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Koyanagi Kanako

Faculty of Information Science and Technology　Bioengineering and Bioinformatics　BioinformaticsAssociate Professor
Office of Diversity Equity and InclusionAssociate Professor
Institute for Academic InnovationAssociate Professor

Researcher basic information

■ Degree
  • PhD, Kyoto University
■ URL
researchmap URLホームページURL■ Various IDs
J-Global ID■ Research Keywords and Fields
Research Keyword
  • phylogenetic analysis
  • epigenetics
  • Cell lineage
  • Cell differentiation
  • rice
  • human
  • virus
  • comparative genomics
  • genome organization
  • regulation of gene expression
  • molecular evolution
  • evolution
  • genome
Research Field
  • Life Science, Genetics
  • Life Science, System genome science
  • Life Science, Evolutionary biology
  • Life Science, Genome biology
■ Educational Organization

Career

■ Career
Career
  • 2019 - Present
    Hokkaido University, Faculty of Information Science and Technology, Associate Professor
  • 2007 - 2019
    Hokkaido University, Graduate School of Information Science and Technology, Associate Professor
  • 2004 - 2007
    Hokkaido University, Graduate School of Information Science and Technology, Associate Professor
  • 2003 - 2004
    Nara Institute of Science and Technology, Information Science, Assistant Professor
  • 2001 - 2003
    Japan Biological Information Research Center, Postdoctoral researcher
  • 2000 - 2001
    Kyoto University, Graduate School of Science, Postdoctoral researcher
Committee Memberships
  • Apr. 2021 - Mar. 2023
    文部科学省 科学技術・学術政策研究所 (NISTEP), 専門調査員, Government
  • 2021 - 2022
    日本遺伝学会第94回大会実行委員
  • 2016 - 2019
    日本進化学会, 2019年大会準備委員, Society
  • 2016 - 2017
    IIBMP2017, 実行委員, Society

Research activity information

■ Awards
  • 2021, 公益財団法人 秋山記念生命科学振興財団 研究助成〈一般〉
    リアルタイム選別による未知DNA配列解読－北海道イネゲノム難解読領域への応用－
    小柳香奈子;渡邉日出海
  • 2005, 日本遺伝学会, 第７７回日本遺伝学会BP賞
    脊椎動物特異的なゲノム構造進化の発見
    小柳香奈子;伊藤剛;萩原正人;五條堀孝;今西規
■ Papers
  • Genomic footprints of historical introgression between ancient lineages of wild Oryza AA-genome species with widely separated contemporary distributions
    Kanako O. Koyanagi; Yuta Kotoku; Yuji Kishima
    bioRxiv, openRxiv, 15 Jan. 2026, [Lead author, Corresponding author]
    English, Abstract

    Phylogenetic incongruence is increasingly recognized as pervasive, yet the extent to which reticulate evolution occurs between groups separated by substantial geographical distances and deep phylogenetic divergence remains poorly characterized. In the Oryza AA-genome group—a model for plant speciation and domestication—the traditional bifurcation model posits that Australian Oryza meridionalis and African Oryza longistaminata occupy basal branches, distinct from the more recently diversified monophyletic clade comprising Asian and other African lineages, including major cultivars. However, recent evidence from endogenous viral sequences has hinted at unexpected genetic relatedness between African O. longistaminata and Asian Oryza sativa , which are geographically and phylogenetically distant. Here, we conducted a genome-wide survey across 11 Oryza species to systematically identify genomic regions exhibiting phylogenetic incongruence. Widespread phylogenetic discordance was observed, notably involving genomic segments in which O. longistaminata showed phylogenetic proximity to Asian species, contradicting their established deep divergence. To distinguish between introgression and incomplete lineage sorting, we performed four-taxon ABBA-BABA tests, which provided statistical support for introgression. Furthermore, divergence time estimates for these incongruent regions were younger than the species divergence times, suggesting historical introgression between the ancestors of lineages that are currently separated by vast geographical distances. Systematic assessments indicated that potential analytical artifacts, such as compositional bias and substitution saturation, were unlikely to explain the observations. These convergent lines of evidence suggest that ancient introgression had occurred between currently geographically separated and evolutionarily divergent Oryza lineages, leaving detectable footprints across their modern genomes.
  • Inferring chromatin accessibility during murine hematopoiesis through phylogenetic analysis.
    Kanako O Koyanagi
    BMC research notes, 16, 1, 222, 222, 19 Sep. 2023, [Lead author, Corresponding author], [International Magazine]
    English, Scientific journal, OBJECTIVE: Diversification of cell types and changes in epigenetic states during cell differentiation processes are important for understanding development. Recently, phylogenetic analysis using DNA methylation and histone modification information has been shown useful for inferring these processes. The purpose of this study was to examine whether chromatin accessibility data can help infer these processes in murine hematopoiesis. RESULTS: Chromatin accessibility data could partially infer the hematopoietic differentiation hierarchy. Furthermore, based on the ancestral state estimation of internal nodes, the open/closed chromatin states of differentiating progenitor cells could be predicted with a specificity of 0.86-0.99 and sensitivity of 0.29-0.72. These results suggest that the phylogenetic analysis of chromatin accessibility could offer important information on cell differentiation, particularly for organisms from which progenitor cells are difficult to obtain.
  • Phylogenetic analysis of endogenous viral elements in the rice genome reveals local chromosomal evolution in Oryza AA-genome species.
    Nozomi Saito; Sunlu Chen; Katsuya Kitajima; Zhitong Zhou; Yohei Koide; Jaymee R Encabo; Maria Genaleen Q Diaz; Il-Ryong Choi; Kanako O Koyanagi; Yuji Kishima
    Frontiers in plant science, 14, 1261705, 1261705, 2023, [Corresponding author], [International Magazine]
    English, Scientific journal, INTRODUCTION: Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae. These viral elements, known as endogenous RTBV-like sequences (eRTBVLs), comprise five subfamilies, eRTBVL-A, -B, -C, -D, and -X. Four subfamilies (A, B, C, and X) are present to a limited degree in the genomes of the Asian cultivated rice Oryza sativa (spp. japonica and indica) and the closely related wild species Oryza rufipogon. METHODS: The eRTBVL-D sequences are widely distributed within these and other Oryza AA-genome species. Fifteen eRTBVL-D segments identified in the japonica (Nipponbare) genome occur mostly at orthologous chromosomal positions in other AA-genome species. The eRTBVL-D sequences were inserted into the genomes just before speciation of the AA-genome species. RESULTS AND DISCUSSION: Ten eRTBVL-D segments are located at six loci, which were used for our evolutionary analyses during the speciation of the AA-genome species. The degree of genetic differentiation varied among the eRTBVL-D segments. Of the six loci, three showed phylogenetic trees consistent with the standard speciation pattern (SSP) of the AA-genome species (Type A), and the other three represented phylogenies different from the SSP (Type B). The atypical phylogenetic trees for the Type B loci revealed chromosome region-specific evolution among the AA-genome species that is associated with phylogenetic incongruences: complex genome rearrangements between eRTBVL-D segments, an introgression between the distant species, and low genetic diversity of a shared eRTBVL-D segment. Using eRTBVL-D as an indicator, this study revealed the phylogenetic incongruence of local chromosomal regions with different topologies that developed during speciation.
  • Adenovirus-associated uveitis with necrotizing retinitis.
    Sunao Sugita; Yoshihiko Usui; Hidemi Watanabe; Laura Panto; Miyabi Iida; Keisuke Suginoshita; Kanako O Koyanagi; Akihiro Nishida; Yasuo Kurimoto; Masayo Takahashi; Tatsuya Shindo; Hiroaki Nishioka; Masahiko Takano; Takeshi Kezuka; Hiroshi Goto; Nobuyoshi Kitaichi
    Ophthalmology, 130, 4, 443, 445, 23 Dec. 2022, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Translation of continuous artificial selection on phenotype into genotype during rice breeding programs
    Fujino Kenji; Kawahara Yoshihiro; Koyanagi Kanako O.; Shirasawa Kenta
    Breeding Science, 71, 2, 125, 133, Japanese Society of Breeding, 2021, [Peer-reviewed], [Domestic magazines]
    English, Scientific journal,

    Understanding genetic diversity among local populations is a primary goal of modern crop breeding programs. Here, we demonstrated the genetic relationships of rice varieties in Hokkaido, Japan, one of the northern limits of rice cultivation around the world. Furthermore, artificial selection during rice breeding programs has been characterized using genome sequences. We utilized 8,565 single nucleotide polymorphisms and insertion/deletion markers distributed across the genome in genotype-by-sequencing for genetic diversity analyses. Phylogenetics, genetic population structure, and principal component analysis showed that a total of 110 varieties were classified into four distinct clusters according to different populations geographically and historically. Furthermore, the genome sequences of 19 rice varieties along with historic representations in Hokkaido, nucleotide diversity and FST values in each cluster revealed that artificial selection of elite phenotypes focused on chromosomal regions. These results clearly demonstrated the history of the selections on agronomic traits as genome sequences among current rice varieties from Hokkaido.

  • Inferring changes in histone modification during cell differentiation by ancestral state estimation based on phylogenetic trees of cell types: Human hematopoiesis as a model case
    Kanako O. Koyanagi
    Gene, 721S, 100021, 100021, Sep. 2019, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
    English, Scientific journal
  • Biosynthetic Short Neuropeptides: A Rational Theory Based on Experimental Results for the Missing Pain-Relief Opioid Endomorphin Precursor Gene
    Ayami Matsushima; Jun Sese; Kanako O. Koyanagi
    ChemBioChem, 20, 16, 2054, 2058, 16 Aug. 2019, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii
    Marcin Jakalski; Kazutaka Takeshita; Mathieu Deblieck; Kanako O. Koyanagi; Izabela Makałowska; Hidemi Watanabe; Wojciech Makałowski
    Biology Direct, 11, 1, 35, 35, 04 Aug. 2016, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Genome-wide association mapping focusing on a rice population derived from rice breeding programs in a region
    Kenji Fujino; Mari Obara; Toshiaki Shimizu; Kanako O. Koyanagi; Tomohito Ikegaya
    Breeding Science, 65, 5, 403, 410, 19 Dec. 2015, [Peer-reviewed], [Domestic magazines]
    English, Scientific journal
  • DNA barcoding of Oeneis butterflies newly sampled in Mongolia
    Takatoshi Abe; Hidemi Watanabe; Kanako O. Koyanagi; Botaro Inoue
    GENOME, 58, 5, 185, 185, May 2015, [Peer-reviewed]
    English
  • Inferring cell differentiation processes based on phylogenetic analysis of genome-wide epigenetic information: Hematopoiesis as a model case
    Kanako O. Koyanagi
    Genome Biology and Evolution, 7, 3, 699, 705, Mar. 2015, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
    English, Scientific journal
  • Interregional coevolution analysis revealing functional and structural interrelatedness between different genomic regions in human mastadenovirus D
    Gabriel Gonzalez; Kanako O. Koyanagi; Koki Aoki; Hidemi Watanabe
    Journal of Virology, 89, 12, 6209, 6217, 2015, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Rice genomes recorded ancient pararetrovirus activities: Virus genealogy and multiple origins of endogenization during rice speciation
    Sunlu Chen; Ruifang Liu; Kanako O. Koyanagi; Yuji Kishima
    Virology, 471-473, 141, 152, 01 Dec. 2014, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • A Novel Complex Recombinant Form of Type 48-Related Human Adenovirus Species D Isolated in Japan (vol 67, pg 282, 2014)
    Tsuguto Fujimoto; Shotaro Yamane; Tomoko Ogawa; Nozomu Hanaoka; Atsushi Ogura; Chiemi Hotta; Takeshi Niwa; Yakou Chiba; Gabriel Gonzalez; Koki Aoki; Kanako Ono Koyanagi; Hidemi Watanabe
    JAPANESE JOURNAL OF INFECTIOUS DISEASES, 67, 5, 416, 416, Sep. 2014, [Peer-reviewed]
    English
  • Intertypic modular exchanges of genomic segments by homologous recombination at universally conserved segments in human adenovirus species D
    Gabriel Gonzalez; Kanako O. Koyanagi; Koki Aoki; Nobuyoshi Kitaichi; Shigeaki Ohno; Hisatoshi Kaneko; Susumu Ishida; Hidemi Watanabe
    Gene, 547, 1, 10, 17, 15 Aug. 2014, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • A novel complex recombinant form of type 48-related human adenovirus species d isolated in Japan
    Tsuguto Fujimoto; Shotaro Yamane; Tomoko Ogawa; Nozomu Hanaoka; Atsushi Ogura; Chiemi Hotta; Takeshi Niwa; Yakou Chiba; Gabriel Gonzalez; Koki Aoki; Kanako Ono Koyanagi; Hidemi Watanabe
    Japanese Journal of Infectious Diseases, 67, 4, 282, 287, 2014, [Peer-reviewed], [Domestic magazines]
    English, Scientific journal
  • Bidirectional Gene Pairs in the Human Genome
    Kanako O Koyanagi; Tadashi Imanishi; Takashi Gojobori
    eLS. John Wiley & Sons, Ltd: Chichester, Dec. 2013, [Peer-reviewed], [Invited], [Lead author]
    English, Scientific journal
  • Identification of contamination in the american type culture collection stock of human adenovirus type 8 by whole-genome sequencing
    Shotaro Yamane; Amanda Wei Ling Lee; Nozomu Hanaoka; Gabriel Gonzalez; Hisatoshi Kaneko; Susumu Ishida; Nobuyoshi Kitaichi; Shigeaki Ohno; Kanako O. Koyanagi; Koki Aoki; Tsuguto Fujimoto; Nobuyo Yawata; Hidemi Watanabe
    Journal of Virology, 87, 2, 1285, 6, 2, Jan. 2013, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Evolutionary force of AT-rich repeats to trap genomic and episomal DNAs into the rice genome: Lessons from endogenous pararetrovirus
    Ruifang Liu; Kanako O. Koyanagi; Sunlu Chen; Yuji Kishima
    Plant Journal, 72, 5, 817, 828, Dec. 2012, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • In silico and in vivo identification of the intermediate filament vimentin that is downregulated downstream of Brachyury during Xenopus embryogenesis
    Atsuko Yamada; Kanako O. Koyanagi; Hidemi Watanabe
    Gene, 491, 2, 232, 236, 10 Jan. 2012, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Toward an Integrated Human Adenovirus Designation System That Utilizes Molecular and Serological Data and Serves both Clinical and Fundamental Virology
    Koki Aoki; Maria Benkoe; Andrew J. Davison; Marcela Echavarria; Dean D. Erdman; Balazs Harrach; Adriana E. Kajon; David Schnurr; Goran Wadell
    JOURNAL OF VIROLOGY, 85, 11, 5703, 5704, Jun. 2011
    English
  • Recombination analysis of intermediate human adenovirus type 53 in Japan by complete genome sequence
    Hisatoshi Kaneko; Koki Aoki; Susumu Ishida; Shigeaki Ohno; Nobuyoshi Kitaichi; Hiroaki Ishiko; Tsuguto Fujimoto; Yoshifumi Ikeda; Masako Nakamura; Gabriel Gonzalez; Kanako O. Koyanagi; Hidemi Watanabe; Tatsuo Suzutani
    Journal of General Virology, 92, 6, 1251, 1259, Jun. 2011, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Complete genome analysis of a novel intertypic recombinant human adenovirus causing epidemic keratoconjunctivitis in Japan
    Hisatoshi Kaneko; Koki Aoki; Shigeaki Ohno; Hiroaki Ishiko; Tsuguto Fujimoto; Masayuki Kikuchi; Seiya Harada; Gabriel Gonzalez; Kanako O. Koyanagi; Hidemi Watanabe; Tatsuo Suzutani
    Journal of Clinical Microbiology, 49, 2, 484, 490, Feb. 2011, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Highly diversified molecular evolution of downstream transcription start sites in rice and arabidopsis
    Tsuyoshi Tanaka; Kanako O. Koyanagi; Takeshi Itoh
    Plant Physiology, 149, 3, 1316, 1324, Mar. 2009, [Peer-reviewed], [International Magazine]
    English, International conference proceedings
  • Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees
    Akihiro Matsuya; Ryuichi Sakate; Yoshihiro Kawahara; Kanako O. Koyanagi; Yoshiharu Sato; Yasuyuki Fujii; Chisato Yamasaki; Takuya Habara; Hajime Nakaoka; Fusano Todokoro; Kaori Yamaguchi; Toshinori Endo; Satoshi Oota; Wojciech Makalowski; Kazuho Ikeo; Yoshiyuki Suzuki; Kousuke Hanada; Katsuyuki Hashimoto; Momoki Hirai; Hisakazu Iwama; Naruya Saitou; Aiko T. Hiraki; Lihua Jin; Yayoi Kaneko; Masako Kanno; Katsuhiko Murakami; Akiko Ogura Noda; Naomi Saichi; Ryoko Sanbonmatsu; Mami Suzuki; Jun Ichi Takeda; Masayuki Tanaka; Takashi Gojobori; Tadashi Imanishi; Takeshi Itoh
    Nucleic Acids Research, 36, SUPPL. 1, D787, D792, Jan. 2008, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
    Chisato Yamasaki; Katsuhiko Murakami; Yasuyuki Fujii; Yoshiharu Sato; Erimi Harada; Jun Ichi Takeda; Takayuki Taniya; Ryuichi Sakate; Shingo Kikugawa; Makoto Shimada; Motohiko Tanino; Kanako O. Koyanagi; Roberto A. Barrero; Craig Gough; Hong Woo Chun; Takuya Habara; Hideki Hanaoka; Yosuke Hayakawa; Phillip B. Hilton; Yayoi Kaneko; Masako Kanno; Yoshihiro Kawahara; Toshiyuki Kawamura; Akihiro Matsuya; Naoki Nagata; Kensaku Nishikata; Akiko Ogura Noda; Shin Nurimoto; Naomi Saichi; Hiroaki Sakai; Ryoko Sanbonmatsu; Rie Shiba; Mami Suzuki; Kazuhiko Takabayashi; Aiko Takahashi; Takuro Tamura; Masayuki Tanaka; Susumu Tanaka; Fusano Todokoro; Kaori Yamaguchi; Naoyuki Yamamoto; Toshihisa Okido; Jun Mashima; Aki Hashizume; Lihua Jin; Kyung Bum Lee; Yi Chueh Lin; Asami Nozaki; Katsunaga Sakai; Masahito Tada; Satoru Miyazaki; Takashi Makino; Hajime Ohyanagi; Naoki Osato; Nobuhiko Tanaka; Yoshiyuki Suzuki; Kazuho Ikeo; Naruya Saitou; Hideaki Sugawara; Claire O'Donovan; Tamara Kulikova; Eleanor Whitfield; Brian Halligan; Mary Shimoyama; Simon Twigger; Kei Yura; Kouichi Kimura; Tomohiro Yasuda; Tetsuo Nishikawa; Yutaka Akiyama; Chie Motono; Yuri Mukai; Hideki Nagasaki; Makiko Suwa; Paul Horton; Reiko Kikuno; Osamu Ohara; Doron Lancet; Eric Eveno; Esther Graudens; Sandrine Imbeaud; Marie Anne Debily; Yoshihide Hayashizaki; Clara Amid; Michael Han; Andreas Osanger; Toshinori Endo; Michael A. Thomas; Mika Hirakawa; Wojciech Makalowski; Mitsuteru Nakao; Nam Soon Kim; Hyang Sook Yoo; Sandro J. De Souza; Maria De Fatima Bonaldo; Yoshihito Niimura; Vladimir Kuryshev; Ingo Schupp; Stefan Wiemann; Matthew Bellgard
    Nucleic Acids Research, 36, SUPPL. 1, D793, D799, Jan. 2008, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • The Rice Annotation Project Database (RAP-DB): 2008 update
    Tsuyoshi Tanaka; Baltazar A. Antonio; Shoshi Kikuchi; Takashi Matsumoto; Yoshiaki Nagamura; Hisataka Numa; Hiroaki Sakai; Jianzhong Wu; Takeshi Itoh; Takuji Sasaki; Ryo Aono; Yasuyuki Fujii; Takuya Habara; Erimi Harada; Masako Kanno; Yoshihiro Kawahara; Hiroaki Kawashima; Hiromi Kubooka; Akihiro Matsuya; Hajime Nakaoka; Naomi Saichi; Ryoko Sanbonmatsu; Yoshiharu Sato; Yuji Shinso; Mami Suzuki; Junichi Takeda; Motohiko Tanino; Fusano Todokoro; Kaori Yamaguchi; Naoyuki Yamamoto; Chisato Yamasaki; Tadashi Imanishi; Toshihisa Okido; Masahito Tada; Kazuho Ikeo; Yoshio Tateno; Takashi Gojobori; Yao Cheng Lin; Fu Jin Wei; Yueie Hsing; Qiang Zhao; Bin Han; Melissa R. Kramer; Richard W. McCombie; David Lonsdale; Claire C. O’donovan; Eleanor J. Whitfield; Rolf Apweiler; Kanako O. Koyanagi; Jitendra P. Khurana; Saurabh Raghuvanshi; Nagendra K. Singh; Akhilesh K. Tyagi; Georg Haberer; Masaki Fujisawa; Satomi Hosokawa; Yukiyo Ito; Hiroshi Ikawa; Michie Shibata; Mayu Yamamoto; Richard M. Bruskiewich; Douglas R. Hoen; Thomas E. Bureau; Nobukazu Namiki; Hajime Ohyanagi; Yasumichi Sakai; Satoshi Nobushima; Katsumi Sakata; Roberto A. Barrero; Yutaka Sato; Alexandre Souvorov; Brian Smith-White; Tatiana Tatusova; Suyoung An; Gynheung An; Satoshi Oota; Galina Fuks; Joachim Messing; Karen R. Christie; Damien Lieberherr; Hyeran Kim; Andrea Zuccolo; Rod A. Wing; Kan Nobuta; Pamela J. Green; Cheng Lu; Blake C. Meyers; Cristian Chaparro; Benoit Piegu; Olivier Panaud; Manuel Echeverria
    Nucleic Acids Research, 36, SUPPL. 1, D1028, 33, Database issue, 01 Jan. 2008, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes
    Hiroaki Sakai; Kanako O. Koyanagi; Tadashi Imanishi; Takeshi Itoh; Takashi Gojobori
    Gene, 389, 2, 196, 203, 15 Mar. 2007, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana: The Rice Annotation Project
    Takeshi Itoh; Tsuyoshi Tanaka; Roberto A. Barrero; Chisato Yamasaki; Yasuyuki Fujii; Phillip B. Hilton; Baltazar A. Antonio; Hideo Aono; Rolf Apweiler; Richard Bruskiewich; Thomas Bureau; Frances Burr; Antonio Costa De Oliveira; Galina Fuks; Takuya Habara; Georg Haberer; Bin Han; Erimi Harada; Aiko T. Hiraki; Hirohiko Hirochika; Douglas Hoen; Hiroki Hokari; Satomi Hosokawa; Yue Ie Hsing; Hiroshi Ikawa; Kazuho Ikeo; Tadashi Imanishi; Yukiyo Ito; Pankaj Jaiswal; Masako Kanno; Yoshihiro Kawahara; Toshiyuki Kawamura; Hiroaki Kawashima; Jitendra P. Khurana; Shoshi Kikuchi; Setsuko Komatsu; Kanako O. Koyanagi; Hiromi Kubooka; Damien Lieberherr; Yao Cheng Lin; David Lonsdale; Takashi Matsumoto; Akihiro Matsuya; W. Richard McCombie; Joachim Messing; Akio Miyao; Nicola Mulder; Yoshiaki Nagamura; Jongmin Nam; Nobukazu Namiki; Hisataka Numa; Shin Nurimoto; Claire O'Donovan; Hajime Ohyanagi; Toshihisa Okido; Satoshi OOta; Naoki Osato; Lance E. Palmer; Francis Quetier; Saurabh Raghuvanshi; Naomi Saichi; Hiroaki Sakai; Yasumichi Sakai; Katsumi Sakata; Tetsuya Sakurai; Fumihiko Sato; Yoshiharu Sato; Heiko Schoof; Motoaki Seki; Michie Shibata; Yuji Shimizu; Kazuo Shinozaki; Yuji Shinso; Nagendra K. Singh; Brian Smith-White; Jun Ichi Takeda; Motohiko Tanino; Tatiana Tatusova; Supat Thongjuea; Fusano Todokoro; Mika Tsugane; Akhilesh K. Tyagi; Apichart Vanavichit; Aihui Wang; Rod A. Wing; Kaori Yamaguchi; Mayu Yamamoto; Naoyuki Yamamoto; Yeisoo Yu; Hao Zhang; Qiang Zhao; Kenichi Higo; Benjamin Burr; Takashi Gojobori; Takuji Sasaki
    Genome Research, 17, 2, 175, 183, 2, Feb. 2007, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs
    Jun Ichi Takeda; Yutaka Suzuki; Mitsuteru Nakao; Roberto A. Barrero; Kanako O. Koyanagi; Lihua Jin; Chie Motono; Hiroko Hata; Takao Isogai; Keiichi Nagai; Tetsuji Otsuki; Vladimir Kuryshev; Masafumi Shionyu; Kei Yura; Mitiko Go; Jean Thierry-Mieg; Danielle Thierry-Mieg; Stefan Wiemann; Nobuo Nomura; Sumio Sugano; Takashi Gojobori; Tadashi Iman ishi
    Nucleic Acids Research, 34, 14, 3917, 3928, 2006, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • A web tool for comparative genomics: G-compass
    Yasuyuki Fujii; Takeshi Itoh; Ryuichi Sakate; Kanako O. Koyanagi; Akihiro Matsuya; Takuya Habara; Kaori Yamaguchi; Yayoi Kaneko; Takashi Gojobori; Tadashi Imanishi
    Gene, 364, 1-2, 45, 52, 30 Dec. 2005, [Peer-reviewed], [International Magazine]
    English, International conference proceedings
  • Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB)
    Chisato Yamasaki; Kanako O. Koyanagi; Yasuyuki Fujii; Takeshi Itoh; Roberto Barrero; Takuro Tamura; Yumi Yamaguchi-Kabata; Motohiko Tanino; Jun Ichi Takeda; Satoshi Fukuchi; Satoru Miyazaki; Nobuo Nomura; Sumio Sugano; Tadashi Imanishi; Takashi Gojobori
    Gene, 364, 1-2, 99, 107, 30 Dec. 2005, [Peer-reviewed], [International Magazine]
    English, International conference proceedings
  • Comparative genomics of bidirectional gene pairs and its implications for the evolution of a transcriptional regulation system
    Kanako O. Koyanagi; Masato Hagiwara; Takeshi Itoh; Takashi Gojobori; Tadashi Imanishi
    Gene, 353, 2, 169, 176, 04 Jul. 2005, [Peer-reviewed], [Lead author], [International Magazine]
    English, Scientific journal
  • Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Tadashi Imanishi; Takeshi Itoh; Yutaka Suzuki; Claire O'Donovan; Satoshi Fukuchi; Kanako O. Koyanagi; Roberto A. Barrero; Takuro Tamura; Yumi Yamaguchi-Kabata; Motohiko Tanino; Kei Yura; Satoru Miyazaki; Kazuho Ikeo; Keiichi Homma; Arek Kasprzyk; Tetsuo Nishikawa; Mika Hirakawa; Jean Thierry-Mieg; Danielle Thierry-Mieg; Jennifer Ashurst; Libin Jia; Mitsuteru Nakao; Michael A. Thomas; Nicola Mulder; Youla Karavidopoulou; Lihua Jin; Sangsoo Kim; Tomohiro Yasuda; Boris Lenhard; Eric Eveno; Yoshiyuki Suzuki; Chisato Yamasaki; Jun Ichi Takeda; Craig Gough; Phillip Hilton; Yasuyuki Fujii; Hiroaki Sakai; Susumu Tanaka; Clara Amid; Matthew Bellgard; Maria de Fatima Bonaldo; Hidemasa Bono; Susan K. Bromberg; Anthony J. Brookes; Elspeth Bruford; Piero Carninci; Claude Chelala; Christine Couillault; Sandro J. de Souza; Marie Anne Debily; Marie Dominique Devignes; Inna Dubchak; Toshinori Endo; Anne Estreicher; Eduardo Eyras; Kaoru Fukami-Kobayashi; Gopal R. Gopinath; Esther Graudens; Yoonsoo Hahn; Michael Han; Ze Guang Han; Kousuke Hanada; Hideki Hanaoka; Erimi Harada; Katsuyuki Hashimoto; Ursula Hinz; Momoki Hirai; Teruyoshi Hishiki; Ian Hopkinson; Sandrine Imbeaud; Hidetoshi Inoko; Alexander Kanapin; Yayoi Kaneko; Takeya Kasukawa; Janet Kelso; Paul Kersey; Reiko Kikuno; Kouichi Kimura; Bernhard Korn; Vladimir Kuryshev; Izabela Makalowska; Takashi Makino; Shuhei Mano; Regine Mariage-Samson; Jun Mashima; Hideo Matsuda; Hans Werner Mewes; Shinsei Minoshima; Keiichi Nagai; Hideki Nagasaki; Naoki Nagata; Rajni Nigam; Osamu Ogasawara; Osamu Ohara; Masafumi Ohtsubo; Norihiro Okada; Toshihisa Okido; Satoshi Oota; Motonori Ota; Toshio Ota
    PLoS Biology, 2, 6, e162, 6, 2004, [Peer-reviewed], [International Magazine]
    English, Scientific journal
  • TTOP: A System for Phylogenetic Tree Editing and Evolutionary Annotation of Genes
    Kundu Srinesh; Hagiwara Masato; Koyanagi Kanako O.; Imanishi Tadashi; Itoh Takeshi
    GI, 14, 583, 584, Japanese Society for Bioinformatics, 2003
    English
  • Detection of Processed Pseudogenes Based on cDNA Mapping to the Human Genome
    Sakai Hiroaki; Koyanagi Kanako O.; Itoh Takeshi; Imanishi Tadashi; Gojobori Takashi
    GI, 14, 452, 453, Japanese Society for Bioinformatics, 2003
    English
  • gLdraw: A General Tool for a Comparison of Chromosome Maps
    Hayakawa Yousuke; Koyanagi Kanako; Tamura Takuro; Gojobori Takashi; Imanishi Tadashi
    GI, 12, 466, 468, Japanese Society for Bioinformatics, 2001
    English
  • Protein tyrosine phosphatases from amphioxus, hagfish, and ray: Divergence of tissue-specific isoform genes in the early evolution of vertebrates
    Kanako Ono-Koyanagi; Hiroshi Suga; Kazutaka Katoh; Takashi Miyata
    Journal of Molecular Evolution, 50, 3, 302, 311, 2000, [Peer-reviewed], [Lead author]
    English, Scientific journal
  • Extensive gene duplication in the early evolution of animals before the parazoan-eumetazoan split demonstrated by G proteins and protein tyrosine kinases from sponge and hydra
    H Suga; M Koyanagi; D Hoshiyama; K Ono; N Iwabe; K Kuma; T Miyata
    JOURNAL OF MOLECULAR EVOLUTION, 48, 6, 646, 653, Jun. 1999, [Peer-reviewed]
    English, Scientific journal
  • Multiple protein tyrosine phosphatases in sponges and explosive gene duplication in the early evolution of animals before the parazoan-eumetazoan split
    K Ono; H Suga; N Iwabe; K Kuma; T Miyata
    JOURNAL OF MOLECULAR EVOLUTION, 48, 6, 654, 662, Jun. 1999, [Peer-reviewed], [Lead author]
    English, Scientific journal
  • Multiple TGF-beta receptor related genes in sponge and ancient gene duplications before the parazoan-eumetazoan split
    H Suga; O Kanako; T Miyata
    FEBS LETTERS, 453, 3, 346, 350, Jun. 1999, [Peer-reviewed]
    English, Scientific journal
  • Phospholipase C cDNAs from sponge and hydra: antiquity of genes involved in the inositol phospholipid signaling pathway
    M Koyanagi; K Ono; H Suga; N Iwabe; T Miyata
    FEBS LETTERS, 439, 1-2, 66, 70, Nov. 1998, [Peer-reviewed]
    English, Scientific journal
  • Ancient gene duplication and domain shuffling in the animal cyclic nucleotide phosphodiesterase family
    M Koyanagi; H Suga; D Hoshiyama; K Ono; N Iwabe; K Kuma; T Miyata
    FEBS LETTERS, 436, 3, 323, 328, Oct. 1998, [Peer-reviewed]
    English, Scientific journal
  • Sponge Pax cDNA related to Pax-2/5/8 and ancient gene duplications in the Pax family
    Daisuke Hoshiyama; Hiroshi Suga; Naoyuki Iwabe; Mitsumasa Koyanagi; Naruo Nikoh; Kei-Ichi Kuma; Fumihiko Matsuda; Tasuku Honjo; Takashi Miyata
    Journal of Molecular Evolution, 47, 6, 640, 648, 1998, [Peer-reviewed]
    English, Scientific journal
  • Intermittent divergence of the protein tyrosine kinase family during animal evolution
    H Suga; K Kuma; N Iwabe; N Nikoh; K Ono; M Koyanagi; D Hoshiyama; T Miyata
    FEBS LETTERS, 412, 3, 540, 546, Aug. 1997, [Peer-reviewed]
    English, Scientific journal
■ Other Activities and Achievements
■ Books and other publications
  • 進化―分子・個体・生態系
    ニコラス・H. バートン; ジョナサン・A. アイゼン; デイビッド・B; ゴールドステイン; ニパム・H. パテル; デレク・E.G. ブリッグス
    メディカルサイエンスインターナショナル, 08 Dec. 2009, 4895926214, 908
■ Lectures, oral presentations, etc.
  • Investigating phylogenetic incongruence in wild Oryza species through genome-wide phylogenomic analysis
    Koyanagi KO; Kotoku Y; Kishima Y
    The Annual Meeting of the Society for Molecular Biology & Evolution, 29 Jun. 2026, English, Poster presentation
    28 Jun. 2026 - 02 Jul. 2026
  • Estimating the temporal origins of mutations associated with domestication and improvement in Oryza sativa ssp. japonica
    Kanako O. Koyanagi
    第48回日本分子生物学会年会 シンポジウム3AS-13「ゲノムエポックが引き起こした大進化を探す」, 05 Dec. 2025, Nominated symposium
    [Invited]
  • Estimating the temporal origins of mutations associated with domestication and improvement in Oryza sativa ssp. japonica
    小柳香奈子; 川原善浩; 周止桐; 渡邉日出海
    日本育種学会第148回講演会, 11 Sep. 2025, Poster presentation
  • Exploration and validation of introgressed regions between AA-genome species of the genus Oryza
    Kanako Koyanagi; Yuta Kotoku; Yuji Kishima
    日本進化学会第27回大会, 20 Aug. 2025, Poster presentation
  • オミクス情報の系統解析による細胞分化過程の理解
    小柳香奈子
    木村資生記念第5回進化学セミナー, 15 Dec. 2024, Japanese, Public discourse
    [Invited]
  • Exploration of historical introgressed regions between AA-genome species of the genus Oryza
    小柳香奈子; 神徳雄太; 貴島祐治
    日本進化学会第26回大会, 21 Aug. 2024, English, Poster presentation
    21 Aug. 2024 - 24 Aug. 2024
  • 比較ゲノム解析によるO. sativa ssp. japonicaとイネ属AAゲノム種のイントログレッション領域の探索
    小柳 香奈子; 神徳 雄太; 貴島 祐治
    日本育種学会第145回講演会, 17 Mar. 2024, Japanese, Oral presentation
  • オミクス情報の系統解析による細胞分化過程推定の可能性
    小柳香奈子
    第46回日本分子生物学会年会 フォーラム1F-15「ゲノム起源を討論する学問所」, 06 Dec. 2023
    神戸市, Japan, [Invited]
  • オープンクロマチン情報の系統解析による細胞分化過程の推定
    小柳香奈子
    日本遺伝学会第95回大会, 08 Sep. 2023, Oral presentation
  • エピゲノム情報の系統解析による細胞分化過程の推定
    小柳香奈子
    遺伝研研究集会「生命科学を支える分子系統学」, 03 Aug. 2022
    03 Aug. 2022 - 04 Aug. 2022, [Invited]
  • Inferring cell differentiation processes based on phylogenetic analysis of epigenomes
    Kanako O. Koyanagi
    The 24th Hokkaido University – Seoul National University Joint Symposium, 05 Nov. 2021, English, Invited oral presentation
    [Invited]
  • Inferring cell type tree based on phylogenetic analysis of genome-wide epigenetic information
    Kanako O. Koyanagi
    EMBO | EMBL Symposium: The Identity and Evolution of Cell Types, 06 May 2021, English, Poster presentation
    04 May 2021 - 07 May 2021
  • Inferring cell differentiation processes based on phylogenetic analysis of genome-wide epigenetic information
    Kanako O. Koyanagi
    SMBE 2018, 11 Jul. 2018, English, Poster presentation
    [International presentation]
  • Inferring cell differentiation processes based on the phylogenetic analysis of genome-wide epigenetic information: mammalian hematopoiesis as a model case
    Kanako O. Koyanagi
    ConBio 2017, 07 Dec. 2017, English, Nominated symposium
    [Invited], [Domestic Conference]
  • Inferring cell differentiation processes based on phylogenetic analysis of genome-wide epigenetic information
    Kanako O. Koyanagi
    CDB symposium 2017, 27 Mar. 2017, English, Poster presentation
    [International presentation]
  • Inferring cell differentiation processes based on phylogenetic analysis of genome-wide epigenetic information
    Kanako O. Koyanagi
    THE 40th NAITO CONFERENCE on Epigenetics―From Histone Code to Therapeutic Strategy, 17 Sep. 2015, English, Poster presentation
    [International presentation]
  • Development of web application "FATESer" for the FATES analysis
    Kanako O. Koyanagi
    日本育種学会 第128回講演会・新潟, 11 Sep. 2015, Japanese, Public symposium
    [Domestic Conference]
  • Inferring cell differentiation processes based on the phylogenetic analysis of genome-wide histone modification data: Human hematopoiesis as a model case
    Kanako O. Koyanagi
    日本進化学会 第17回大会・東京, 22 Aug. 2015
  • Inferring cell differentiation processes based on the phylogenetic analysis of genome-wide DNA methylation data: Hematopoiesis as a model case
    Kanako O. Koyanagi
    Keystone Symposia Conference (Z1: DNA Methylation), 31 Mar. 2015, English, Poster presentation
    [International presentation]
  • アデノウイルスのゲノム進化を可能にする組換えと置換の特徴
    小柳香奈子
    第15回アデノウィルス研究会 品川インターシティ, 08 Nov. 2014
    [Invited]
  • エピジェネティック情報の最尤推定による細胞分化過程の推定 ーマウス血球系細胞をモデルとして
    小柳香奈子
    日本進化学会 第16回大会・高槻, 22 Aug. 2014, Japanese, Poster presentation
    [Domestic Conference]
  • Inferring cell differentiation processes based on the phylogenetic analysis of genome-wide epigenetic information: mouse hematopoietic cells as a model case
    Kanako O. Koyanagi
    日本分子生物学会 第36回・神戸, 05 Dec. 2013, Japanese, Poster presentation
    [Domestic Conference]
  • エピジェネティック情報の系統解析による細胞分化過程の推定 ーマウス血球系細胞をモデルとして
    小柳香奈子
    日本進化学会 第15回大会・つくば, 30 Aug. 2013, Japanese, Oral presentation
    [Domestic Conference]
■ Syllabus
  • 大学院共通授業科目（一般科目）：自然科学・応用科学, 2024年, 修士課程, 大学院共通科目
  • ゲノム情報科学特論, 2024年, 修士課程, 情報科学院
  • 情報科学特論, 2024年, 博士後期課程, 獣医学院
  • 情報科学特論, 2024年, 博士後期課程, 国際感染症学院
  • ゲノム情報科学特論, 2024年, 博士後期課程, 情報科学研究科
  • ゲノム情報科学特論, 2024年, 博士後期課程, 情報科学院
  • 一般教育演習(ﾌﾚｯｼｭﾏﾝｾﾐﾅｰ), 2024年, 学士課程, 全学教育
  • 生体機能学, 2024年, 学士課程, 工学部
  • 生体医工学基礎, 2024年, 学士課程, 工学部
  • 生体工学概論, 2024年, 学士課程, 工学部
  • 生体情報工学実験Ⅰ, 2024年, 学士課程, 工学部
  • 生体情報工学実験Ⅱ, 2024年, 学士課程, 工学部
■ Research Themes
  • Estimating mutation ages associated with crop domestication and improvement and comparing them across species
    Grants-in-Aid for Scientific Research
    01 Apr. 2026 - 31 Mar. 2029
    小柳 香奈子; 川原 善浩
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Hokkaido University, 26K08749
  • Inferring epigenomic changes during cell differentiation at single cell resolution
    Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
    Apr. 2022 - Mar. 2026
    小柳 香奈子
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Hokkaido University, 22K06330
  • Inferring cell differentiation process based on phylogenetic analysis of histone modifications of human cells
    Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
    01 Apr. 2016 - 31 Mar. 2020
    Koyanagi Kanako
    For understanding the development of animals, it is important to reveal the landscape of epigenetic changes in cells during differentiation process. However, analyzing whole differentiation processes in various cell types is laborious and impossible for some organisms. In this study, phylogenetic analysis is applied to reconstruct developmental processes based on the developmental changes of epigenomes of differentiated cells. Using epigenomes of eight types of differentiated human hematopoietic cells, ancestral state estimation based on a phylogenetic tree was applied to map the epigenomic changes of six kinds of histone modifications onto the hierarchical cell differentiation process of hematopoiesis. As a result, it was shown that this approach could infer an appropriate landscape of histone modification changes during hematopoiesis.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Hokkaido University, Principal investigator, Competitive research funding, 16K07458
  • Inferring cell differentiation processes based on phylogenetic analysis of genome-wide epigenetic information
    Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
    01 Apr. 2013 - 31 Mar. 2017
    Koyanagi Kanako
    How cells divide and differentiate is a fundamental question in organismal development; however, analyzing differentiation processes in various cell types is laborious and sometimes impossible. Phylogenetic analysis is usually used to reconstruct evolutionary processes based on inherent characters. It could also be used to reconstruct developmental processes based on the developmental changes during cell proliferation and differentiation. In this study, genome-wide epigenetic information from differentiated cells was used to perform phylogenetic analyses. As a result, it was shown that the hierarchical differentiation processes and epigenetic status of differentiating progenitor cells could be inferred based on genom-wide DNA methylation information for murine hematopoiesis. This analysis was also applied to various differentiated cells of human.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Hokkaido University, Principal investigator, Competitive research funding, 25440186
  • An analgesic neuropeptide endomorphin may be produced by RNA editing induced by oxidative stress
    Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research
    01 Apr. 2014 - 31 Mar. 2016
    Matsushima Ayami; KOYANAGI KANAKO
    Endomorphin-1 and -2 are neuropeptides consisting of only 4 amino acid residues. Various biological functions of these peptides are known, for instance analgesic activity that is stronger than that of morphine and a relation with itching. However, to date a precursor protein of these peptides has never been uncovered. Many scientists today consider that the limited information from short peptide sequence makes it difficult to find peptide genes by in silico genomic searches. In the present study, we intended to perform RNA-seq determinations combined with an in silico genomic search for the peptide precursor protein. We succeeded in finding an endomorphin-like peptide, although this was not exactly the same as endomorphins. The synthetic peptide corresponding to the endomorphin-like amino acid sequence has a weak binding affinity for opioid receptors.
    Japan Society for the Promotion of Science, Grant-in-Aid for Challenging Exploratory Research, Kyushu University, 26670288
  • 地域の育種集団におけるFNPsハプロタイプを用いた高速ゲノム育種法の開発
    農林水産業・食品産業科学技術研究推進事業 シーズ創出ステージ
    2013 - Mar. 2016
    藤野 賢治
    農林水産省, Competitive research funding
  • Study of the occurrence of mutations and adaptive genome evolution via genomic analyses
    Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
    01 Apr. 2010 - 31 Mar. 2015
    WATANABE Hidemi; KOYANAGI Kanako
    In order to obtain the fundamental properties of occurrence of genomic mutations so as to identify genomic changes that have led to adaptive evolution, i.e., genome adaptation, via finding significant deviations from the expectations calculated with the properties of the occurrence of mutations, we artificially introduced random double-strand breaks (DSBs) to the budding yeast genome and detected occurred mutations during repair of the DSBs by sequencing the whole genomes. In addition, we have computationally traced back genomic changes of natural human adenoviruses (HAdV), and it was suggested that HAdVs have changed via homologous recombination events between distant relatives. The statistical properties of this type of changes in HAdV indicate that the recombinant forms have been selected for adaptation.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Hokkaido University, Coinvestigator not use grants, Competitive research funding, 22125009
  • エピゲノミクスとファイロゲノミクスの融合による哺乳類細胞系譜再構築の試み
    大学院情報科学研究科若手研究費
    Jul. 2012 - Mar. 2013
    小柳香奈子
    北海道大学大学院情報科学研究科
  • Functional analysis on endogenous pararetrovirus in rice genome-relationship with rice tungro disease-
    Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    2010 - 2012
    KISHIMA Yuji; KOYANAGI Kanako; YASUI Hideshi
    We have addressed two questions as to endogenous RTBV; theinsertion mechanism of ERTBV into rice genome and the relationship between ERTBVand RTBV resistance. ERTBVs are preferentially present in AT-rich repeats in ricegenome, and we described that AT-rich repeats have integrated chromosomal andepisomal DNAs, which would have been suspended in the nucleus. We also identified atolerance allele against RTBV, qTDR5, located on chromosome 5 by the genetic analysesusing the progenies between an African rice strain Oryza glaberrima WK18 and a japonicarice strain Taichung 65. The region in qTDR5 contains an ERTBV sequence.
    Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 22380001
  • Interaction among human chromosomes and its relationship to spatial organization of chromosomes in a nucleus
    Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)
    2006 - 2008
    KOYANAGI Kanako
    本研究の目的は、ヒトゲノム情報解析から染色体間の相互作用を示す情報を抽出し、核内における染色体の核内配置との関連性を検証することである。本研究では、染色体間の相互作用を示す情報として、ヒトゲノム中にみられるプロセス型偽遺伝子とゲノム内重複領域の染色体分布を解析し、染色体間の偏りを検出した。またこの研究の過程において、種特異的な重複領域を高精度に同定する目的で、分子進化解析に基づくゲノム直系領域の同定方法を開発した。
    Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (B), Hokkaido University, Principal investigator, Competitive research funding, 18710159
  • 比較ゲノム解析に基づくヒト固有遺伝情報の同定と機能推定
    科学研究費助成事業 特定領域研究
    2006 - 2007
    渡邉 日出海; 小柳 香奈子
    本研究課題の目的は、ヒト固有形質に密接に関連すると推定されるヒト固有遺伝情報を同定することである。この目的のために、ヒトとチンパンジーの種分岐後にヒトゲノムに生じたヒト固有遺伝情報ならびにヒト特異的進化状態を示すゲノム領域の同定を行った。まず、基盤となるデータとして、ヒト-チンパンジー一マカク間の高精度なゲノム直系領域多重アラインメントの作成を行った。具体的には、曖昧なゲノム領域の実験による確認、ゲノム概要配列に加えてBACクローン配列を用いた解析、詳細な分子進化学的解析によるゲノム直系領域の推定を行った。次にこのゲノムアラインメントに基づき、ヒト系統に特異的な、挿入・欠失および塩基置換・アミノ酸置換速度変化を同定した。特に、従来は解析が困難であるために対象外とされていた、ヒトとチンパンジーの種分岐後に遺伝子重複が起きた遺伝子群についても解析を行った。その結果、ヒト固有形質に関連する候補遺伝子が推定された。これら候補遺伝子のさらなる機能解析等により、ヒト固有形質の理解が進むことが期待される。上記の研究過程では、プログラムによる自動処理に加えて、人間の目によるデータの精査も重要となる。そこで、このデータ精査を支援するための解析ツールの開発も行った。このツールは、長大なゲノム間の対応領域を可視化し、それを自由に拡大縮小したり、対応領域の各ゲノム上における位置情報や塩基相違度等の必...
    日本学術振興会, 特定領域研究, 北海道大学, Coinvestigator not use grants, Competitive research funding, 18017002
  • ヒトゲノム構造にみられる遺伝子位置の偏りの意義とその進化過程に関する研究
    科学研究費助成事業 若手研究(B)
    2004 - 2005
    小柳 香奈子
    申請者のこれまでの研究から、ヒトゲノム上の遺伝子位置及びその構造に偏りがあることが明らかとなっていた。そこで、本課題ではこの偏りの意義の解明すること(目的1)、さらにこの遺伝子構造の進化過程を明らかにすること(目的2)、を目的として研究を行った。まず、ヒトゲノム上で偏りのみられたhead-to-head遺伝子ペアについて、成人における組織特異性に関する発現情報を用いて、遺伝子ペア間の発現パターンの比較を行った。その結果、遺伝子ペア間では弱いながら発現組織に相関がみられることがわかった。また、遺伝子ペア間において何か共通の特徴はないか、機能アノテーション情報を比較したが、機能アノテーションには特徴的な偏りはみられないことがわかった。これらのことから、ヒトゲノム構造にみられる偏りと遺伝子発現調節との間に関連性のあることが示唆された。次に、ヒトゲノム上でみられたゲノム構造の偏りが他の生物種でも保存しているか、それはヒトに至る進化の過程でいつ頃進化したのか、また他の生物種にその生物種固有のヒトとは異なった偏りや特徴がないか、といった点について解明する目的で、ヒト以外の生物種(マウス、フグ、ホヤ、ハエ、カ、線虫)についてゲノム構造の比較解析を行った。その結果、この遺伝子構造は哺乳類に特異的にみられるものであり、その他の真核生物にはみられない新しく進化した構造であること、という結果を得た...
    日本学術振興会, 若手研究(B), 北海道大学, Principal investigator, Competitive research funding, 16710142
  • ゲノム配列の種間・種内比較に基づく進化過程の推定
    科学研究費助成事業 特定領域研究
    2004 - 2004
    渡邉 日出海; 小柳 香奈子
    理化学研究所が中心となって日独中韓台の9センターで編成したコンソーシアムにおいて、霊長類の染色体としては世界で初めてのチンパンジー22番染色体(PTR22)の完成配列を決定し、Nature誌のArticleとして発表した。この論文において本研究代表者は比較解析全般を担当し、ヒト相同染色体であるヒト21番染色体(HSA21)および他の類人猿との間で種間比較解析を行った。本研究の目的は、500-700万年前にヒトとチンパンジーが分岐した後に、それぞれの系統において生じてきたゲノムの構造変化の詳細を明らかにすることである。同コンソーシアムによる先行研究(Fujiyama et al.,2002)において両ゲノムは塩基配列レベルで平均1.23%の塩基置換が起きていることをあきらかにしていたが、PTR22-HSA21間では若干高い1.44%の平均塩基置換率になっていた。これは主としてテロメア側半分ではGC含量が高くCpGのメチル化脱アミノ化による塩基置換(C:G→T:A)が高頻度で起こっていることによることがわかった。他に、PTR22はHSA21よりも約1%小さいこと、多くの挿入・欠失が存在し短いものほど頻度が高いこと、300bp以上の長さの挿入は大部分が散在性反復配列の挿入によるものであること、挿入はHSA21で高頻度で起こっている一方、欠失は両染色体で完全に同じ傾向をしめしているこ...
    日本学術振興会, 特定領域研究, 北海道大学, Coinvestigator not use grants, Competitive research funding, 16011239
■ Academic and Social Contribution Activities/Other
Social Contribution Activities
  • 国立大学法人8大学情報系大学院合同開催イベント「情報学 for all by all」
    15 Mar. 2026
    Panelist
  • 北大道新アカデミー 情報科学から見える景色
    12 Oct. 2024
    Lecturer
  • 北海道札幌東高等学校模擬授業
    04 Nov. 2022
    Lecturer
  • 北大セミナー in オホーツク2015
    10 Oct. 2015
    Lecturer
  • 北海道大学 公開講座
    31 Jul. 2014
    Lecturer
  • 日本植物学会 第4回男女共同参画セミナー
    13 Sep. 2013
    Panelist
  • 日本遺伝学会 男女共同参画ランチョンワークショップ
    21 Sep. 2010
    Panelist
  • 第47回サイエンス・カフェ札幌
    03 Oct. 2009
    Appearance