Genome Concept Centennial Conference
Dates: February 15-17, 2021
Purely Online using zoom
Hosted by
National Institute of Genetics
andMEXT Yaponesia Genome Project
Organizers
IKEO Kazuho, National Institute of Genetics, Mishima, Japan (chair)
SAITOU Naruya, National Institute of Genetics, Mishima, JapanSATTA Yoko, Graduate University for Advanced Studies, SOKENDAI, Hayama, Japan
TAMURA Koichiro, Tokyo Metropolitan University, Tokyo, Japan
Conference Home Page: http://molevo.sakura.ne.jp/DnaData_lab/GCC2021.html
National Institute of Genetics (NIG) Home Page: https://www.nig.ac.jp/nig/
MEXT Yaponesia Genome Project Home Page: http://www.yaponesian.jp/index_e.php
1Keynote Speakers (30min talk + 5min discussion)
Dr. GOJOBORI Takashi (Distinguished Professor & Associate Director of Computational Bioscience Research Center, KAUST)
Dr. Dan GRAUR (Moores Professor, Department of Biology and Biochemistry, University of Houston, Houston)Dr. LI Wen-Hsiung (Distinguished Research Fellow, Biodiversity Research Center, Academia Sinica, Taipei)
Dr. LI Yi-Xue (Director, Shanghai Center for Bioinformation Technology, Shanghai)
Dr. Mark STONEKING (Professor, University of Leipzig, Leipzig)

Invited Speakers oversea (20min talk+ 5 min discussion)
Dr. FU Qiaomei (Professor, CAS Institute of Paleontology and Paleoanthropology, Beijing)
Dr. Aida ANDRES (Professor, University College London, London)
Dr. Arndt von HAESELER (Professor, University of Vienna, Vienna)
Dr. CHAW Shu-Miaw (Research Fellow, Academia Sinica, Taipei)
Dr. Tal DAGAN (Professor, University of Kiel, Kiel)
Dr. Yun-Xin FU (Professor, University of Texas at Houston, Houston)Dr. MINETA Katsuhiko (Researcher, KAUST, Jedda)
Dr. SHIMIZU Kentaro (Professor, University of Zurich, Zurich)
Dr. SHIMIZU Hiroshi (Researcher, KAUST, Jedda)
Dr. Anne STONE (Professor, Arizona State University, Phoenix)
Dr. SU Bing (Professor, CAS Kunming Institue of Zoology , Kunming)

Invited Speakers from Japan (20min talk+ 5 min discussion)
Dr. FUJIMOTO Akihiro (Professor, University of Tokyo, Tokyo) *Dr. HANADA Kousuke (Associate Professor, Kyushu Institute of Technology , Tobata) *Dr. HASEBE Mitsuyasu (Professor, National Institute of Basic Biology, Okazaki)
Dr. IMANISHI Tadashi (Professor, Tokai University, Isehara) *Dr. INOUE Jun (Assistant Professor, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa)
Dr. ITOH Takeshi (Advanced Analysis Center Leader, The National Agriculture and Food Research Organization, Tsukuba) *2

Dr. KANZAWA-KIRIYAMA Hideaki (Associate Curator, National Museum of Nature and Science, Tsukuba) *Dr. KIMURA Ryosuke (Associate Professor, University of Ryukyu, Okinawa) *Dr. KINOSHITA Tetsu (Professor, Yokohama City University , Yokohama)Dr. OOTA Hiroki (Professor, University of Tokyo, Tokyo) *Dr. OSADA Naoki (Associate Professor, Hokkaido University , Sapporo) *Dr. SASAKI Hiroyuki (Professor, Kyushu University, Fukuoka)
Dr. SATTA Yoko (Professor, Graduate University for Advanced Studies, Hayama)
Dr. SHINODA Ken-Ichi, (Senior Director in Research, National Museum of Nature and Science, Tokyo/Tsukuba) *Dr. SHINZATO Chuya (Associate Professor, University of Tokyo, Kashiwa)
Dr. SUZUKI Hitoshi (Professor, Hokkaido University, Sapporo) *Dr. TAKEYAMA Haruko (Professor, Waseda University, Tokyo)
Dr. TAMURA Koichiro (Professor, Tokyo Metropolitan University, Tokyo)

Invited Speakers from National Institute of Genetics (NIG) (20min talk+ 5 min discussion)
Dr. Hiroshi AKASHI (Professor, Division of Evolutionary Genetics, NIG, Mishima)
Dr. IKEO Kazuho (Associate Professor, Laboratory for DNA Data Analysis, NIG, Mishima)
Dr. INOUE Ituro (Professor, Division of Human Genetics, NIG, Mishima) *Dr. Timothy A. JINAM (Assistant Professor, Population Genetics Laboratory, NIG, Mishima) *Dr. KITANO Jun (Professor, Division of Ecological Genetics, NIG, Mishima)
Dr. Kirill KRYUKOV (Specially Appointed Associate Professor, Population Genetics Laboratory, NIG, Mishima)
Dr. NAKAMURA Yasukazu (Professor, Genome Informatics Laboratory, NIG, Mishima)
Dr. SAITOU Naruya (Professor, Population Genetics Laboratory, NIG, Mishima) *Dr. SUZUKI Rumiko (Project Associate Professor, Population Genetics Laboratory, NIG, Mishima)* Member of Yaponesia Genome Project3

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Program Day 1: Monday, February 15, 2021===================================
13:00 - 13:10 Opening remarks
Dr. IKEO Kazuho, Chair of GCCC, National Institute of Genetics
Dr. HANAOKA Fumio, Director-General, National Institute of Genetics
13:10 - 15:00 Session 1 (Chair: Dr. SATTA Yoko)
13:10 - 13:45 Keynote talk 1 by Dr. Wen-Hsiung Li, Taipei
Talk title: Evolutionary insights from microbial genomes
13:45 - 14:10 Invited talk 1 by Dr. SU Bing, Kunming
Talk title: Comparative brain 3D genome analysis reveals evolutionary innovations of human corticogenesis
14:10 - 14:35 Invited talk 2 by Dr. FU Qiaomei, Beijing
Talk title: The prehistory of East Asian using insights from ancient DNA
14:35 - 15:00 Invited talk 3 by Dr. CHAW Shu-Miaw, Taipei
Talk title: Stout camphor tree (Laurel family) genome fills gaps in understanding of flowering plant genome evolution
15:00 - 15:20 Tea break
15:20 - 16:45 Session 2 (Chair: Dr. TAMURA Koichiro)
15:20 - 15:55 Keynote talk 2 by Dr. GOJOBORI Takashi, KAUST
Talk title: Genome evolution in Asian rice domestication
15:55 - 16:20 Invited talk 4 by Dr. SHIMIZU Hiroshi, KAUST
Talk title: Behavior of cnidarian hydra : dominance of foot nervous system in behavioral regulation
16:20 - 16:45 Invited talk 5 by Dr. MINETA Katsuhiko, KAUST
Talk title: Population genomics of indigenous inhabitants of Arabia
16:45 - 17:05 Tea break
17:05 - 18:30 Session 3 (Chair: Dr. SAITOU Naruya)
17:05 - 17:40 Keynote talk 3 by Dr. Mark STONEKING, Leipzig
Talk title: Genes, Culture, and Human Evolution
17:40 - 18:05 Invited talk 6 by Dr. SHINODA Ken-ichi, Tsukuba
Talk title: Contribution of ancient genome analysis to the origin of the Japanese - Looking back on the research history of the past 30 years418:05 - 18:30 Invited talk 7 by Dr. Arndt von HAESELER, Vienna
Talk title: Lineage size evolution in developing organoids===================================
Program Day 2: Tuesday, February 16, 2021===================================
9:00 - 10:25 Session 4 (Chair: Dr. IKEO Kazuho)
9:00 - 9:35 Keynote talk 4 by Dr. Dan GRAUR, Houston
Talk title: The selectionist pandemic and the emperor's new clothes: examining the evidence for soft selective sweeps in humans
9:35 - 10:00 Invited talk 8 by Dr. Anne STONE, Phoenix
Talk title: Mycobacterium leprae genomic variation and evolutionary history in the Pacific
10:00 - 10:25 Invited talk 9 by Dr. Yun-Xin FU, Houston
Talk title: Tetrahymena amitosis strategy: from sex determination to whole genome sequencing
10:25 - 10:45 Tea break
10:45 - 12:10 Session 5 (Chair: Dr. KITANO Jun)
10:45 - 11:20 Keynote talk 5 by Dr. LI Yi-Xue, Shanghai
Talk title: A pharmaco-genomic landscape in human liver cancers
11:20 - 11:45 Invited talk 10 by Dr. KINOSHITA Tetsu, Yokohama
Talk title: Overcoming the species hybridization barrier by ploidy manipulation in the genus Oryza
11:45 - 12:10 Invited talk 11 by Dr. HASEBE Mitsuyasu, Okazaki
Talk title: Evolution of carnivory and movement in plants
12:10 - 13:30 Lunch
13:30 - 14:45 Session 6 (Chair: Dr. NAKAMURA Yasukazu)
13:30 - 13:55 Invited talk 12 by Dr. SASAKI Hiroyuki, Fukuoka
Talk title: DNA methylation in development and disease
13:55 - 14:20 Invited talk 13 by Dr. INOUE Jun, Kashiwa
Talk title: dbCNS: a new database for conserved non-coding sequences
14:20 - 14:45 Invited talk 14 by Dr. SHINZATO Chuya, Kashiwa
Talk title: Using genomics to reveal novel insights into coral biology
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14:45 - 15:05 Tea break
15:05 - 16:45 Session 7 (Chair: Dr. SUZUKI Rumiko)
15:05 - 15:30 Invited talk 15 by Dr. Hiroshi AKASHI, NIG
Talk title: Population genomics of weak evolutionary forces: Base composition evolution in Drosophila
15:30 - 15:55 Invited talk 16 by Dr. NAKAMURA Yasukazu, NIG
Talk title: A chromosome-level assembly of a domestic cat of American Shorthair
15:55 - 16:20 Invited talk 17 by Dr. KITANO Jun, NIG
Talk title: Genetics of adaptive radiation in stickleback and medaka fishes
16:20 - 16:45 Invited talk 18 by Dr. INOUE Ituro, NIG
Talk title: Genomics and cultivation of new virus world
16:45 - 17:05 Tea break
17:05 - 18:45 Session 8 (Chair: Dr. AKASHI Hiroshi)
17:05 - 17:30 Invited talk 19 by Dr. TAMURA Koichiro, Tokyo
Talk title: Genome evolution for cold adaptation in experimental populations of Drosophila albomicans
17:30 - 17:55 Invited talk 20 by Dr. Tal DAGAN, Kiel
Talk title: Plasmids as turtles in an evolutionary race
17:55 - 18:20 Invited talk 21 by Dr. SHIMIZU Kentaro, Zurich
Talk title: Polyploid wheat as the traditional model of genome analysis and the last frontier of genome sequencing
18:20 - 18:45 Invited talk 22 by Dr. Aida ANDRES, London
Talk title: Dissecting genomes to identify local adaptations in humans and other primates====================================
Program Day 3: Wednesday, February 17, 2021====================================
9:00 - 10:40 Session 9 (Chair: Dr. IMANISHI Tadashi)
9:00 - 9:25 Invited talk 23 by Dr. SATTA Yoko, Hayama
Talk title: Population genomics on the origin of lactase persistence in Europe and South Asia
9:25 - 9:50 Invited talk 24 by Dr. IKEO Kazuho, NIG
Talk title: Reconstruction of cell lineage trees by using single-cell RNA sequence data
9:50 - 10:15 Invited talk 25 by Dr. OSADA Naoki, Sapporo
Talk title: Genome-wide genetic diversity of wild house mice across Eurasia
610:15 - 10:40 Invited talk 26 by Dr. KIMURA Ryosuke, Okinawa
Talk title: Pleiotropic effects of the EDAR 370V/A variant on East Asian phenotypes
10:40 - 11:00 Tea break
11:00 - 12:15 Session 10 (Chair: Dr. INOUE Ituro)
11:00 - 11:25 Invited talk 27 by Dr. TAKEYAMA Haruko, Tokyo
Talk title: high-resolution analysis of environmental microbes by massively parallel single-cell genome sequencing
11:25 - 11:50 Invited talk 28 by Dr. FUJIMOTO Akihiro, Tokyo
Talk title: Whole genome sequencing with long-reads reveals complex structure and origin of structural variation in human genetic variations
and somatic mutations in cancer
11:50 - 12:15 Invited talk 29 by Dr. OOTA Hiroki, Tokyo
Talk title: Genome of Jomon people and peopling history of East Eurasians
12:15 - 13:30 Lunch
13:30 - 14:45 Session 11 (Chair: Dr. OSADA Naoki)
13:30 - 13:55 Invited talk 30 by Dr. SUZUKI Hitoshi, Sapporo
Talk title: Geographic shift of the house mouse Mus musculus following humans during the past 15,000 years
13:55 - 14:20 Invited talk 31 by Dr. ITOH Takeshi, Tsukuba
Talk title: Genomics of plants: the genome concept made real
14:20 - 14:45 Invited talk 32 by Dr. HANADA Kousuke, Tobata
Talk title: Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants
14:45 - 15:05 Tea break
15:05 - 16:20 Session 12 (Chair: Dr. FUJIMOTO Akihiro)
15:05 - 15:30 Invited talk 33 by Dr. IMANISHI Tadashi, Isehara
Talk title: Rapid profiling of drug-resistant bacteria using a single-molecule DNA sequencer
15:30 - 15:55 Invited talk 34 by Dr. KANZAWA-KIRIYAMA Hideaki, Tsukuba
Talk title: Genome from the initial to final Jomon: Genetic history throughout the Jomon period
15:55 - 16:20 Invited talk 35 by Dr. Timothy A. JINAM, NIG
Talk title: Population substructure within mainland Japanese suggests multiple waves of migration
16:20 - 16:40 Tea break7

16:40 - 17:55 Session 13 (Chair: Dr. Timothy A. JINAM)
16:40 - 17:05 Invited talk 36 by Dr. SUZUKI Rumiko, NIG
Talk title: Genome mapping of F1 hybrid camels
17:05 - 17:30 Invited talk 37 by Dr. Kirill KRYUKOV, NIG
Talk title: GenomeSync: streamlining access to current genome data
17:30 - 17:55 Invited talk 38 by Dr. SAITOU Naruya, NIG
Talk title: AGTC, iDarwin, and Yaponesia Genome Project
17:55 - 18:00 Closing Remarks
SATTA Yoko, Graduate University for Advanced Studies, SOKENDAI, Hayama, Japan
TAMURA Koichiro, Tokyo Metropolitan University, Tokyo, Japan

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Profile of Keynote talk 1 Speaker: Dr. Wen-Hsiung Li, Taipei
Talk time: Monday, February 15, 13:10 - 13:45 (12:10-12:45 Taipei time)
Talk title: Evolutionary insights from microbial genomes

Academician and Distinguished Research Fellow at the Biodiversity Research Center, Academia Sinica, Taipei
James D. Watson Professor emeritus, University of Chicago, Chicago
Recent publicaitons
1. Li W.-H. (2021) Adventures of a Mathematician in Evolutionary Biology. Genome Biology and Evolution. https://doi.org/10.1093/
gbe/evab012
2. Liu W.-Y. et al. (2020) Maize ANT1 modulates vascular development, chloroplast development, photosynthesis, and plant growth.
Proc. Natl. Acad. Sci. USA 117 (35): 21747-21756. https://doi.org/10.1073/pnas.2012245117
3. Anandharaj M. et al. (2020) Constructing a yeast to express the largest cellulosome complex on the cell surface. Proc. Natl. Acad.
Sci. USA 117 (5): 2385-2394. https://doi.org/10.1073/pnas.1916529117

Profile of Keynote talk 2 Speaker: Dr. GOJOBORI Takashi, KAUST
Talk time: Monday, February 15, 15:20 - 15:55 (9:20-9:55 Jedda time)
Talk title: Genome evolution in Asian rice domestication
Distinguished Professor of Bioscience, King Abdullah University of Science and Technology
Acting Director, Computational Bioscience Research Center, King Abdullah University of Science and Technology
Professor emeritus, National Institute of Genetics, Mishima
Recent publicaitons
1. Mineta K. et al. (2021) Population structure of indigenous inhabitants of Arabia. Plos Genetics 17 (1) e1009210. https://doi.org/
10.1371/journal.pgen.1009210
2. Gojobori T. et al. (2019) Marine Metagenomics: Technological Aspects and Applications. Springer. https://doi.org/
10.1007/978-981-13-8134-8
3. Behzad H., Mineta K., and Gojobori T. (2018) Global ramifications of dust and sandstorm microbiota. Genome Biology and
Evolution 10 (8): 1970-1987. https://doi.org/10.1093/gbe/evy134
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Profile of Keynote talk 3 Speaker: Dr. Mark STONEKING, Leipzig
Talk time: Monday, February 15, 17:05 - 17:40 (9:05 - 9:40 Leipzig time)
Talk title: Genes, Culture, and Human Evolution
Group Leader, Max Planck Institute for Evolutionary Anthropology, Leipzig
Honorary Professor of Biological Anthropology, University of Leipzig, Leipzig
Recent publicaitons
1. Pugach I. et al. (2021) Ancient DNA from Guam and the peopling of the Pacific. Proc. Natl. Acad. Sci. USA 118 (1)e2022112118. https://doi.org/10.1073/pnas.2022112118
2. Yang M. A. et al. (2020) Ancient DNA indicates human population shifts and admixture in northern and southern China.
Science 369 (6501): 282-288. DOI: 10.1126/science.aba0909
3. Liu D. et al. (2020) Extensive ethnolinguistic diversity in Vietnam reflects multiple sources of genetic diversity. Molecular
Biology and Evolution 37 (9): 2503–2519. https://doi.org/10.1093/molbev/msaa099

Profile of Keynote talk 4 Speaker: Dr. Dan GRAUR, Houston
Talk time: Tuesday, February 16, 9:00 - 9:35 (Monday, February 15, 18:00 - 18:35 Houston time)
Talk title: The selectionist pandemic and the emperor's new clothes: examining the evidence for soft selective sweeps in humans
John and Rebecca Moores Professor, Department of Biology and Biochemistry, University of Houston, Houston
Professor, Department of Biomedical Engineering, Cullen College of Engineering, University of Houston
Professor emeritus of Zoology, Tel Aviv University, Tel Aviv
Recent publications
1. Zheng Y., Graur D., and Azevedo R. B. R. (2018) Correlated selection on amino acid deletion and replacement in mammalianprotein sequences. Journal of Molecular Evolution 86: 365-378.
2. Graur D. (2017) An upper limit on the functional fraction of the human genome. Genome Biology and Evolution 9 (7):1880-1885. https://doi.org/10.1093/gbe/evx121
3. Graur D. (2017) Rubbish DNA: The functionless fraction of the human genome. Pp. 19-60, Evolution of the Human Genome
I. Springer.

10Profile of Keynote talk 5 Speaker: Dr. LI Yi-Xue, Shanghai
Talk time: Tuesday, February 16, 10:45 - 11:20 (9:45-10:20, Shanghai time)
Talk title: A pharmaco-genomic landscape in human liver cancers
Professor, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai
Director, Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai
Director, Shanghai Center for Bioinformation Technology, Shanghai
Recent publications
1. Li C. et al. (2020) Integrated omics of metastatic colorectal cancer. Cancer Cell 38 (5) 734-747. https://doi.org/10.1016/
j.ccell.2020.08.002
2. Li Q. et al. (2020) DysRegSig: an R package for identifying gene dysregulations and building mechanistic signatures incancer. Bioinformatics btaa688. https://doi.org/10.1093/bioinformatics/btaa688
3. Chen X.-M. et al. (2019) A novel mutation KCNQ1p.Thr312del is responsible for long QT syndrome type 1. Heart andVessels 34: 177–188.

Profile of Invited talk 1 Speaker: Dr. SU Bing, Kunming
Talk time: Monday, February 15, 13:45 - 14:10 (12:45 - 13:10 Kunming Time)
Talk title: Comparative brain 3D genome analysis reveals evolutionary innovations of human corticogenesis
Professor, State Key Laboratory of Genetic Resources and Evolution, CAS Kunming Institute of Zoology, Kunming
Recent publications
1. He Y. et al. (2019) Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structuralvariants. Nature Communications 10, 4233.
2. Shi L. et al. (2019) Transgenic rhesus monkeys carrying the human MCPH1 gene copies show human-like neoteny of brain
development. National Science Review 6 (3): 480-493.
3. Peng Y. et al. (2017) Down-regulation of EPAS1 transcription and genetic adaptation of Tibetans to high-altitude hypoxia.
Molecular Biology and Evolution 34 (4): 818-830.

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Profile of Invited talk 2 Speaker: Dr. FU Qiaomei, Beijing
Talk time: Monday, February 15, 14:10 - 14:35 (13:10 - 13:35 Beijing Time)
Talk title: The prehistory of East Asian using insights from ancient DNA
Professor, CAS Institute of Vertebrate Paleontology and Paleoanthropology, Beijing
Recent publications
1.Yang M. A. et al. (2020) Ancient DNA indicates human population shifts and admixture in northern and southern China. Science
369 (6501): 282-288.
2. Ding M. et al. (2020) Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day
Tibetans. Proceedings of the Royal Society B 287: 20192968.
3. Yang M. A. et al. (2017) 40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia.
Current Biology 27 (20): 3202-3208.

Profile of Invited talk 3 Speaker: Dr. CHAW Shu-Miaw, Taipei
Talk time: Monday, February 15, 14:35 - 15:00 (13:35 - 14:00 Taipei Time)
Talk title: Stout camphor tree (Laurel family) genome fills gaps in understanding of flowering plant genome evolution
Distinguished Research Fellow, Biodiversity Research Center, Academia Sinica, Taipei
Recent publications
1.Wu C.-S. et al. (2020) Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses. Scientific Reports 10(1) 20650.
2. Sudianto E., Wu C.-S., and Chaw S. M. (2020) The origin and evolution of plastid genome downsizing in Southern Hemisphericcypresses (Cupressaceae). Frontiers in Plant Science 11, 901.
3. Chaw S.-M. et al. (2020) The origin and underlying driving forces of the SARS-CoV-2 outbreak. Journal of Biomedical
Science 27 (1) 73.

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Profile of Invited talk 4 Speaker: Dr. SHIMIZU Hiroshi, KAUST
Talk time: Monday, February 15, 15:55 - 16:20 (9:55 - 10:20 Jedda time)
Talk title: Behavior of cnidarian hydra : dominance of foot nervous system in behavioral regulation
Senior Research Scientist, Gojobori Group, King Abdullah University of Science and Technology
Recent publications
1. Noro Y. et al. (2020) A single neuron subset governs a single coactive neuron circuit in Hydra vulgaris, representing a
prototypic feature of neural evolution. bioRxive https://doi.org/10.1101/2020.11.22.392985
2. Noro Y. et al. (2019) Regionalized nervous system in Hydra and the mechanism of its development. Gene Expression
Patterns 31: 42-59.
3. Ishikawa M. et al. (2016) Different endosymbiotic interactions in two hydra species reflect the evolutionary history ofendosymbiosis. Genome Biology and Evolution 8 (7): 2155-2163.

Profile of Invited talk 5 Speaker: Dr. MINETA Katsuhiko, KAUST
Talk time: Monday, February 15, 16:20 - 16:45 (10:20 - 10:45 Jedda time)
Talk title: Population genomics of indigenous inhabitants of Arabia
Principal Research Scientist, Computational Bioscience Research Center, King Abdullah University of Science andTechnology
Recent publications
1. Mineta K. et al. (2021) Population structure of indigenous inhabitants of Arabia. Plos Genetics 17 (1) e1009210.
2. Mineta K. et al. (2020) Indigenous Arabs have an intermediate frequency of a Neanderthal-derived COVID-19 risk
haplotype compared with other world populations. Clinical Genetics 10, 1111.
3. Behzad H., Mineta K., and Gojobori T. (2018) Global ramifications of dust and sandstorm microbiota. Genome Biology
and Evolution 10 (8): 1970-1987.

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Profile of Invited talk 6 Speaker: SHINODA Ken-ichi, Tokyo
Talk time: Monday, February 15, 17:40 - 18:05
Talk title: Contribution of ancient genome analysis to the study of the origin of the Japanese - Looking back on the research history of
the past 30 years
Senior Director in Research, National Museum of Nature and Science, Tokyo
Chair, Department of Anthropology, National Museum of Nature and Science, Tsukuba
Recent publications
1. Eisenhower R., Kanzawa-Kiriyama H., Shinoda K., and Weyrich L. S. (2020) Investigating the demographic history of Japan
using ancient oral microbiota. Proceedings of the Royal Society B 287. https://doi.org/10.1098/rstb.2019.0578
2. Kanzawa-Kiriyama H. et al. (2019) Late Jomon male and female genome sequences from the Funadomari site in Hokkaido,
Japan. Anthropological Science 127(2): 83-108.
3. Adachi N., Kakuda T., Takahashi R., Kanzawa-Kiriyama H., and Shinoda K. (2017) Ethnic derivation of the Ainu inferredfrom ancient mitochondrial DNA data. American Journal of Physical Anthropology 165:139–148.

Profile of Invited talk 7 Speaker: Dr. Arndt von HAESELER, Vienna
Talk time: Monday, February 15, 18:05 - 18:30 (10:05 - 10:30 Vienna time)
Talk title: Lineage size evolution in developing organoids
Dean, Center of Molecular Biology at the University of Vienna, Vienna
Head, Center for Medical Biochemistry, Medical University of Vienna, Vienna
Professor, University of Vienna and Medical University of Vienna, Vienna
Scientific Director, Center for Integrative Bioinformatics, Vienna
Recent publications
1. Leuchtenberger A. F. et al. (2020) Distinguishing Felsenstein zone from Farris zone using neural networks. Molecular Biology
and Evolution 37 (12): 3632–3641.
2. Jain A. et al. (2019) The evolutionary traceability of a protein. Genome Biology and Evolution 11 (2): 531-545.
3. Plug F. G. And von Haeseler A. (2018) TRUmiCount: correctly counting absolute numbers of molecules using unique molecular
identifiers. Bioinformatics 34 (18): 3137-3144.
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Profile of Invited talk 8 Speaker: Dr. Anne STONE, Phoenix
Talk time: Tuesday, February 16, 9:35 - 10:00 (Monday, February 15, 17:35 - 18:00 Phoenix time)
Talk title: Mycobacterium leprae genomic variation and evolutionary history in the PacificRegents Professor, School of Human Evolution and Social Change, Arizona State University, Phoenix
Recent publications
1. Housman G. et al. (2018) Assessment of DNA methylation patterns in the bone and cartilage of a nonhuman primate model ofosteoarthritis. Cartilage 10 (3): 335-345.
2. Honap T. et al. (2018) Mycobacterium leprae genomes from naturally infected nonhuman primates. PLoS Neglected Tropical
Diseases 12 (1): e0006190.
3. Nieves-Colón M. A. et al. (2018) Comparison of two ancient DNA extraction protocols for skeletal remains from tropicalenvironments. American Journal of Physical Anthropology 166: 824–836.

Profile of Invited talk 9 Speaker: Dr. Yun-Xin FU, Houston
Talk time: Tuesday, February 16, 10:00 - 10:25 (Monday, February 15, 19:00 - 19:25 Houston time)
Talk title: Tetrahymena amitosis strategy: from sex determination to whole genome sequencing
Director and Professor, Computational Genomics Section, Human Genetics Center and Division of Biostatistics School of Public
Health, The University of Texas at Houston, Houston
Visiting Professor, National Institute of Genetics, Mishima
Recent publications
1. Fu Y.-X. et al. (2020) Amitosis as a strategy of cell division - Insight from the proliferation of Tetrahymena thermophila
macronucleus. bioRxiv https://doi.org/10.1101/2020.08.11.247031
2. Liu X. And Fu Y.-X. (2020) Stairway Plot 2: demographic history inference with folded SNP frequency spectra. Genome
Biology 21, 280.
3. Liu Q. et al. (2020) Mycobacterium tuberculosis clinical isolates carry mutational signatures of host immune environments.
Science Advances 6 (22) eaba4901.

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Profile of Invited talk 10 Speaker: Dr. KINOSHITA Tetsu, Yokohama
Talk time: Tuesday, February 16, 11:20 - 11:45
Talk title: Overcoming the species hybridization barrier by ploidy manipulation in the genus Oryza
Professor, Epigenome Laboratory, Kihara Institute for Biological Research, Yokohama City University, Yokohama
Recent publications
1. Ohnishi Y. et al. (2019) Sperm Entry into the Egg Cell Induces the Progression of Karyogamy in Rice Zygotes. Plant & cell
physiology 60 (8):1656 – 1665.
2. Kim M. Y. et al. (2019) DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proc. Natl.
Acad. Sci. USA 116: 9652-9657.
3. Kinoshita T. (2018) A parental tug-of-war. Nature Plants 4:329–330.

Profile of Invited talk 11 Speaker: Dr. HASEBE Mitsuyasu, Okazaki
Talk time: Tuesday, February 16, 11:45 - 12:10
Talk title: Evolution of carnivory and movement in plants
Professor, Division of Evolutionary Biology, National Institute of Basic Biology, Okazaki
Recent publications
1. Suda H. et al. (2020) Calcium dynamics during trap closure visualized in transgenic Venus flytrap. Nature Plants 6:1219–
1224.
2. Gu N. et al. (2020) DNA damage triggers reprogramming of differentiated cells into stem cells in Physcomitrella. Nature
Plants 6:1098–1105.
3. Palfalvi G. et al. (2020) Genomes of the Venus flytrap and close relatives unveil the roots of plant carnivory. Current Biology
30: 1-9.

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Profile of Invited talk 12 Speaker: Dr. SASAKI Hiroyuki, Fukuoka
Talk time: Tuesday, February 16, 13:30 - 13:55
Talk title: DNA methylation in development and disease
Dean, Kyushu University Institute for Advanced Study, Fukuoka
Professor, Medical Institute of Bioregulation, Kyushu University, Fukuoka
Recent publications
1.Albert J. R. et al. (2020) Maternal DNMT3A-dependent de novo methylation of the paternal genome inhibits gene expression
in the early embryo. Nature Communications 11: 5417.
2. Ishiuchi T. et al. (2020) Reprogramming of the histone H3.3 landscape in the early mouse embryo. Nature Structural andMolecular Biology 28: 38–49.
3. Yeung W. K. A. et al. (2019) Histone H3K9 methyltransferase G9a in oocytes is essential for preimplantation development
but dispensable for CG methylation protection. Cell Reports 27 (1): 282-293.

Profile of Invited talk 13 Speaker: Dr. INOUE Jun, Kashiwa
Talk time: Tuesday, February 16, 13:55 - 14:20
Talk title: dbCNS: a new database for conserved non-coding sequences
Assistant Professor, Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa
Recent publications
1. Inoue J. and Saitou N. (2020) dbCNS: a new database for conserved noncoding sequences. Molecular Biology and Evolution
doi:10.1093/molbev/msaa29
2. Inoue J. and Satoh N. (2019) ORTHOSCOPE: an automatic web tool for phylogenetically inferring bilaterian orthogroups withuser-selected taxa. Molecular Biology and Evolution 36 (3): 621-631.
3. Inoue J. and Satoh N. (2018) Deuterostome Genomics: Lineage-Specific Protein Expansions That Enabled Chordate Muscle
Evolution. Molecular Biology and Evolution 35 (4): 914-924.
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Profile of Invited talk 14 Speaker: Dr. SHINZATO Chuya, Kashiwa
Talk time: Tuesday, February 16, 14:20 - 14:45
Talk title: Using genomics to reveal novel insights into coral biology
Associate Professor, Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa
Recent publications
1. Sinzato C. et al. (2020) Eighteen coral genomes reveal the evolutionary origin of Acropora strategies to accommodate
environmental changes. Molecular Biology and Evolution 38 (1): 16-30.
2. Yoshioka Y. Et al. (2020) Whole-genome transcriptome analyses of native symbionts reveal host coral genomic
novelties for establishing coral-algae symbioses. Genome Biology and Evolution 13 (1) doi:10.1093/gbe/evaa24
3. Sinzato C. et al. (2018) Using seawater to document coral-zoothanthella diversity: A new approach to coral reefmonitoring using environmental DNA. Frontiers in Marine Science 5, 28.

Profile of Invited talk 15 Speaker: Dr. Hiroshi AKASHI, NIG
Talk time: Tuesday, February 16, 15:05 - 15:30
Talk title: Population genomics of weak evolutionary forces: Base composition evolution in Drosophila
Professor, Evolutionary Genetics Laboratory, National Institute of Genetics, Mishima
Recent publications
1. Matsumoto T. and Akashi H. (2018) Distinguishing Among Evolutionary Forces Acting on Genome-Wide BaseComposition: Computer Simulation Analysis of Approximate Methods for Inferring Site Frequency Spectra of Derived
Mutation. G3 8: 1755-1769.
2. Matsumoto T. et al. (2016) Codon usage selection can bias estimation of the fraction of adaptive amino acid fixations.
Molecular Biology and Evolution 33: 1580-1589.
3. Matsumoto T., Akashi H., and Yang Z. (2015) Evaluation of Ancestral Sequence Reconstruction Methods to Infer
Nonstationary Patterns of Nucleotide Substitution. Genetics 200: 873-890.
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Profile of Invited talk 16 Speaker: Dr. NAKAMURA Yasukazu, NIG
Talk time: Tuesday, February 16, 15:30 - 15:55
Talk title: A chromosome-level assembly of a domestic cat of American Shorthair
Professor, Genome Informatics Laboratory, National Institute of Genetics, Mishima
Recent publications
1. Montgomery S. A. et al. (2020) Chromatin organization in early land plants reveals an ancestral association between
H3K27me3, transposons, and constitutive heterochromatin. Current Biology 30 (4): R161-R163.
2. Isobe S. et al. (2020) AnAms1.0: A high-quality chromosome-scale assembly of a domestic cat Felis catus of American
Shorthair breed. bioRxiv https://doi.org/10.1101/2020.05.19.103788
3. Tanizawa Y., Fujisawa T., and Nakamura Y. (2018) DFAST: a flexible prokaryotic genome annotation pipeline for fastergenome publication. Bioinformatics 36 (6): 1037–1039.

Profile of Invited talk 17 Speaker: Dr. KITANO Jun, NIG
Talk time: Tuesday, February 16, 15:55 - 16:20
Talk title: Genetics of adaptive radiation in stickleback and medaka fishes
Professor, Ecological Genetics Laboratory, National Institute of Genetics, Mishima
Recent publications
1.Ansai. S. et al. (2021) Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes.
Nature Communications (in press).
2. Yamasaki Y. Y. et al. (2020) Genome-wide patterns of divergence and introgression after secondary contact between
Pungitius sticklebacks. Philosophical Transactions of the Royal Society B 375, 20190548.
3. Ishikawa A. et al. (2019) A key metabolic gene for recurrent freshwater colonization and radiation in fishes. Science 364:886-889.

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Profile of Invited talk 18 Speaker: Dr. INOUE Ituro, NIG
Talk time: Tuesday, February 16, 16:20 - 16:45
Talk title: Genomics and cultivation of new virus world
Professor, Human Genetics Laboratory, National Institute of Genetics, Mishima
Recent publications
1. Nishimura L. et al. (2020) Identification of ancient viruses from metagenomic data of the Jomon people. Journal of
Human Genetics 66: 287–296
2. Sugimoto R. et al. (2020) De novo virus inference and host prediction from metagenome using CRISPR spacers. bioRxiv
https://doi.org/10.1101/2020.09.04.282665
3. Romero V. et al. (2018) High order formation and evolution of hornerin in primates. Genome Biology and Evolution 10(12): 3167–317.

Profile of Invited talk 19 Speaker: Dr. TAMURA Koichiro, Tokyo
Talk time: Tuesday, February 16, 17:05 - 17:30
Talk title: Genome evolution for cold adaptation in experimental populations of Drosophila albomicans
Director, Reseach Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo
Professor, Department of Biological Sciences, Tokyo Metropolitan University, Tokyo
Recent publications
1. Moriguchi N. et al. (2019) Inferring the demographic history of Japanese cedar, Cryptomeria japonica, using ampliconsequencing. Heredity 123: 371-383.
2. Tamura K., Qiqing Tao, and Kumar S. (2018) Theoretical foundation of the RelTime method for estimating divergencetimes from variable evolutionary rates. Molecular Biology and Evolution 35 (7): 1770-1782.
3. Kumar S. et al. (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular
Biology and Evolution 35 (6): 1547-1549.

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Profile of Invited talk 20 Speaker: Dr. Tal DAGAN, Kiel
Talk time: Tuesday, February 16, 17:30 - 17:55 (9:30 - 9:55 Kiel time)
Talk title: Plasmids as turtles in an evolutionary race
Professor, Institute of Microbiology, University of Kiel, Kiel
Recent publications
1. Yu L. et al. (2020) Somatic genetic drift and multilevel selection in a clonal seagrass. Nature Ecology and Evolution 4 (7):952-962.
2. Hammerschmidt K. et al. (2020) The order of trait emergence in the evolution of cyanobacterial multicellularity. Genome
Biology and Evolution, evaa249.
3. Ilhan J. et al. (2019) Segregational drift and the interplay between plasmid copy number and evolvability. Molecular Biology
and Evolution 36 (3): 472-486.

Profile of Invited talk 21 Speaker: Dr. SHIMIZU Kentaro, Zurich
Talk time: Tuesday, February 16, 17:55 - 18:20 (9:55 - 10:20 Zurich time)
Talk title: Polyploid wheat as the traditional model of genome analysis and the last frontier of genome sequencing
Professor, Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich
Recent publications
1. Walkowiak S. et al. (2020) Multiple wheat genomes reveal global variation in modern breeding. Nature 588: 277–283.
2. Hatakeyama M. et al. (2018) Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop. DNA
Research, 25(1):39-47.
3. Paape T. et al. (2018) Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica.
Nature Communications 9: 3909.

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Profile of Invited talk 22 Speaker: Dr. Aida ANDRES, London
Talk time: Tuesday, February 16, 18:20 - 18:45 (9:20 - 9:45 London time)
Talk title: Dissecting genomes to identify local adaptations in humans and other primates
Associate Professor, Division of Biosciences, University College London, London
Recent publications
1. Rees J. S., Castellano S., and Andrés A. M. (2020) The genomics of human local adaptation. Trends in Genetics 36 (6):415-428.
2. Giner-Delgado C. et al. (2019) Evolutionary and functional impact of common polymorphic inversions in the humangenome. Nature Communications 10 (1): 1-14.
3. Key F. M. et al. (2018) Human local adaptation of the TRPM8 cold receptor along a latitudinal cline. PLoS Genetics 14(5), e1007298.

Profile of Invited talk 23 Speaker: Dr. SATTA Yoko, Hayama
Talk time: Wednesday, February 17, 9:00 - 9:25
Talk title: Population genomics on the origin of lactase persistence in Europe and South Asia
Professor, School of Advanced Sciences, Graduate University for Advanced Studies, Hayama
Recent publications
1. Iwasaki R. L. et al. (2020) Evolutionary history of the risk of SNPs for diffuse-type gastric cancer in the Japanese
population. Genes 11 (7), 775. https://doi.org/10.3390/genes11070775
2. Satta Y. et al. (2019) Two-dimensional site frequency spectrum for detecting, classifying and dating incomplete selective
sweeps. Genes and Genetic Systems 94: 283-300. https://doi.org/10.1266/ggs.19-00012
3. Fujito N. T. et al. (2018) Positive selection on schizophrenia-associated ST8SIA2 gene in post-glacial Asia. PLoS ONE 13(7): e0200278. https://doi.org/10.1371/journal. pone.0200278.

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Profile of Invited talk 24 Speaker: Dr. IKEO Kazuho, NIG
Talk time: Wednesday, February 17, 9:25 - 9:50
Talk title: Reconstruction of cell lineage trees by using single-cell RNA sequence data
Associate Professor, DNA Data Analysis Laboratory, National Institute of Genetics, Mishima
Recent publications
1. Yaguchi S. et al. (2020) Establishment of homozygous knock-out sea urchins. Current Biology 30 (10): R427-R429.
2. Sun J. et al. (2020) The Scaly-foot Snail genome and implications for the origins of biomineralised armour. Nature
Communications 11, 1657.
3. Kinjo S. et al. (2018) Maser: one-stop platform for NGS big data from analysis to visualization. Database 2018, bay027.

Profile of Invited talk 25 Speaker: Dr. OSADA Naoki, Sapporo
Talk time: Wednesday, February 17, 9:25 - 9:50
Talk title: Genome-wide genetic diversity of wild house mice across Eurasia
Associate Professor, Division of Bioengineering and Bioinformatics, Graduate School of Information Science and Technology,
Hokkaido University, Sapporo
Recent publications
1. Osada N. and Kawai Y. (2021) Exploring models of human migration to the Japanese archipelago using genome-wide genetic
data. Anthropological Science 129 (in press).
2. Li Y. et al. (2020) House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete
mitochondrial genome sequences. Heredity 126: 132-147.
3. Satomura K., Osada N., and Endo T. (2019) Achiasmy and sex chromosome evolution. Ecological Genetics and Genomics
13, 100046.

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Profile of Invited talk 26 Speaker: Dr. KIMURA Ryosuke, Okinawa
Talk time: Wednesday, February 17, 10:15 - 10:40
Talk title: Pleiotropic effects of the EDAR 370V/A variant on East Asian phenotypes
Associate Professor, Department of Human Biology and Anatomy, Graduate School of Medicine, University of the
Ryukyu, Okinawa
Recent publications
1. Matsunami M. et al. (2021) Fine-scale genetic structure and demographic history in the Miyako Islands of the Ryukyu
Archipelago. Molecular Biology and Evolution msab005 published online.
2. Gakuhari T. et al. (2020) Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian
populations. Communications Biology 3, 437.
3. Gamage C. et al. (2020) Understanding leptospirosis eco-epidemiology by environmental DNA metabarcoding ofirrigation water from two agro-ecological regions of Sri Lanka. PLoS Neglected Tropical Diseases 14(7): e0008437.

Profile of Invited talk 27 Speaker: Dr. TAKEYAMA Haruko, Tokyo
Talk time: Wednesday, February 17, 11:00 - 11:25
Talk title: high-resolution analysis of environmental microbes by massively parallel single-cell genome sequencing
Professor, Biomolecular Engineering Laboratory, Department of Life Science and Medical Bioscience, Waseda University,
Tokyo
Recent publications
1. Chijiiwa R. et al. (2020) Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut
microbiota. Microbiome 8, 5.
2. Yumoto M. et al. (2020) Evaluation of the effects of cell-dispensing using an inkjet-based bioprinter on cell integrity by
RNA-seq analysis. Scientific Reports 10, 7158.
3. Yamazaki M. et al. (2020) Effective microtissue RNA extraction coupled with Smart-seq2 for reproducible and robust
spatial transcriptome analysis. Scientific Reports 10, 7083.

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Profile of Invited talk 28 Speaker: Dr. FUJIMOTO Akihiro, Tokyo
Talk time: Wednesday, February 17, 11:25 - 11:50
Talk title: Whole genome sequencing with long-reads reveals complex structure and origin of structural variation in human genetic
variations and somatic mutations in cancer
Professor, Department of Human Genetics, The University of Tokyo, Graduate School of Medicine, Tokyo
Recent publications
1. Fujimoto A. et al. (2020) Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite
instability across 21 cancer types. Genome Research 30: 334-346.
2. Mizuno K. et al. (2019) eVIDENCE: a practical variant filtering for low-frequency variants detection in cell-free DNA.
Scientific Reports 9, 15017.
3. Ton N. D. et al. (2018) Whole genome sequencing and mutation rate analysis of trios with paternal dioxin exposure. Human
Mutation 39: 1384–1392.

Profile of Invited talk 29 Speaker: Dr. OOTA Hiroki, Tokyo
Talk time: Wednesday, February 17, 11:50 - 12:15
Talk title: Genome of Jomon people and peopling history of East Eurasians
Professor, Laboratory of Genome Anthropology, Department of Biological Sciences, Graduate School of Science, University ofTokyo, Tokyo
Recent publications
1. Koganebuchi K. and Oota H. (2021) Paleogenomics of human remains in East Asia and Yaponesia focusing on current
advances and future directions. Anthropological Science 129 (in press).
2. Gakuhari T. et al. (2020) Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian
populations. Communications Biology 3, 437.
3 Schmidt R. W. et al. (2020) Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the Late
Neolithic-Chalcolithic Cucuteni–Tripolye culture. Anthropological Science 128 (1) : 1-10.
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Profile of Invited talk 30 Speaker: Dr. SUZUKI Hitoshi, Sapporo
Talk time: Wednesday, February 17, 13:30 - 13:55
Talk title: Geographic shift of the house mouse Mus musculus following humans during the past 15,000 years
Professor, Hokkaido University, Sapporo
Recent publications
1. Suzuki H. (2021) The time-dependent evolutionary rate of mitochondrial DNA in small mammals inferred from biogeographic
calibration points with reference to the late Quaternary environmental changes. Anthropological Science 129 (in press).
2. Li Y. et al. (2020) House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete
mitochondrial genome sequences. Heredity 126: 132-147.
3. Thomson V. et al. (2018) A perspective for resolving the systematics of Rattus, the vertebrates with the most influence on humanwelfare. Zootaxa 4459 (3): 431–452.

Profile of Invited talk 31 Speaker: Dr. ITOH Takeshi, Tsukuba
Talk time: Wednesday, February 17, 13:55 - 14:20
Talk title: Genomics of plants: the genome concept made real
Leader, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba
Recent publications
1. Itoh T. et al. (2020) Foreign DNA detection by high-throughput sequencing to regulate genome-edited agricultural products.
Scientific Reports 10(1): 4914 - 4914.
2. Endo M. et al. (2019) Genome editing in plants by engineered CRISPR–Cas9 recognizing NG PAM. Nature Plants 5: 14-17.
3. Itoh T., Kawahara Y., and Tanaka T. (2018) Databases for rice omics studies. Pp. 541-554 in In: Sasaki T. and Ashikari M. (eds)
Rice Genomics, Genetics, and Breeding. Springer, Singapore.

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Profile of Invited talk 32 Speaker: Dr. HANADA Kousuke, Iizuka
Talk time: Wednesday, February 17, 14:20 - 14:45
Talk title: Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants
Professor, Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
Recent publications
1. Ezoe A., Shirai K., and Hanada K. (2021) Degree of functional divergence in duplicates is associated with distinct roles in plant
evolution. Molecular Biology and Evolution (in press).
2. Higuchi-Takeuchi M. et al. (2020) Effect of small coding genes on the circadian rhythms under elevated CO 2 conditions inplants. Plant Molecular Biology 104(1), 55-65.
3. Nakaminami K. et al. (2018) AtPep3 is a hormone-like peptide that plays a role in the salinity stress tolerance of plants. Proc.
Natl. Acad. Sci. USA 115 (22): 5810-5815.

Profile of Invited talk 33 Speaker: Dr. IMANISHI Tadashi, Isehara
Talk time: Wednesday, February 17, 15:05 - 15:30
Talk title: Rapid profiling of drug-resistant bacteria using a single-molecule DNA sequencer
Professor, Biomedical Informatics Laboratory, Department of Molecular Life Science, Tokai University School of Medicine
Recent publications
1. Ohno A. et al. (2021) Rapid profiling of drug resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer.
Scientific Reports 11: 3436.
2. Hashimoto S. et al. (2020) Implications of HLA diversity among regions for bone marrow donor searches in Japan. HLA 96:
24-42.
3. Asogawa M. et al. (2020) Human short tandem repeat identification using a nanopore-based DNA sequencer: a pilot study.
Journal of Human Genetics 65 (1): 21-24.

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Profile of Invited talk 34 Speaker: Dr. KANZAWA-KIRIYAMA Hideaki, Tsukuba
Talk time: Wednesday, February 17, 15:30 - 15:55
Talk title: Genome from the initial to final Jomon: Genetic history throughout the Jomon period
Associate Curator, Department of Anthropology, National Museum of Nature and Science, Tsukuba
Recent publications
1. Eisenhower R., Kanzawa-Kiriyama H., Shinoda K., and Weyrich L. S. (2020) Investigating the demographic history of Japan
using ancient oral microbiota. Proceedings of the Royal Society B 287. https://doi.org/10.1098/rstb.2019.0578
2. Kanzawa-Kiriyama H. et al. (2019) Late Jomon male and female genome sequences from the Funadomari site in Hokkaido,
Japan. Anthropological Science 127(2): 83-108.
3. Kanzawa-Kiriyama H. et al. (2017) A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan.
Journal of Human Genetics 62: 213-221.

Profile of Invited talk 35 Speaker: Dr. Timothy A. JINAM, NIG
Talk time: Wednesday, February 17, 15:55 - 16:20
Talk title: Population substructure within mainland Japanese suggests multiple waves of migration
Assistant Professor, Population Genetics Laboratory, National Institute of Genetics, Mishima
Recent publications
1. Jinam T. A., Kawai Y., and Saitou N. (2021) Modern human DNA analyses with special reference to the Inner-Dual structure
model of Yaponesian. Anthropological Science 129 (in press).
2. Jinam T. A. et al. (2021) Genome-wide SNP data of Izumo and Makurazaki populations support inner- dual structure model for
origin of Yamato people. Journal of Human Genetics online. https://doi.org/10.1038/s10038-020-00898-3
3. Jinam T. A. et al. (2017) Discerning the origins of the negritos, First Sundaland People: deep divergence and archaic admixture.
Genome Biology and Evolution 9 (8): 2013-2022.

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Profile of Invited talk 36 Speaker: Dr. SUZUKI Rumiko, NIG
Talk time: Wednesday, February 17, 16:40 - 17:05
Talk title: Genome mapping of F1 hybrid camels
Project Associate Professor, Population Genetics Laboratory, National Institute of Genetics, Mishima
Recent publications
1. Ono T. et al. (2020) Discovery of unique African Helicobacter pylori CagA-multimerization motif in the Dominican Republic.
World Journal of Gastroenterology 26 (45): 7118–7130.
2. Suzuki R. et al. (2019) Genome-wide mutation analysis of Helicobacter pylori after inoculation to Mongolian gerbils. Gut
Pathogens 11, 45.
3. Wastito L. A. et al. (2018) Distribution and clinical associations of integrating conjugative elements and cag pathogenicity
islands of Helicobacter pylori in Indonesia. Scientific Reports 8, 6073.

Profile of Invited talk 37 Speaker: Dr. Kirill KRYUKOV, NIG
Talk time: Wednesday, February 17, 17:05 - 17:30
Talk title: GenomeSync: streamlining access to current genome data
Specially Appointed Associate Professor, Population Genetics Laboratory, National Institute of Genetics, Mishima
Recent publications
1. Kryukov K. et al. (2020) Sequence Compression Benchmark (SCB) database — a comprehensive evaluation of reference-freecompressors for FASTA-formatted sequences. GigaScience 9 (7), giaa072.
2. Kryukov K. et al. (2019) Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA
sequences. Bioinformatics 35 (19): 3826-3828.
3. Kryukov K. et al. (2019) Systematic survey of non-retroviral virus-like elements in eukaryotic genomes. Virus Research 262:
30-36.
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Profile of Invited talk 38 Speaker: Dr. SAITOU Naruya, NIG
Talk time: Wednesday, February 17, 17:30 - 17:55
Talk title: AGTC, iDarwin, and Yaponesia Genome Project
Professor, Population Genetics Laboratory, National Institute of Genetics, Mishima
Specially appointed Professor Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus
Recent publications
1. Saber M. M. et al. (2021) Possible roles for the hominid-specific DSCR4 gene in human cells. Genes and Genetic Systems (inpress).
2. Saitou N. (2021) “My Thoughts on Biological Evolution” by KIMURA (2020) – translation of KIMURA (1988) – . iDarwin 1:
37-53.
4. Babarinde I. A. and Saitou N. (2020) The dynamics, causes, and impacts of mammalian evolutionary rates revealed by the
analyses of capybara draft genome sequences. Genome Biology and Evolution 12 (8):1444–1458.

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"Genome” was proposed in Winkler (1920); see cover of this book at right.
Winkler H. (1920) Verbreitung und Ursache der Parthenogenesis im Pflanzenund Tierreiche. Verlag von Gustav Fischer, Jena.
At page 165 of this book, “Distribution and cause of parthenogenesis in plants
and animals” in English, he wrote:
Ich schlage vor, für den haploiden Chromosomensatz, der im Verein mit
dem zugehörigen Protoplasma die materielle Grundlage dersystematischen Einheit darstellt, den Ausdruck: das Genom zu verwenden,…
This can be translated into English:
I suggest to use the word 'genome' for the haploid chromosome set, whichis the material basis of the systematic unit in combination with theassociated protoplasm, …
(translated by Dr. SUZUKI Rumiko, invited speaker of GCCC)
Hans Karl Albert Winkler (1877-1945)
He was professor of botany in Hamburg University when he published thisbook at age of 53. He also coined “gene conversion”.
His photo below is taken from:https://www.ranker.com/review/hans-winkler/1127023?ref=wiki_1070897

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Introduction of KIHARA Hitoshi
KIHARA Hitoshi conducted “genome analysis” of wheats in 1920s. Kihara (1982) wrote at page 69, in section “4.1 The Concept of the Genome” of Chapter 4“Genome Analysis I”.
At the time when cytological analysis on the intra- and intergroup hybrids among three Triticum
groups attained a certain stage, the term genome analysis was introduced to give an appropriate name tothis kind of study.
The term “genome” was coined by H. Winkler (1920), and was defined by him as follows;
The present writer proposes a term “GENOME” (Genome) for a haploid set of chromosomes.
Such a set of chromosomes gives a substantial basis as the taxonomical unit in corporation withcytoplasm to which it belongs. And the cells or the organism, whose nuclei contain two or more
identical genomes are called homogenomic, and the ones which contain two or more kinds ofgenomes are called heterogenomic.
As Winkler did not define the homologous chromosomes, I have defined them as follows:
Homologous chromosomes have their homologous loci in identical sequence as well as indistance. Therefore when two genomes are homologous, an exchange of homologous partners
causes no physiological damage to the gametes or to the zygotes.
Non-homologous chromosomes may have different loci or the same loci different in sequence
or in distance. When there are no homologous chromosomes between two genomes, these arenonhomologous genomes; if there are some, they are partially homologous.
These principles and definitions were set out in the article entitled “Genome analysis, III” (1932), andthe first report in the same series was devoted to a presentation of the principles and actual data of theanalysis.
Kihara H. (1982) Wheat Studies – Retrospect and Prospects –. Kodansha, Tokyo and Elsevier Science Publishing Company, Amsterdam.
KIHARA Hitoshi (1893-1986)
1927-1956, Professor, Faculty of Agriculture, Kyoto University, Kyoto.
1942-1984, Director, Kihara Institute for Biological Research, Kyoto/Mishima/Yokohama.
1955-1969, Director-General, National Institute of Genetics, Mishima.
His photo shown above is taken from: https://kihara.or.jp/kihara/dr_kihara.html

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Introduction of National Institute of Genetics, Mishima, Japan
Institute Home Page: https://www.nig.ac.jp/nig/
Director-General
Dr. HANAOKA Fumio
There are four Departments in this Institute:
Department of Informatics (5 laboratories)
Department of Genomics and Evolutionary Biology (7 laboratories)
Department of Gene Function and Phenomics (11 laboratories)
Department of Chromosome Science (5 laboratories)
There are five Centers in this Institute:
Center for Frontier Research (2 laboratories)
Bioinformatics and DDBJ Center (3 divisions)
Advanced Genomics Center (2 divisions)
Genetic Resource Center (4 divisions)Support Center (3 units)

Many researchers are involved in genome and chromosome studies in National Institute of Genetics. Eight GCCC speakers from thisInstitute belong to Department of Genomics and Evolutionary Biology. KIMURA Motoo (1924-1994), who studied in this institute until
he passed away, proposed the neutral theory of evolution in 1968. This neutral theory is now fundamental for evolutionary genomics.
Therefore, it is natural for us to celebrate Genome Concept Centennial.

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Introduction of Yaponesian Genome Project
Project Home Page: http://www.yaponesian.jp/index_e.php

There was first wave of immigration to Yaponesia (Japanese Archipelago) about 40,000 years ago, followed by several more waves afterwards. In this timeframe, we try to understand what kind of ethnic groups the Japanese Archipelago humans were originated from, and how the process of it’s establishment anddevelopment in Yaponesia took place, by determining and conducting comparative analysis on the genomic sequences of 500 modern humans selected fromvarious area, and 100 ancient humans of Paleolithic - Historic times, to further elucidate the Yaponesian Genome history. Together with the analysis on human,
we also elucidate the history of animals and plants immigrated to Yaponesia, by the genomic sequence comparison. We reconstruct the details of history for the
past population fluctuations by the existing or newly developed methods estimating by genomic sequences. To investigate the Yaponesians history from various
directions, our genome research team collaborates with the Archaeological research team incorporating the age dating method, and the linguistic research teamanalyzing the Japanese and Ryukyu dialects. From the collaborations we establish the new research filed integrated with social science and science.
This research received the grant from MEXT (Ministry of Education, Culture, Sports, Science and Technology), as a New Academic Field Research,
titled as “Elucidating the Origin and Establishment of Yaponesians” (Abbreviated as: Yaponesian Genome).
Following 13people of this Yaponesian Genome Project give talks in GCCC:
FUJIMOTO Akihiro (B03 group member)
IMANISHI Tadashi (A04 group member)
ITOH Tsuyoshi (A03 group member)
KANZAWA-KIRIYAMA Hideaki (A02 group member)
OOTA Hiroki (A04 group member)
SAITOU Naruya (Project P.I. and A01group leader)
SUZUKI Hitoshi (A03 group leader)

HANADA Kosuke (A04 group member)
INOUE Ituro (A01 group member)
Timothy A. JINAM (A01 group member)
KIMURA Ryosuke (A04 group member)
OSADA Naoki (B03 group leader)
SHINODA Ken-ichi (A02 group leader)34