Genome Evolution at Mishima

Dates: Monday, March 27th, Tuesday, March 28th, and Wednesday, March 29th, 2017
Place: Lecture Hall, National Institute of Genetics, Mishima, Japan
 Map of NIG campus (Lecture Hall is building D)

Evolutionary study is now at the center of all biology, and genome evolution 
is basis of evolution at any level of organisms. Neutral evolution is a very
important mechanism for genomes to evolve. We at National Institute of 
Genetics are thus proud of being here, the birth place of the neutral theory 
of evolution, started by late Motoo Kimura in 1960s and expanded by Tomoko Ohta and others later. 

We would like to discuss many aspects of genome evolution from virus to human in this symposium, 
"Genome Evolution at Mishima" or GEM. Twenty six invited speakers and six GEM talk speakers present 
current status of researches in genome evolution. We also have 22 poster presentations in this symposium.

GEM Invited Speakers

Dr. Hiroshi Akashi (Professor, Division of Evolutionary Genetics, National Institute of Genetics, Japan) Dr. Jaume Bertranpetit (Professor, CEXS-Universitat Pompeu Fabra, Spain) Dr. Shu-Miaw Chaw (Research Fellow, Academia Sinica, Taiwan) Dr. Yun-Xin Fu (Professor, University of Texas at Houston, USA) Dr. Takashi Gojobori (Project Professor, National Institute of Genetics, Japan / Distinguished Professor & Associate Director of Computational Bioscience Research Center, KAUST, Saudi Arabia) Dr. Mitsuyasu Hasebe (Professor, National Institute for Basic Biology, Japan) Dr. Kazuho Ikeo (Associate Professor, Laboratory for DNA Data Analysis, National Institute of Genetics, Japan) Dr. Ituro Inoue (Professor, Division of Human Genetics, National Institute of Genetics, Japan) Dr. Sachiko Isobe (Group Leader, Kazusa DNA Research Institute, Japan) Dr. Timothy A. Jinam (Assistant Professor, Division of Population Genetics, National Institute of Genetics,, Japan) Dr. Lynn Jorde (Professor, University of Utah School of Medicine, USA / Visiting Professor, Division of Applied Genetics, National Institute of Genetics, Japan) Dr. Sanguk Kim (Professor, Pohang University of Science and Technology, Korea) Dr. Jun Kitano (Professor, Division of Ecological Genetics, National Institute of Genetics, Japan) Dr. Ichizo Kobayashi (Visiting Professor, University of Paris-Saclay, France) Dr. Ken Kurokawa (Professor, Genome Evolution Laboratory, National Institute of Genetics, Japan) Dr. Olivier Lichtarge (Professor, Baylor College of Medicine, USA) Dr. Takashi Makino (Associate Professor, Tohoku University, Japan) Dr. William Martin (Professor, Heinrich Heine University, Germany) Dr. Klaus Mayer (Group Leader, Plant Genome and Systems Biology, Germany) Dr. Yasukazu Nakamura (Professor, Genome Informatics Laboratory, National Institute of Genetics, Japan) Dr. Rasmus Nielsen (Professor, UC Berkeley Center for Theoretical Evolutionary Genomics, USA) Dr. Yukinori Okada (Professor, Osaka University, Japan) Dr. Hiroki Oota (Associate Professor, Kitazato University, Japan) Dr. Noriyuki Satoh (Professor, Okinawa Institute of Science and Technology, Japan) Dr. Yoko Satta (Professor, Graduate University for Advanced Studies, Japan) Dr. Koichiro Tamura (Professor, Tokyo Metropolitan University, Japan)

Program

Day 1 (Monday, March 27th, 2017) 10:20 - 10:30 Opening remarks 10:30 - 11:00 Invited talk 1: William Martin Title: Endosymbiotic origin and differential loss of eukaryotic genes 11:00 - 11:30 Invited talk 2: Takashi Gojobori Title: Unseen world of bacterial community seen from comparative marine metagenomics 11:30 - 12:00 Invited talk 3: Rasmus Nielsen Title: The genetic basis of human physiological adaptation 12:00 - 12:30 Invited talk 4: Hiroki Oota Title: A trial for reconstructing human population history in the Japanese archipelago through the simulation based on genome-wide data and ancient DNA analyses 12:30 - 14:00 Lunch break 14:00 - 14:30 Invited talk 5: Jaume Bertranpetit Title: The detection and interpretation of adaptive selection in human populations. Much Ado About Nothing? 14:30 - 15:00 Invited talk 6: Yoko Satta Title: The demographic histories in primate lineages based on whole genome sequences 15:00 - 15:30 Invited talk 7: Lynn Jorde Title: Genetics of high-altitude adaptation 15:30 - 16:00 Invited talk 8: Ituro Inoue Title: Landscape of regulatory elements derived from human endogenous retroviruses 16:00 - 16:30 Tea Break 16:30 - 17:00 Invited talk 9: Noriyuki Satoh Title: Genome evolution involved in chordate origins 17:00 - 17:30 Invited talk 10: Klaus Mayer Title: The genes of (western) civilization 17:30 - 18:00 Invited talk 11: Sachiko Isobe Title: Did the journey to strawberry start from Japan? 18:00 - 19:00 Poster Presentation 1 19:00 - 20:30 Buffet & Poster Presentation 1 Day 2 (Tuesday, March 28th, 2017) 10:00 - 10:30 Invited talk 12: Takashi Makino Title: Invasive animal genomes with high duplicated gene content 10:30 - 11:00 Invited talk 13: Jun Kitano Title: Genetics of physiological adaptation in sticklebacks 11:00 - 11:30 Invited talk 14: Olivier Lichtarge Title: Evolution versus disease: a new look at an old calculus 11:30 - 12:00 Invited talk 15: Yukinori Okada Title: Statistical genetics, disease biology, and novel drug discovery 12:00 - 13:30 Lunch break 13:30 - 14:00 Invited talk 16: Yun-Xin Fu Title: Genome sorting in Tetrahymena 14:00 - 14:30 Invited talk 17: Mitsuyasu Hasebe Title: The genome of Australian pitcher plant Cephalotus reveals genetic changes associated with carnivory 14:30 - 15:00 Invited talk 18: Shu-Miaw Chaw Title: Evolution of cupressophyte (conifers II) plastomes 15:00 - 15:30 Invited talk 19: Yasukazu Nakamura Title: Towards better genome annotation 15:30 - 16:00 Tea Break 16:00 - 16:30 Invited talk 20: Sanguk Kim Title: Evolution of the modular architecture of protein-protein interaction network 16:30 - 17:00 Invited talk 21: Koichiro Tamura Title: Divergence time estimation using genome-scale sequence data 17:00 - 17:30 Invited talk 22: Hiroshi Akashi Title: Transcriptional constraints in Drosophila genome evolution 17:30 - 18:20 Poster Presentation 2 19:00 - 21:00 Symposium Dinner at Nihonkai Shoya (front of Mishima JR Station south exit) Day 3 (Wednesday, March 29th, 2017) 10:00 - 10:30 Invited talk 23: Ichizo Kobayashi Title: Epigenome-based adaptive evolution 10:30 - 11:00 Invited talk 24: Ken Kurokawa Title: Microbial diversity of an active continental serpentinite-hosted hydrothermal system 11:00 - 11:30 Invited talk 25: Kazuho Ikeo Title: Integration of protein and genome information to know function 11:30 - 12:00 Invited talk 26: Timothy A. Jinam Title: Exploration of archaic human admixture in Southeast Asian populations 12:00 - 13:30 Lunch break 13:30 - 13:50 GEM talk 1: Yuseob Kim, Ewha Womans University, Korea Title: Neutral and selective processes in the molecular evolution of influenza virus H3N2 13:50 - 14:10 GEM talk 2: Hiroki Shibata, Medical Institute of Bioregulation, Kyushu University, Japan Title: Accelerated evolution of venom protein genes in the habu genome 14:10 - 14:30 GEM talk 3: Hiroshi Mori, National Institute of Genetics, Japan Title: Phylogenomic and morphological analyses of extinct Palaeognathae 14:30 - 14:50 GEM talk 4: Tomotaka Matsumoto, National Institute of Genetics, Japan Title: Codon usage selection biases estimates of the fraction of adaptive amino acid substitutions 14:50 - 15:10 GEM talk 5: Takeshi Kawashima, National Institute of Genetics, Japan Title: Reconsidering Evolutionary Study of Metabolic Pathways in Eukaryotes 15:10 - 15:30 GEM talk 6: Hirofumi Nakaoka, National Institute of Genetics, Japan Title: Clonal expansion of KRAS-mutated epithelial cells in human endometriosis 15:30 - 15:40 Ending remarks

Poster Presentations

P1. Interaction among nucleoporins and reproductive isolation in Drosophila Kyoichi Sawamura (Presenter)1, Zhuo Wang2, Kohei Miura2, Takaaki Hayashi2, Kazuyuki Hirai3, Takeshi Awasaki3, Moe Wada4, Yoko Keira4, Hiroyuki O. Ishikawa4 1 Faculty of Life and Environmental Sciences, University of Tsukuba 2 Graduate School of Life and Environmental Sciences, University of Tsukuba 3 Kyorin University School of Medicine 4 Gdaduate School of Science, Chiba University P2. Habu snake genome reveals the evolutionary strategy for generating the venom-related genes Tomohisa Ogawa (Presenter)1, Takahito Chijiwa2, Naoko Oda-Ueda3, Hitomi Nakamura3, Kazuaki Yamaguchi2, Shousaku Hattori4, Kazumi Matsubara5, Yoichi Matsuda6, Kazuki Mori7, Kosuke Tashiro7, Satoru Kuhara7, Shinichi Yamasaki8, Manabu Fujie8, Hiroki Goto8, Ryo Koyanagi8, Takeshi Takeuchi9, Yasuyuki Fukumaki1, Motonori Ohno3, Eiichi Shoguchi9, Kanako Hisata9, Noriyuki Satoh9*, Hiroki Shibata7,10 1) Department of Biomolecular Science, Graduate School of Life Sciences, Tohoku University 2) Department of Applied Life Science, Faculty of Bioscience and Biotechnology, Sojo University, Kumamoto 3) Department of Biochemistry, Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto 4) Institute of Medical Science, University of Tokyo, Oshima-gun, Kagoshima 5) Department of Information and Biological Sciences, Graduate School of Natural Sciences, Nagoya City University, Nagoya 6) Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 7) Graduate School of Systems Life Sciences, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka 8) DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 9) Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 10) Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka P3. Genome Identifier: A tool for phylogenetic analysis using whole genome data Tokumasa Horiike (Presenter)1 and Yuki Shimoyama2 1) College of Agriculture, Academic Institute, Shizuoka University 2) Graduate School of Integrated Science and Technology, Shizuoka University P4. Expression divergence of chemosensory genes between Drosophila sechellia and its sibling species and its implications for host shift Meng-Shin Shiao1,2 , Jia-Ming Chang3,4,5, Wen-Lang Fan1,6, Mei-Yeh Jade Lu1, Cedric Notredame3,4, Shu Fang1, Rumi Kondo7 (Presenter) and Wen-Hsiung Li1,8 1) Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 2) Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand 3) Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain 4) Universitat Pompeu Fabra (UPF), Barcelona, Spain 5) Institute of Human Genetics (IGH), UPR 1142, CNRS, Montpellier, France 6) Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan 7) Department of Biologial Sciences, Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo 8) Department of Ecology and Evolution, University of Chicago, USA P5. A study on attractive odorant and chemosensory genes between Drosophila sechellia and its sibling species and its implications for host shift Yumi Nakajo (Presenter)1 and Rumi Kondo1 1) Department of Biologial Sciences, Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo P6. 153 genes phylogenetic analysis indicated a newly single-celled eukaryote, strain SRT308, as a deep-branching Euglenozoan Euki Yazaki (Presenter)1, Takashi Shiratori1, Tetsuo Hashimoto1,2, Ken-ichiro Ishida1, Yuji Inagaki1,2 1) Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba 2) Center for Computational Science, University of Tsukuba, Tsukuba P7. Structure and evolution of the repeated region of the S100'Fused' type genes across primates Vanessa Romero (Presenter)1,2, Hirofumi Nakaoka1,2, and Ituro Inoue1,2 1) Division of Human Genetics, National Institute of Genetics, Mishima 2) Department of Genetics, SOKENDAI, Mishima P8. Silencing effect of Hominoid highly conserved non-coding sequences on embryonic brain development Morteza Mahmoudi Saber (Presenter)1,2 and Saitou Naruya1,2 1) Division of Population Genetics, National Institute of Genetics, Mishima 2) Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo P9. Exome sequencing of Toque Macaque (Macaca sinica) Nilmini Hettiarachchi (Presenter)1,2, Morteza Mahmoudi Saber1,3, Naoki Osada4, Takashi Hayakawa5, Hirofumi Nakaoka6, Ituro Inoue6, and Saitou Naruya1 1) Division of Population Genetics, National Institute of Genetics, Mishima 2) Laboraty of Biological Network, National Institute of Genetics, Mishima 3) Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 4) Graduate School of Information Science and Technology, Hokkaido University, Sapporo 5) Primate Research Institute, Kyoto University, Inuyama 6) Division of Human Genetics, National Institute of Genetics, Mishima P10. Detecting human contamination in genome databases Kirill Kryukov (Presenter)1 and Tadashi Imanishi1 1) Department of Molecular Life Science, Tokai University School of Medicine, Isehara P11. Evolution of Cnidarian eyes inferred from transcriptomes Junichi Imoto (Presenter)1 and Kazuho Ikeo1 1) Laboratory for DNA Data Analysis, National Institute of Genetics, Mishima P12. Analysis of HLA polymorphisms in East Africans reveals evidence of gene flow from Asia to the Sudanese Arab Waleed H. Omer (Presenter)1,2, Hirofumi Nakaoka1,2, Hisham Y. Hassan3, Kazuyoshi Hosomichi4, Martin Jaeger5, Mihai G. Neata5, and Ituro Inoue1,2 1) Division of Human Genetics, National Institute of Genetics, Mishima 2) Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima 3) Banoon ART and Cytogenetics Centre, Bahrain Defence Force Hospital, Manama, Bahrain 4) Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa 5) Radboud Center for Infectious Diseases, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands P13. Germline variants of prostate cancer in Japanese families Takahide Hayano(Presenter)1 , Hiroshi Matsui2, Hirofumi Nakaoka1, Nobuaki Ohtake2, Kazuyoshi Hosomichi3, Kazuhiro Suzuki2, and Ituro Inoue1 1) Division of Human Genetics, National Institute of Genetics, Mishima 2) Department of Urology, Gunma University Graduate School of Medicine, Maebashi 3) Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa P14. Draft genome sequencing of capybara Isaac Babarinde1,2 and Saitou Naruya (Presenter)1,2 1) Division of Population Genetics, National Institute of Genetics, Mishima 2) Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima P15. Comparative genome analysis to identify a responsible gene for morphological evolution through the study of non-model organisms Tomoyo Iizuka (Presenter)1,2, Masafumi Nozawa 3, Kazuho Ikeo 1,2 1) Laboratory for DNA Data Analysis, National Institute of Genetics, Mishima 2) Department of Genetics, SOKENDAI, Mishima 3) Department of Biological Sciences, Tokyo Metropolitan University, Tokyo P16. Systematic identification and characterization of regulatory elements derived from Human Endogenous Retroviruses Jumpei Ito (Presenter)1,2, Ryota Sugimoto 1, Hirofumi Nakaoka 1, Shiro Yamada 1, Tetsuaki Kimura 1, Takahide Hayano 1, and Ituro Inoue 1,2 1) Division of Human Genetics, National Institute of Genetics, Mishima 2) Department of Genetics, SOKENDAI, Mishima P17. Molecular basis of EGT and HGT: How transgenes acquire transcriptional competence in the foreign genome? Takayuki Hata (Presenter)1, Soichirou Satoh1, Naoto Takada1, Tomohiro Uchikoba2, Makoto Tachikawa1, Mitsuhiro Matsuo1, Sergei Kushnir3, and Junichi Obokata1,2 1) Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 2) Faculty of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 3) Vale Institute of Technology Sustainable Development, Belem, Brazil P18. Evolutionary roles of SL-trans-splicing in the primary endosymbiosis Mitsuhiro Matsuo1, Atsushi Katahata1, Soichirou Satoh1, Motomichi Matsuzaki2, Mami Nomura3, Ken-ichiro Ishida3, Yuji Inagaki4, and Junichi Obokata (presenter)1 1) Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 2) Graduate School of Medicine, The University of Tokyo, Tokyo 3) Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 4) Center for Computational Sciences, University of Tsukuba, Tsukuba P19. Genomic history of Japonesians, people on Japanese Archipelago Timothy A. Jinam1 and Saitou Naruya (Presenter)1 1) Division of Population Genetics, National Institute of Genetics, Mishima P20. Development of knowledge based analysis platform for NGS type of genomic research Norikazu Monma1, Sonoko Kinjo (Presenter)1, Sadahiko Misu1, Norikazu Kitamura1, Junichi Imoto1, and Kazuho Ikeo1 1) Center for Information Biology, National Institute of Genetics, Mishima P21. Genetic and molecular mechanisms underlying variation in seasonal reproduction between stickleback ecotypes Asano Ishikawa (Presenter)1 and Jun Kitano1 1) Division of Ecological Genetics, National Institute of Genetics, Mishima P22. Genomic insights into the relationship between Jomon and modern East Eurasians H. Kanzawa-Kiriyama (Presenter)1, N. Adachi2, T. Kakuda2, Y. Nakagaki1, T.A. Jinam3, K. Hosomichi4, A. Tajima4, K. Kryukov5, A. Saso6,7, G. Suwa7, S. Ueda6, M. Yoneda6, I. Inoue8,9, N. Saitou3,9, and K. Shinoda1 1) Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan 2) Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi 3) Division of Population Genetics, National Institute of Genetics, Mishima, Japan 4) Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan 5) Department of Molecular Life Science, School of Medicine, Tokai University, Isehara, Japan 6) Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan 7) The University Museum, The University of Tokyo, Tokyo, Japan 8) Division of Human Genetics, National Institute of Genetics, Mishima, Japan 9) Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan

Organizing Committee for NIG Symposium on Genome Evolution at Mishima

Dr. Kazuho Ikeo (Laboratory for DNA Data Analysis, NIG) Dr. Ituro Inoue (Division of Human Genetics, NIG) Dr. Jun Kitano (Division of Ecological Genetics, NIG) Dr. Naruya Saitou (Division of Population Genetics, NIG), Chair Dr. Yasukazu Nakamura (Genome Informatics Laboratory, NIG)

GEM administrative office:

Saitou Lab National Institute of Genetics Mishima, 411-8540, Japan email: saitounr@nig.ac.jp phone: +81-55-981-6790 fax: +81-55-981-6789 Funded by National Institute of Genetics Updated on March 26, A.S. 0017 (2017 A.D.)