, F. Sakurai, N. Osada, J. Kusuda, T. Hayakawa, K. Yamanishi, H. Mizuguchi
    GENE THERAPY 14 (16) 1199 - 1207 0969-7128 2007/08 [Refereed][Not invited]
     
    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.
  • Naoki Osada, Katsuyuki Hashimoto, Momoki Hirai, Jun Kusuda
    GENE 392 (1-2) 151 - 156 0378-1119 2007/05 [Refereed][Not invited]
     
    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.
  • 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 1544-9173 2007/02 [Refereed][Not invited]
     
    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.
  • 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 1079-9907 2007/01 [Refereed][Not invited]
     
    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.
  • Naoki Osada, Michael H. Kohn, Chung-I Wu
    MOLECULAR BIOLOGY AND EVOLUTION 23 (8) 1585 - 1591 0737-4038 2006/08 [Refereed][Not invited]
     
    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.
  • 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 0737-4038 2006/04 [Refereed][Not invited]
     
    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.
  • 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 0737-4038 2005/10 [Refereed][Not invited]
     
    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.
  • JA Alipaz, S Fang, N Osada, CI Wu
    AMERICAN NATURALIST 165 (4) 420 - 428 0003-0147 2005/04 [Refereed][Not invited]
     
    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.
  • N Osada, CI Wu
    GENETICS 169 (1) 259 - 264 0016-6731 2005/01 [Refereed][Not invited]
     
    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.
  • 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 0737-4038 2003/09 [Refereed][Not invited]
     
    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.
  • FM Mesak, N Osada, K Hashimoto, QY Liu, CE Ng
    BMC GENOMICS 4 32  1471-2164 2003/08 [Refereed][Not invited]
     
    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.
  • 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 1088-9051 2003/05 [Refereed][Not invited]
     
    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.
  • N Osada, J Kusuda, M Hirata, R Tanuma, M Hida, S Sugano, M Hirai, K Hashimoto
    GENOMICS 79 (5) 657 - 662 0888-7543 2002/05 [Refereed][Not invited]
     
    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.
  • Osada N, Hida M, Kusuda J, Tanuma R, Hirata M, Hirai M, Terao K, Suzuki Y, Sugano S, Hashimoto K
    Genome biology 1 3 RESEARCH0006  1465-6906 2002 [Refereed][Not invited]
  • N Osada, M Hida, J Kusuda, R Tanuma, M Hirata, Y Suto, M Hirai, K Terao, S Sugano, K Hashimoto
    BMC GENOMICS 3 36  1471-2164 2002 [Refereed][Not invited]
     
    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.
  • Naoki Osada, Munetomo Hida, Jun Kusuda, Reiko Tanuma, Makoto Hirata, Momoki Hirai, Keiji Terao, Yutaka Suzuki, Sumio Sugano, Katsuyuki Hashimoto
    GENOME BIOLOGY 3 (1) 1474-760X 2002 [Refereed][Not invited]
     
    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.
  • 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 0378-1119 2001/09 [Refereed][Not invited]
     
    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.
  • 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 1088-9051 2001/05 [Refereed][Not invited]
     
    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.
  • N Osada, J Kusuda, Y Suzuki, S Sugano, K Hashimoto
    JOURNAL OF HUMAN GENETICS 45 (6) 374 - 377 1434-5161 2000 [Refereed][Not invited]
     
    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.

MISC

  • 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  2022/06  [Not refereed][Invited]
  • 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  2021/08  
    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  [Not refereed][Invited]
  • ソフトウェア紹介9：TreeMixとqpGraph
    長田直樹  Yaponesian  3-  (はる)  37  -39  2021  [Not refereed][Not invited]
  • 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  [Not refereed][Invited]
  • 長田直樹  Yaponesian  2-  (なつ)  9  -10  2020/09  [Not refereed][Invited]
  • ソフトウェア紹介1：FastQC
    長田直樹  Yaponesian  1-  (はる)  20  -21  2019/05  [Not refereed][Invited]
  • 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  2019/04  [Not refereed][Not invited]
  • ソフトウェア紹介はじまります
    Naoki Osada  Yaponesian  0-  (0)  27  -28  2019/03  [Not refereed][Not invited]
  • 研究計画B03班の紹介
    Naoki Osada  Yaponesian  0-  (0)  16  -17  2019/03  [Not refereed][Not invited]
  • Naoki Osada, Ryutaro Miyagi, Aya Takahashi  GENES & GENETIC SYSTEMS  91-  (6)  372  -372  2016/12  [Not refereed][Not invited]
  • Sangeetha Udani Ratnayake, Toshinori Endo, Naoki Osada  GENES & GENETIC SYSTEMS  91-  (6)  345  -345  2016/12  [Not refereed][Not invited]
  • Yasuaki Takada, Aya Takahashi, Ryutaro Miyagi, Toshinori Endo, Naoki Osada  GENES & GENETIC SYSTEMS  91-  (6)  372  -372  2016/12  [Not refereed][Not invited]
  • 古代ゲノムの解析手法（情報編）
    長田直樹  細胞工学  34-  1092  -1095  2015/11  [Not refereed][Invited]
  • Naoki Osada  Genes and Genetic Systems  90-  (3)  121  -122  2015/10/27  [Not refereed][Not invited]
  • 長田直樹  実験医学Webコラム  2015/08  [Not refereed][Invited]
  • 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-  2015/06  [Not refereed][Not invited]
  • Neha Mishra, Tomotaka Matsumoto, Naoki Osada, Hiroshi Akashi  GENES & GENETIC SYSTEMS  89-  (6)  277  -277  2014/12  [Not refereed][Not invited]
  • FUKUTA Kentaro, NOGUCHI Hideki, TOYODA Atsushi, OSADA Naoki, GO Yasuhiro, ISHIDA Takahumi, ISA Tadashi, FUJIYAMA Asao  Primate Research Supplement  30-  (0)  49  -49  2014  
    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  [Not refereed][Not invited]
  • Ryutaro Miyagi, Naoki Osada, Aya Takahashi  GENES & GENETIC SYSTEMS  88-  (6)  367  -367  2013/12  [Not refereed][Not invited]
  • Hiromitsu Kono, Masaru Tamura, Naoki Osada, Kunihiro Ohta, Toshihiko Shiroishi  GENES & GENETIC SYSTEMS  88-  (6)  368  -368  2013/12  [Not refereed][Not invited]
  • 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  2013/05  [Not refereed][Invited]
  • Hiromitsu Kono, Masaru Tamura, Naoki Osada, Hitoshi Suzuki, Kazuo Moriwaki, Kunihiro Ohta, Toshihiko Shiroishi  GENES & GENETIC SYSTEMS  87-  (6)  401  -401  2012/12  [Not refereed][Not invited]
  • Aya Takahashi, Naoki Osada  GENES & GENETIC SYSTEMS  87-  (6)  416  -416  2012/12  [Not refereed][Not invited]
  • HIGASHINO Atsunori, SAKATE Ryuichi, KAMEOKA Yosuke, TAKAHASHI Ichiro, HIRATA Makoto, TANUMA Reiko, MASUI Tohru, YASUTOMI Yasuhiro, OSADA Naoki  Primate Research Supplement  28-  (0)  61  -61  2012  [Not refereed][Not invited]
     
    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．
  • 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  [Not refereed][Not invited]
  • Hiroshi Akashi, Naoki Osada  GENES & GENETIC SYSTEMS  86-  (6)  388  -388  2011/12  [Not refereed][Not invited]
  • Naoki Osada, Yasuhiro Uno  GENES & GENETIC SYSTEMS  86-  (6)  443  -443  2011/12  [Not refereed][Not invited]
  • Naoki Osada, Hiroshi Akashi  GENES & GENETIC SYSTEMS  85-  (6)  439  -439  2010/12  [Not refereed][Not invited]
  • 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  [Not refereed][Not invited]
  • Naoki Osada, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao  GENES & GENETIC SYSTEMS  83-  (6)  523  -523  2008/12  [Not refereed][Not invited]
  • 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  2008/11  [Not refereed][Not invited]
  • 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  [Not refereed][Invited]
  • Y Suto, N Osada, M Hirai, S Misawa, K Omoto  ANTHROPOLOGICAL SCIENCE  111-  (1)  74  -74  2003/01  [Not refereed][Not invited]
  • N Osada, Y Suto, M Hida, M Hirai, J Kusuda, R Tanuma, K Iseki, M Hirata, K Hashimoto  ANTHROPOLOGICAL SCIENCE  110-  (1)  81  -81  2002/01  [Not refereed][Not invited]
  • 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  2001/10  [Not refereed][Not invited]
  • 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  [Not refereed][Not invited]
  • 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  [Not refereed][Not invited]
  • N Osada, F Kasai, K Terao, Y Mori, Hayasaka, I, M Hirai  ANTHROPOLOGICAL SCIENCE  107-  (1)  56  -56  1999/01  [Not refereed][Not invited]
  • OSADA Naoki, KASAI Fumio, ISEKI Kanako, KUSUDA Jun, HASHIMOTO Katuyuki, HIRAI Momoki  日本分子生物学会年会プログラム・講演要旨集  21-  363  -363  1998/12/01
  • N Osada, M Hirai  ANTHROPOLOGICAL SCIENCE  106-  (2)  166  -166  1998/04  [Not refereed][Not invited]

Books etc

Presentations

  • Naoki Osada
    SMBE Regional Meeting in Taiwan  2024/03
  • 長田直樹
    第一回統合生物考古学セミナー  2023/12
  • 長田 直樹
    第33回モロシヌス研究会  2023/11
  • ほぼ中立説と弱有害変異について―霊長類・げっ歯類ゲノム研究の視点から  [Invited]
    長田直樹
    日本遺伝学会第95回大会  2023/09
  • 長田直樹
    日本進化学会第25回沖縄大会  2023/08
  • 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”  2023/08
  • Genomic Insights into the Hybridization of House Mouse Subspecies in East Asia
    Naoki Osada
    SMBE2023  2023/07
  • Hybrids meet in Japan: pattern and mode of genomic admixture between subspecies of wild house mice (Mus musculus) in East Asia  [Not invited]
    Kazumichi Fujiwara, Shunpei Kubo, Tomoki Yano, Toshinori Endo, Toyoyuki Takada, Toshihiko Shiroishi, Hitoshi Suzuki, Naoki Osada
    IMGC2023  2023/03
  • 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  2023/03
  • 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  [Invited]
    長田直樹
    サイエンスカフェ  2022/10
  • 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  2022/10
  • 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  [Invited]
    長田直樹
    第二回名古屋産学官・医連携研究会（NJK）  2022/08
  • くにうみやわらか講座：ゲノム解析の基礎と考え方  [Invited]
    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  2022/03
  • 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  2022/03
  • 東アジアから俯瞰する二重構造説  [Invited]
    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  2021/11
  • 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  [Invited]
    長田直樹
    日本人類遺伝学会第67回大会  2021/10
  • 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  [Invited]
    長田直樹
    第75回日本人類学会  2021/10
  • 現代・古代東アジア人の遺伝的構造について  [Invited]
    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  2021/03
  • Genome-wide genetic diversity of wild house mice across Eurasia  [Invited]
    Naoki Osada
    Genome Concept Centennial Symposium  2021/02
  • マカク属7種のゲノム解析による進化モデルの構築  [Not invited]
    長田直樹, 松平一成, 濱田穣, Malaivijitnond Suchinda
    第36回日本霊長類学会  2020/12
  • Inference of East and Northeast Asian Population Histories using Present-day and Ancient Genome Sequence Data  [Invited]
    Naoki Osada
    The First Meeting of the Academic Year 2020 Joint Research Project on “Studies in Asian and African Geolinguistics”, ILCAA  2020/10
  • 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  [Invited]
    長田直樹
    第22回日本進化学会オンライン大会  2020/09
  • Big data in biology: perspectives of genomic diversity studies  [Invited]
    Naoki Osada
    2019 Winter International Symposium on Big-Data, Cybersecurity and IoT  2019/12
  • ソフトウェア講習  [Invited]
    長田直樹
    第3回木村資生記念進化学セミナー  2019/08
  • 霊長類種間における遺伝子浸透様式の解析  [Not invited]
    長田直樹
    ヤポネシアゲノム若手研究集会  2019/01
  • 移住率の性による偏りをゲノムデータから探る  [Not invited]
    長田直樹
    ヤポネシアゲノムB02班班会議  2019/01
  • ゲノムからたどる人類進化の歴史  [Invited]
    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」  2018/12
  • 性による移住率の偏りをゲノムデータから推定する  [Invited]
    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  2018/10  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  [Not invited]
    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  2018/09
  • Dissecting genetic and epigenetic gene expression regulatory variations in diploid organisms  [Invited]
    Naoki Osada
    14th Japanese-German Frontiers of Science Symposium  2018/09
  • ゲノム進化解析ソフトウェアの使い方  [Not invited]
    長田直樹
    第2回木村資生記念進化学セミナー  2018/09
  • 集団遺伝学とゲノム進化学  [Invited]
    長田直樹
    第11回生物学基礎論研究会特別講演  2017/09
  • 環境変動と集団サイズ変動の関係を考える  [Not invited]
    Naoki Osada
    日本列島（ヤポネシア）人のゲノム歴史学  2017/08
  • Quantifying genetic and epigenetic control of gene expression in Drosophila and mice  [Invited]
    Naoki Osada
    The 5th international symposium “Frontier Science in Ecology, Genetics and Genomics”  2017/03
  • 集団遺伝学データ解析  [Invited]
    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  2016/12
  • Genomics of non-human primates: application to biomedical studies  [Invited]
    Naoki Osada
    2016 HU/SNU joint symposium  2016/11
  • Population genomics of non-human primates: a case of Mauritian cynomolgus macaques (Macaca fascicularis)  [Not invited]
    Naoki Osada, Soichi Sakurai
    5th Asian Primate Symposium  2016/10
  • An impact of population bottleneck on genomes: a case of Mauritian cynomolgus macaques (Macaca fascicularis)  [Invited]
    Naoki Osada
    13th Japanese-German Frontiers of Science Symposium  2016/10
  • 集団遺伝学データ解析  [Not invited]
    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  2015/12  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  [Not invited]
    Naoki Osada
    12th Japanese-German Frontiers of Science Symposium  2015/10
  • 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  [Not invited]
    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  2015/07
  • Effect of strong population bottleneck on genomes: a case of Mauritian cynomolgus macaques  [Not invited]
    Naoki Osada
    遺伝研研究集会「ビッグデータ時代の分子進化」  2015/06
  • 集団遺伝学データ解析：ABCのABC  [Not invited]
    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  2014/12
  • Challenge of population genomics in non-model organisms  [Not invited]
    長田直樹
    Frontiers in Genomic Research  2014/12
  • 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  [Not invited]
    長田直樹
    木村資生博士生誕90周年記念シンポジウム  2014/11
  • Compensatory Evolution  [Not invited]
    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  2014/10
  • 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」  [Not invited]
    長田直樹
    第86回日本遺伝学会大会  2014/09
  • Allele-specific gene expression among Drosophila melanogaster hybrid lines revealed abundant cis-regulatory mutations  [Not invited]
    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  2014/03
  • Finding evidence for weak compensatory evolution  [Not invited]
    Naoki Osada, Hiroshi Akashi
    SMBE Satellite Meeting/NIG International Workshop: The Causes of Genome Evolution  2014/03
  • 帰無モデルとしての中立説と歴史推定  [Not invited]
    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  2013/12
  • Dissecting regulatory mechanisms of transcriptome variation in Drosophila melanogaster  [Not invited]
    Naoki Osada
    Seminar at Academia Sinica  2013/11
  • Dissecting regulatory mechanisms of transcriptome variation in Drosophila melanogaster  [Not invited]
    Naoki Osada
    ISEGB2013  2013/11
  • 霊長類のゲノム進化  [Not invited]
    長田直樹
    日本人類学会大会  2013/11
  • 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  [Not invited]
    長田直樹, 宮城竜太郎, 高橋文
    日本遺伝学会大会  2013/09
  • Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis  [Not invited]
    Naoki Osada, Shigeki Nakagome, Shuhei Mano, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao
    SMBE2013  2013/07
  • Finding evidence for weak compensatory evolution  [Not invited]
    長田直樹
    NIG Collaborative Workshop: Evolution of Junk DNAs  2013/06
  • 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  [Not invited]
    長田直樹
    インシリコ・メガバンク研究会  2013/05
  • Evolution of rice photoperiod genes  [Not invited]
    長田直樹
    NIG collaborative research meeting: Evolutionary Genetics and Proteomics of Natural Resources in Asia  2013/02
  • Ecological and Evolutionary Genomics of non-model organisms in Asia  [Not invited]
    長田直樹
    CKJ meeting: Genomics, Proteomics, and Bioinformatics with the Asian Perspective  2012/12
  • 実験用霊長類のゲノムとその多様性  [Not invited]
    長田直樹
    霊長類医科学研究フォーラム  2012/11
  • 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  [Not invited]
    長田直樹
    日本人類学会大会  2012/11
  • ゲノムの分岐パターンから探る-歴史，種分化，適応  [Not invited]
    長田直樹
    みちのく進化生物セミナー  2012/10
  • Genetic diversity of humans and nonhuman primates and its evolutionary implications  [Not invited]
    Naoki Osada
    Seminar at Academia Sinica  2012/09
  • Inference of population history from genomic data  [Not invited]
    Naoki Osada
    Arabidopsis symposium  2012/09
  • 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  [Not invited]
    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  2012/08
  • Compensatory Evolution between Mitochondrial and Nuclear Genomes  [Not invited]
    Naoki Osada
    Okazaki Biological Conference 8 (OBC8)  2012/03
  • Inference of natural selection by stratifying individual genome sequences  [Not invited]
    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～  2012/03
  • Genetic diversity and population history of macaque monkeys  [Not invited]
    Naoki Osada
    Genomic Conservation and Diversity of Organisms: Beyond the NGS time of Life Science  2011/12
  • Inference of population history using a single genome data  [Not invited]
    長田直樹
    日本分子生物学会年会  2011/12
  • 多座位データを用いたゲノムヒストリーの推定  [Not invited]
    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  2011/12
  • メタゲノム解析とその応用  [Not invited]
    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  2011/11
  • 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  [Not invited]
    長田直樹, 宇野泰広
    日本遺伝学会大会  2011/09
  • Compensatory evolution between mitochondrial and nuclear genomes: evidence from primate respiratory chain complex genes  [Not invited]
    Naoki Osada
    SMBE2011  2011/07
  • Compensatory Evolution between Mitochondrial and Nuclear Genomes: Evidence from Primate Respiratory Chain Complex Genes  [Not invited]
    Naoki Osada
    Seminar at National Taiwan University  2011/07
  • 霊長類の中のヒト:ゲノム多様性の種間比較  [Not invited]
    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  2011/07
  • ヒトの遺伝的多様性―進化生物学的視点から  [Not invited]
    長田直樹
    日本赤十字第6回学術講演会  2011/06
  • Compensatory Evolution between Mitochondrial and Nuclear Genomes: Evidence from Primate Respiratory Chain Complex Genes  [Not invited]
    Naoki Osada
    Seminar at National Cheng-Kung University  2011/03
  • 人類集団における自然淘汰  [Not invited]
    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  2011/03
  • Genetic analysis using multi-locus DNA sequence data for ecology and evolution research  [Not invited]
    長田直樹
    NIG Collaborative Research Meeting: Toward Next Generation Studies of Biodiversity and Bioresources  2010/11
  • 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  [Not invited]
    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  2010/11
  • Population Genetics of Non-human Primates: How Are We Diverse?  [Not invited]
    Naoki Osada
    International Primatological Society Congress  2010/09
  • 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  [Not invited]
    長田直樹, 明石裕
    日本遺伝学会大会  2010/08
  • 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  [Not invited]
    長田直樹
    日本進化学会大会  2010/08
  • Polymorphism, Divergence, and Speciation: Genomic Perspective  [Not invited]
    Naoki Osada
    Seminar at National Cheng-Kung University  2010/03
  • 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  [Not invited]
    長田直樹
    日本薬学会大会融合型シンポジウム  2010/03
  • カニクイザルのトランスクリプトーム解析  [Not invited]
    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  2010/03
  • 進化生物学への次世代シークエンサーの応用について  [Not invited]
    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  2010/01
  • 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  [Not invited]
    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  2009/12
  • 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  [Not invited]
    長田直樹
    日本遺伝学会大会  2009/09
  • Ecological adaptation and speciation: genomic perspective  [Not invited]
    Naoki Osada
    Eawag CEEB joint workshop: Beyond the gaps among ecology, evolution and biogeochemistry  2009/08
  • Analysis of gene duplication and conversion in the Drosophila melanogaster genome.  [Not invited]
    Naoki Osada, Hideki Innan
    JSPS Japan-Germany International Colloquium  2009/03
  • Polymorphism, Divergence, and Speciation: Genomic Perspective  [Not invited]
    長田直樹
    国立遺伝学研究所 Biological symposium  2009/03
  • カニクイザル骨髄・脾臓・膵臓由来cDNAライブラリーの解析  [Not invited]
    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  2008/12
  • 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  [Not invited]
    長田直樹
    日本人類学会大会  2008/11
  • Deleterious Mutations and Human Diseases: Genomic Perspective  [Not invited]
    長田直樹
    日本進化学会大会  2008/08
  • ヒト疾患とほぼ中立説  [Not invited]
    長田直樹
    国立遺伝学研究所研究集会：中立進化論の現在  2008/07
  • 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  [Not invited]
    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  2008/07
  • Pattern of genetic admixture and differentiation between Macaca fascicularis and M. mulatta genome  [Not invited]
    Naoki Osada, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao
    SMBE2008  2008/06
  • Primate speciation: genes and genome  [Not invited]
    Naoki Osada
    Seminar at National Taiwan University  2008/05
  • Primate speciation: genes and genome  [Not invited]
    Naoki Osada
    Seminar at National Cheng-Kung University  2008/05
  • 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  [Not invited]
    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  2007/12
  • 突然変異にかかる淘汰圧と遺伝子発現の関係について  [Not invited]
    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  2007/10
  • 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  [Not invited]
    長田直樹
    日本遺伝学会大会  2007/09
  • 遺伝子配列と発現パターンから見た霊長類進化  [Not invited]
    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  2007/07
  • 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  [Not invited]
    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  2007/07
  • 高等霊長類でのTMEM30C遺伝子転写の進化  [Not invited]
    長田直樹
    日本進化学会大会  2006/08
  • Collection and analysis of primate disease-related homologs  [Not invited]
    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  2006/06
  • Divergence between human and macaque beyond the protein evolution  [Not invited]
    Naoki Osada, Katsuyuki Hashimoto, Reiko Tanuma, Makoto Hirata, Jun Kusuda
    Human Genome Meeting 2006  2006/05
  • カニクイザルcDNAの解析とデータベース構築  [Not invited]
    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  2005/12
  • 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  [Not invited]
    長田直樹
    日本遺伝学会大会  2005/09
  • ゲノムレベルでわかる霊長類進化  [Not invited]
    長田直樹
    遺伝研生命情報センターCIBセミナー  2005/06
  • Cynomolgus monkey cDNA libraries: Rate and Pattern of 5’UTR evolution in primates  [Not invited]
    Naoki Osada, Makoto Hirata, Reiko Tanuma, Jun Kusuda, Katsuyuki Hashimoto
    Human Genome Meeting 2005  2005/04
  • Rate and pattern of 5’ UTR evolution: comparative analysis between human and cynomolgus monkey  [Not invited]
    Naoki Osada, Makoto Hirata, Jun Kusuda, Reiko Tanuma, Katsuyuki Hashimoto
    International Workshop on Encoding Information in DNA Sequences  2005/02
  • 9. Gene expression of Drosophila melanogaster head with sexual isolation - cis-associated difference and pattern of sex, virginity and genotype  [Not invited]
    Naoki Osada
    日本分子生物学会年会  2004/12
  • Testing the mode of speciation with genomic data  [Not invited]
    Naoki Osada, Chung-I Wu
    Keystone symposia, Natural variation and quantitative genetics in model organism  2004/03
  • Prediction of novel human genes applying cDNA sequence of cynomolgus monkey brain  [Not invited]
    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
    2002/12
  • Identification of human homologs for novel cynomolgus monkey cDNAs  [Not invited]
    Naoki Osada
    Gordon Research Conference: GENOMICS & STRUCTURAL/EVOLUTIONARY BIOINFORMATICS  2002/08
  • 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  [Not invited]
    長田直樹
    哺乳動物遺伝学研究会  2002/06
  • Isolation and sequence analysis of newly identified clones from full-length cynomolgus monkey brain cDNA library  [Not invited]
    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  2001/08
  • Analysis of full-length cynomolgus monkey cDNA library from brain and isolation of unidentified clones  [Not invited]
    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  2000/11
  • Isolation and analysis of unidentified mouse cDNA clones containing CpG islands  [Not invited]
    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  1999/11
  • DNA replication timing of human chromosome 11p15 analyzed by FISH  [Not invited]
    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  1998/11
  • Analysis of DNA replication timing using FISH : A comparative study in primates  [Not invited]
    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  1998/09
  • Analysis of DNA replication timing using FISH method  [Not invited]
    長田直樹, 平井百樹
    日本人類学会大会  1997/11

Association Memberships

  • THE SOCIETY OF BIOSOPHIA STUDIES   JAPANESE SOCIETY FOR BIOINFORMATICS   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   

Research Projects

  • 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)
    Date (from‐to) : 2023/04 -2028/03 
    Author : 長田 直樹
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2023/04 -2028/03 
    Author : 山田 康弘
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2022/04 -2026/03 
    Author : 長田 直樹, 河合 洋介
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2023/04 -2026/03 
    Author : 小林 一三, 長田 直樹, 内山 郁夫, 大崎 敬子, 印南 秀樹
  • 日本学術振興会：科学研究費助成事業 基盤研究(C)
    Date (from‐to) : 2022/04 -2025/03 
    Author : 柿坂 達彦, 蒲池 浩文, 長田 直樹, 神山 俊哉, 折茂 達也
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2018/06 -2023/03 
    Author : 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．
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2018/06 -2023/03 
    Author : 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。
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2014/04 -2017/03 
    Author : Osada Naoki
     
    Compensatory molecular evolution refers to the process where the fixation of multiple mutation that are singly deleterious maintain organismal fitness by compensating their effects. In this research project, we mainly focus on the compensatory weak selection model, where the fixation of slightly advantageous mutations follow the fixation of slightly deleterious mutations in a variety of molecular systems, including protein-protein interaction and gene expression.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2014/04 -2017/03 
    Author : SAITOU NARUYA
     
    Evolutionarily conserved noncoding sequences (CNSs) were analyzed for whole Eukaryotes, Amniotes, Hominoids, and Hominidae by comparing many genome sequences, and series of new CNS characteristics were discovered (mainly conduced by Saitou). Repeat sequence evolution of New World monkeys were analyzed (mainly conduced by Koga). Genomic structure of chimpanzee Rh blood group gene region was analyzed (mainly conduced by Kitano). Whole-genome sequences of Mauritian cynomolgus macaques and Tibetan macaque were analyzed (mainly conduced by Osada). Substitution type mutation pattens were analyzed by using ENU-induced mice (mainly conduced by OOta). Gene annotation of cynomolgus macaque genome was conducted (mainly conduced by Ikeo). These studies deciphered various facets of genome evolution, in particular, of primates.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2011/04 -2016/03 
    Author : Takahashi Aya, OSADA Naoki
     
    This study focused on dopamine biosynthesis pathway genes, which has a pleiotropic effect on both body pigmentation and behavior, as genes potentially involved in reproductive isolation triggered by environmental adaptation. We found unexpectedly complex cis-regulatory polymorphisms in these genes and a genetic variant that is likely to change both pigmentation and behavior. From a wider viewpoint of the “Correlative gene systems”, another contribution of this study was to elucidate various associations between cis/trans-regulatory variations and genomic factors by conducting a novel type of genome-wide transcriptome analysis.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2010/04 -2014/03 
    Author : OSADA Naoki
     
    Understanding the interaction between two different genomes is important issue in evolutionary biology research, especially when the two genomes were incorporated into the same organisms. I analyzed the genomic and expression properties of recently established natural allotetraploid plants, of which parental species are relative to the model species Arabidopsis thaliana. Using massively parallel sequencers, genome sequences of parental species and transcriptome data of allotetraploid species were studied.
  • 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
    Date (from‐to) : 2007/05 -2010/03 
    Author : 寺尾恵治
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research
    Date (from‐to) : 2007 -2008 
    Author : NOMIYAMA Hisayuki, SETOYAMA Chiaki, OSADA Naoki
     
    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.
  • 文部科学省：科学研究費補助金(若手研究(B))
    Date (from‐to) : 2007 -2008 
    Author : 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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