Curriculum Vitae – Shigehiro Kuraku

Shigehiro Kuraku, Ph.D. Unit Leader Laboratory for Phyloinformatics RIKEN Center for Biosystems Dynamics Research Email: [email protected] URL: www.clst.riken.jp/phylo/

GENDER Male YEAR OF BIRTH 1976 NATIONALITY Japanese

Ph.D. Department of Biophysics, Graduate School of Science, Kyoto University January 2005 Discipline: Evolutionary Biology Supervisor: Prof. Yoshinori Shichida (after Prof. Takashi Miyata retired) M.Sc. Department of Biophysics, Graduate School of Science, Kyoto University March 2001 Discipline: Molecular Evolutionary Biology Supervisor: Prof. Takashi Miyata B.Sc. Faculty of Science, Kyoto University March 1999 Discipline: Molecular Evolutionary Biology Supervisor: Prof. Takashi Miyata

Japanese (native) English (fluent) German (Level 3 – Diplom Deutsch in Japan. 1995) Italian (Diploma elementare di Lingua Italiana Firenze - Accadmia italiana di lingua. 1999) 2 Curriculum vitae – Shigehiro Kuraku

Year Appointment 2018- Unit Leader Laboratory for Phyloinformatics RIKEN Center for Biosystems Dynamics Research in Kobe, Japan 2018- Adjunct Associate Professor Graduate School of Science, Kobe University, Japan 2014-2018 Unit Leader Phyloinformatics Unit RIKEN Center for Life Science Technologies in Kobe, Japan 2014- Adjunct Associate Professor Organization of Advanced Science and Technology, Kobe University, Japan 2013- Adjunct Associate Professor Graduate School of Science and Technology, Kwansei Gakuin University, Japan 2012-2014 Unit Leader Genome Resource and Analysis Unit, Center for Developmental Biology, RIKEN in Kobe, Japan 2007-2012 Assistant Professor (Akademischer Rat / Wissenschaftlicher Mitarbeiter) Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany 2005-2007 Research Scientist (postdoctoral) Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN in Kobe, Japan 2004-2005 Research Associate (pre-doctoral) Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN in Kobe, Japan 2003-2004 Junior Research Associate Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN in Kobe, Japan

(Descending order for years of publication; *I am a corresponding author)

Original papers (review papers are numbered separately and listed further below)

2018

69. Yuichiro Hara, Miki Takeuchi, Yuka Kageyama, Kaori Tatsumi, Masahiko Hibi, Hiroshi Kiyonari and Shigehiro Kuraku*. Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes BMC Biology 2018. accepted. doi: 10.1186/s12915-018-0509-4

68. Koh Onimaru, Fumio Motone, Itsuki Kiyatake, Kiyonori Nishida, and Shigehiro Kuraku*. A staging table for the embryonic development of the brownbanded bamboo shark (Chiloscyllium punctatum). Developmental Dynamics 2018. accepted. doi:10.1002/dvdy.24623

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2017 67. Eri Okamoto, Rie Kusakabe, Shigehiro Kuraku, Susumu Hyodo, Alexandre Robert-Moreno, Koh Onimaru, James Sharpe, and Shigeru Kuratani, Mikiko Tanaka. Migratory appendicular muscles precursor cells in the common ancestor to all vertebrates. Nature Ecology & Evolution, 2017. 1, 1784.

66. Osamu Nishimura, Yuichiro Hara, Shigehiro Kuraku*. gVolante for standardizing completeness assessment of genome and transcriptome assemblies. Bioinformatics 2017. 13, 3635-3637. doi: 10.1093/bioinformatics/btx445

65. Mitsutaka Kadota, Yuichiro Hara, Kaori Tanaka, Wataru Takagi, Chiharu Tanegashima, Osamu Nishimura, and Shigehiro Kuraku*. CTCF binding landscape in jawless fish with reference to Hox cluster evolution. Scientific Reports, 2017. 7, 4957. doi:10.1038/s41598-017-04506-x .

2016 64. Miki Takeuchi, Shingo Yamaguchi, Masayoshi Sakakibara, Takuto Hayashi, Koji Matsuda, Yuichiro Hara, Chiharu Tanegashima, Takashi Shimizu, Shigehiro Kuraku and Masahiko Hibi. Gene expression profiling of granule cells and Purkinje cells in the zebrafish cerebellum. Journal of Comparative Neurology, 2016. 525: 1558-1585.

63. Hitoshi Niwa, Akira Nakamura, Makoto Urata, Maki Shirae-Kurabayashi, Shigehiro Kuraku, Steven Russell and Satoshi Ohtsuka. The evolutionally-conserved function of group B1 Sox family members confers the unique role of Sox2 in mouse ES cells. BMC Evolutionary Biology 2016, 16:173.

62. Juliana Gutierrez-Mazariegos, Eswar Kumar Nadendla, Romain A. Studer, Susana Alvarez, Angel R. de Lera, Shigehiro Kuraku, William Bourguet, Michael Schubert & Vincent Laudet. Evolutionary diversification of retinoic acid receptor (RAR) ligand-binding pocket structure by molecular tinkering. Royal Society Open Science 2016, doi: 10.1098/rsos.150484

61. Fumiaki Sugahara, Juan Pascual-Anaya, Yasuhiro Oisi, Shigehiro Kuraku, Shin-ichi Aota, Noritaka Adachi, Wataru Takagi, Tamami Hirai, Noboru Sato, Yasunori Murakami, Shigeru Kuratani. Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain. Nature, 2016, 531: 97-100.

60. Yuuta Moriyama, Fumihiro Ito, Hiroyuki Takeda, Tohru Yano, Masataka Okabe, Shigehiro Kuraku, Fred W. Keeley and Kazuko, Koshiba-Takeuchi. Evolution of the fish heart by sub/neofunctionalization of an elastin gene. Nature Communications, 2016, 7: 10397

59. Genshiro A. Sunagawa, Kenta Sumiyama, Maki Ukai-Tadenuma, Dimitri Perrin, Hiroshi Fujishima, Hideki Ukai, Osamu Nishimura, Shoi Shi, Rei-ichiro Ohno, Ryohei Narumi, Yoshihiro Shimizu, Daisuke Tone, Koji L. Ode, Shigehiro Kuraku, Hiroki R. Ueda. Mammalian reverse genetics without crossing reveals Nr3a as a short-sleeper gene. Cell

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Reports 2016, 14: 662-677. DOI: 10.1016/j.celrep.2015.12.052

58. Yukiko Ogino, Shigehiro Kuraku, Hiroshi Ishibashi, Hitoshi Miyakawa, Eri Sumiya, Shinichi Miyagawa, Hajime Matsubara, Gen Yamada, Michael E. Baker, Taisen Iguchi. Neofunctionalization of androgen receptor (AR) by gain-of-function mutations in teleost Fish lineage. Molecular Biology and Evolution, 2016, 33: 228-244.

2015 57. Yuichiro Hara, Kaori Tatsumi, Michio Yoshida, Eriko Kajikawa, Hiroshi Kiyonari. and Shigehiro Kuraku*. Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation. BMC Genomics 2015, 16: 977.

56. Yoko Yamaguchi, Wataru Takagi, Shigehiro Kuraku, Shunsuke Moriyama, Justin D. Bell, Andre P. Seale, Darren T. Lerner, E. Gordon Grau, Susumu Hyodo. Discovery of conventional prolactin from the holocephalan elephant fish, Callorhinchus milii. General and Comparative Endocrinology 2015, 224: 216-227.

55. Mitsumasa Koyanagi, Seiji Wada, Emi Kawano-Yamashita, Yuichiro Hara, Shigehiro Kuraku, Shigeaki Kosaka, Koichi Kawakami, Satoshi Tamotsu, Hisao Tsukamoto, Yoshinori Shichida, and Akihisa Terakita. Diversification of non-visual photopigment parapinopsin in spectral sensitivity for diverse pineal functions. BMC Biology, 2015, 13: 73.

54. Koh Onimaru, Shigehiro Kuraku, Wataru Takagi, Susumu Hyodo, James Sharpe and Mikiko Tanaka. A shift in anterior-posterior positional information underlies the fin-to-limb evolution. eLife, 2015, 4: e07048. doi: http://dx.doi.org/10.7554/eLife.07048.001.

53. Munazah Andrabi, Shigehiro Kuraku, Nozomu Takata, Yoshiki Sasai and Nick R. Love. Comparative, transcriptome analysis of self-organizing optic tissues. Scientific Data, 2015, 2: Article number: 150030. doi:10.1038/sdata.2015.30.

52. Miyuki Noro, Fumiaki Sugahara, Shigehiro Kuraku*. Reevaluating Emx gene phylogeny: homopolymeric amino acid tracts as a potential factor obscuring orthology signals in cyclostome genes. BMC Evolutionary Biology, 2015, 15:78. doi: 10.1186/s12862-015-0351-z.

51. Kaori Tatsumi, Osamu Nishimura, Kazu Itomi, Chiharu Tanegashima, Shigehiro Kuraku*. Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing. Biotechniques, 2015, 58: 253-257. doi: 10.2144/000114288.

2014 50. Benoit G Godard, Marion Coolen, Sophie Le Panse, Aurelie Gombault, Susana Ferreiro-Galve, Laurent Laguerre, Ronan Lagadec, Patrick Wincker, Julie Poulain, Corinne Da Silva, Shigehiro Kuraku, Wilfrid Carre, Agnes Boutet, and Sylvie Mazan. Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates. Biology Open, doi: 10.1242/bio.20148037.

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49. Nathalie Feiner, Axel Meyer, Shigehiro Kuraku*. Evolution of the vertebrate Pax4/6 class of genes with focus on its novel member, the Pax10 gene. Genome Biology and Evolution, 2014. 6: 1635-1651.

2013 48. Saori Tani, Shigehiro Kuraku, Hiroshi Sakamoto, Kunio Inoue, and Rie Kusakabe. Developmental expression and evolution of muscle-specific microRNAs conserved in vertebrates. Evolution & Development, 2013 15: 293-304.

47. Nathalie Feiner, Yasunori Murakami, Lisa Breithut, Sylvie Mazan, Axel Meyer and Shigehiro Kuraku*. Saltatory evolution of the ectodermal neural cortex (ENC) gene family at the vertebrate origin. Genome Biology and Evolution, 2013. doi:10.1093/gbe/evt104.

46. Adina J. Renz, Axel Meyer and Shigehiro Kuraku*. Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes. PLoS One, 2013. 8(6): e66400. doi:10.1371/journal.pone.0066400.

45. Zhuo Wang, et al (15th out of the 33 authros). The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature Genetics, 2013. 45: 701–706.

44. Shigehiro Kuraku*, Christian M. Zmasek, Osamu Nishimura, and Kazutaka Katoh. aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. Nucleic Acids Research, 2013. 41 (W1): W22-W28.

43. Nao Niwa, Ai Akimoto, Masashi Sakuma, Shigehiro Kuraku, and Shigeo Hayashi. Homeogenetic inductive mechanism of segmentation in polychaete tail regeneration. Developmental Biology, 2013. 381: 460-470.

42. Chris Amemiya, ….. , Shigehiro Kuraku (45th out of the 90 authors), ….. , Eric S. Lander, Axel Meyer and Kerstin Lindblad-Toh. The African coelacanth genome provides insights into tetrapod evolution. Nature, 2013. 496: 311–316.

41. Satoko Fujimoto, Yasuhiro Oisi, Shigehiro Kuraku, Kinya G Ota and Shigeru Kuratani. Non-parsimonious evolution of hagfish Dlx genes. BMC Evolutionary Biology, 2013. 13:15.

40. Jeramiah Smith, Shigehiro Kuraku, …, and Weiming Li (2nd out of the 59 authors). Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nature Genetics, 2013. 45: 415-421.

39. Yasuhiro Oisi, Kinya G. Ota, Shigehiro Kuraku, Satoko Fujimoto and Shigeru Kuratani. Craniofacial development of hagfishes and the evolution of vertebrates. Nature, 2013. 493:175-180.

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38. Bo Xu, Görel Sundström, Shigehiro Kuraku, Ingrid Lundell, and Larhammar Dan. Cloning and pharmacological characterization of the neuropeptide Y receptor Y5 in the sea lamprey, Petromyzon marinus. Peptides, 2013. 39:64-70.

2012 37. Kazumi Matsubara, Shigehiro Kuraku, Hiroshi Tarui, Osamu Nishimura, Chizuko Nishida, Kiyokazu Agata, Yoshinori Kumazawa, and Yoichi Matsuda. Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC3 profiling in snake. BMC Genomics, 2012. 13: 604.

36. Elisabeth Stuerner, Shigehiro Kuraku, Mark Hochstrasser and Stefan G. Kreft. Split-Doa10: a naturally split polytopic eukaryotic membrane protein generated by fission of a nuclear gene. PLoS One, 2012. 7(10): e45194.

35. Sabine Freter, Yuko Muta, Paul O'Neill, Vassil Vassilev, Shigehiro Kuraku and Raj Ladher. Pax2 modulates proliferation during specification of the otic and epibranchial placodes. Developmental Dynamics, 2012. 241:1716-28.

34. Shigehiro Kuraku, Huan Qiu and Axel Meyer. Horizontal transfers of Tc1 elements between teleost fishes and their vertebrate parasites, lampreys. Genome Biology and Evolution. 2012. 4: 929-936.

2011 33. Shigehiro Kuraku* and Shigeru Kuratani. Genome-wide detection of gene extinction in early mammalian evolution. Genome Biology and Evolution, 2011. 3: 1449-1462.

32. Nathalie Feiner, Rolf Ericsson, Axel Meyer, and Shigehiro Kuraku*. Revisiting the origin of the vertebrate Hox14 by including its relict sarcopterygian members. Journal of Experimental Zoology Part B. (Molecular Development and Evolution), 2011. 316B: 515-525.

31. Huan Qiu, Falk Hildebrand, Shigehiro Kuraku*, and Axel Meyer. Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case. BMC Genomics, 2011. 12: 325.

30. Tereza Manousaki, Nathalie Feiner, Gerrit Begemann, Axel Meyer, and Shigehiro Kuraku*. Co-orthology of Pax4 and Pax6 to the fly eyeless gene: molecular phylogenetic, comparative genomic and embryological analyses. Evolution & Development, 2011. 13: 448-459.

29. Christophe Dessimoz, Stefan Zoller, Tereza Manousaki, Huan Qiu, Axel Meyer, and Shigehiro Kuraku*. Comparative genomics approach to detecting split coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). Briefings in Bioinformatics, 2011. 12: 474-484.

28. Fumiaki Sugahara, Shin-ichi Aota, Shigehiro Kuraku, Yasunori Murakami, Yoko Takio-Ogawa, Shigeki Hirano, and Shigeru Kuratani. Involvement of Hedgehog and FGF signalling in the lamprey telencephalon: evolution of regionalization and dorsoventral patterning of the vertebrate forebrain. Development, 2011, 138: 1217-1226.

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27. Rie Kusakabe, Shigehiro Kuraku, and Shigeru Kuratani. Expression and interaction of muscle-related genes in the lamprey imply the evolutionary scenario for vertebrate skeletal muscle, in association with the acquisition of the neck and fins. Developmental Biology, 2011, 350: 217-227.

26. Adina J Renz, Helen M Gunter, Jan Fischer, Huan Qiu, Axel Meyer, and Shigehiro Kuraku*. Ancestral and derived attributes of the dlx gene repertoire, cluster structure and expression patterns in an African cichlid fish. EvoDevo, 2011, 2: 1.

2010 25. Shigehiro Kuraku*, Yoko Takio, Fumiaki Sugahara, Masaki Takechi, and Shigeru Kuratani. Evolution of oropharyngeal patterning mechanisms involving Dlx and endothelins in vertebrates. Developmental Biology, 2010, 341: 315-323.

24. Nobuhiro Kokubo, Manami Matsuura, Koh Onimaru, Eva Tiecke, Shigehiro Kuraku, Shigeru Kuratani and Mikiko Tanaka. Mechanisms of heart development in the Japanese lamprey, Lethenteron japonicum. Evolution & Development, 2010, 12: 34-44.

23. Kathryn Elmer, Shaohua Fan, Helen Gunter, Julia Jones, Sven Boekhoff, Shigehiro Kuraku, and Axel Meyer. Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes. Molecular Ecology, 2010, 19 Suppl. 1: 196-210.

2009 22. Yukiko Ogino, Hironori Katoh, Shigehiro Kuraku and Gen Yamada. Evolutionary history and functional characterization of androgen receptor genes in jawed vertebrates. Endocrinology, 2009, 150: 5415-5427.

21. Nathalie Feiner, Gerrit Begemann, Adina J. Renz, Axel Meyer, and Shigehiro Kuraku*. The origin of bmp16, a novel Bmp2/4 relative, retained in teleost fish genomes. BMC Evolutionary Biology, 2009, 9: 277.

20. Shigehiro Kuraku*, Axel Meyer and Shigeru Kuratani. Timing of genome duplications: did cyclostomes diverge before, or after? Molecular Biology and Evolution, 2009, 26: 47-59.

2008 19. Shigehiro Kuraku*, Yoko Takio, Koji Tamura, Hideaki Aono, Axel Meyer, and Shigeru Kuratani. Non-canonical role of Hox14 revealed by its expression patterns in lamprey and shark. Proc Natl Acad Sci, USA, 2008, 105: 6679-6683.

18. Manami Matsuura, Hidenori Nishihara, Koh Onimaru, Nobuhiro Kokubo, Shigehiro Kuraku, Rie Kusakabe, Norihiro Okada, Shigeru Kuratani, and Mikiko Tanaka. Identification of four Engrailed genes in the Japanese lamprey, Lethenteron japonicum. Developmental Dynamics 2008, 237: 1581-1589.

2007 17. Eva Tiecke, Manami Matsuura, Nobuhiro Kokubo, Shigehiro Kuraku, Rie Kusakabe, Shigeru Kuratani, and Mikiko Tanaka. Identification and developmental expression of two Tbx1/10-related genes in the agnathan Lethenteron japonicum. Development, Genes and Evolution 2007, 217: 691-697.

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16. Yoko Takio, Shigehiro Kuraku, Yasunori Murakami, Massimo Pasqualetti, Filippo M. Rijli, Yuichi Narita, Shigeru Kuratani, and Rie Kusakabe. Hox gene expression patterns in Lethenteron japonicum embryos - insights into the evolution of the vertebrate Hox code. Develepmental Biology 2007, 308: 606-620.

15. Hiroshi Nagashima, Shigehiro Kuraku, Katsuhisa Uchida, Yoshie Kawashima Ohya, Yuichi Narita, and Shigeru Kuratani. On the carapacial ridge in turtle embryos: its developmental origin, function and the chelonian body plan. Development 2007, 134: 2219-2226.

14. Kinya G. Ota, Shigehiro Kuraku, and Shigeru Kuratani. Hagfish embryology with reference to the evolution of the neural crest. Nature 2007, 446: 672-675.

2006 13. Shigehiro Kuraku* and Shigeru Kuratani. Timescale for cyclostome evolution inferred with a phylogenetic diagnosis of hagfish and lamprey cDNA sequences. Zoological Science 2006, 23: 1053-1064.

12. Masaaki Kajiwara, Shigehiro Kuraku, Takako Kurokawa, Kenichi Kato, Shingo Toda, Hidenori Hirose, Shigeru Takahashi, Yasuyuki Shibata, Taisen Iguchi, Toshie Matsumoto, Takashi Miyata, Takashi Miura, and Yuji Takahashi. Tissue preferential expression of estrogen receptor gene in the marine snail, Thais clavigera. General and Comparative Endocrinology 2006, 148: 315-326.

11. Yoshie Kawashima Ohya, Ryo Usuda, Shigehiro Kuraku, Hiroshi Nagashima and Shigeru Kuratani. Unique features of Myf-5 in turtles: nucleotide deletion, alternative splicing, and unusual expression pattern. Evolution & Development 2006, 8: 415-423.

10. Shigehiro Kuraku*, Junko Ishijima, Chizuko Nishida-Umehara, Kiyokazu Agata, Shigeru Kuratani, and Yoichi Matsuda. cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggests a chromosomal size-dependent GC bias shared by sauropsids. Chromosome Research 2006, 14: 187-202.

2005 9. Noriko Funayama, Mikiko Nakatsukasa, Shigehiro Kuraku, Katsuaki Takechi, Mikako Dohi, Naoyuki Iwabe, Takashi Miyata and Kiyokazu Agata. Isolation of Efsilicatein and Eflectin as molecular markers for sclerocytes and cells involved in innate immunity in the fresh water sponge, Ephydatia fluviatilis. Zoological Science 2005, 22: 1113-1122.

8. Shigehiro Kuraku, Ryo Usuda, and Shigeru Kuratani. Comprehensive survey of carapacial ridge-specific genes in turtle implies co-option of some regulatory genes in carapace evolution. Evolution & Development 2005, 7: 3-17. (This paper constitutes the major part of my Ph.D. thesis)

7. Hiroshi Nagashima, Katsuhisa Uchida, Keiko Yamamoto, Shigehiro Kuraku, Ryo Usuda, and Shigeru Kuratani. Turtle-chicken chimera: an experimental approach to understanding evolutionary innovation in the turtle. Developmental Dynamics 2005, 232:149-61.

6. Yoshie Kawashima Ohya, Shigehiro Kuraku and Shigeru Kuratani. Hox code in embryos of

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Chinese soft-shelled turtle Pelodiscus sinensis correlates with the evolutionary innovation in the turtle. Journal of Experimental Zoology Part B (Mol. Dev. Evol.), 2005, 304B: 107-118.

2004 5. Yoko Takio, Massimo Pasqualetti, Shigehiro Kuraku, Shigeki Hirano, Filippo M. Rijli, and Shigeru Kuratani Lamprey Hox genes and the evolution of jaws. Nature 2004, 429; doi:10.1038/nature02616.

4. Kanae Kikugawa, Kazutaka Katoh, Shigehiro Kuraku, Hiroshi Sakurai, Osamu Ishida, Naoyuki Iwabe, and Takashi Miyata. Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes. BMC Biology 2004, 2:3.

2003 3. Katsuhisa Uchida, Yasunori Murakami, Shigehiro Kuraku, Shigeki Hirano and Shigeru Kuratani. Development of the adenohypophysis in the lamprey: evolution of epigenetic pattering programs in organogenesis. Journal of Experimental Zoology Part B (Mol. Dev. Evol.) 2003, 300B: 32-47.

1999 2. Shigehiro Kuraku, Daisuke Hoshiyama, Kazutaka Katoh, Hiroshi Suga and Takashi Miyata. Monophyly of lampreys and hagfishes supported by nuclear DNA-coded genes. Journal of Molecular Evolution 1999, 49:729-35.

1. Hiroshi Suga, Daisuke Hoshiyama, Shigehiro Kuraku, Kazutaka Katoh, Kaoru Kubokawa and Takashi Miyata. Protein tyrosine kinase cDNAs from amphioxus, hagfish, and lamprey: isoform duplications around the divergence of cyclostomes and gnathostomes. Journal of Molecular Evolution 1999, 49: 601-8.

Review papers

2018 R14. Koh Onimaru & Shigehiro Kuraku*. Inference of the ancestral vertebrate phenotype through vestiges of the whole genome duplications. Briefings in Functional Genomics 2018. accepted. doi:10.1093/bfgp/ely008

2016 R13. Shigehiro Kuraku*, Nathalie Feiner, Sean Keeley, Yuichiro Hara. Incorporating tree-thinking and evolutionary time scale into developmental biology. Development Growth and Differentiation 2016, 58: 131-142. DOI: 10.1111/dgd.12258.

2013 R12. Masaki Takechi, Noritaka Adachi, Tamami Hirai, Shigeru Kuratani, and Shigehiro Kuraku. The Dlx genes as clues to vertebrate genomics and craniofacial evolution. Seminars in Cell and Developmental Biology, 2013. 24:110-118.

R11. Shigehiro Kuraku. Impact of asymmetric gene repertoire between cyclostomes and

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gnathostomes. Seminars in Cell and Developmental Biology, 2013. 24:119-127.

2012 R10. Shigehiro Kuraku. Genomic novelty at the vertebrate ancestor. 2012. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0024137]

2011 R9. Hiroshi Nagashima, Shigehiro Kuraku, Katsuhisa Uchida, Yoshie Kawashima-Ohya, Yuichi Narita, Shigeru Kuratani. Body plan of turtles: an anatomical, developmental and evolutionary perspective. Anatomical Science International,, 2011. 87: 1-13.

R8. Shigehiro Kuraku. Hox gene clusters of early vertebrates: do they serve as reliable markers for genome evolution? Genomics, Proteomics & Bioinformatics, 2011. 9: 97-103.

R7. Shigeru Kuratani, Shigehiro Kuraku and Hiroshi Nagashima. Evolutionary developmental perspective for the origin of the turtles: the folding theory for the shell based on the developmental nature of the carapacial ridge. Evolution & Development, 2011. 13: 1-14.

2010 R6. Shigehiro Kuraku*. Palaeophylogenomics of the vertebrate ancestor—impact of hidden paralogy in hagfish and lamprey gene phylogeny. Integrative and Comparative Biology, 2010. 50: 124-129.

2009 R5. Shigehiro Kuraku and Axel Meyer. The evolution and maintenance of Hox gene clusters in vertebrates and the teleost-specific genome duplication. International Journal of Developmental Biology, 2009. 53: 765-773.

R4. Shigehiro Kuraku. Molecular evolutionary studies on Chondrichthyes: in search of the ancestral vertebrate genome. An¥¥graReport of Japanese Society of Elasmobranch Studies, 2009. 45: 17-27 (only abstract in English).

2008 R3. Shigehiro Kuraku and Axel Meyer. Genomic analysis of cichlid fish 'natural mutants'. Current Opinion in Genetics & Development, 2008. 18: 551-558.

R2. Shigehiro Kuraku* Insights into cyclostome phylogenomics: pre-2R or post-2R? Zoological Science, 2008. 25: 960-968.

2002 R1. Shigeru Kuratani, Shigehiro Kuraku, and Yasunori Murakami. Lamprey as an evo-devo model: lessons from comparative embryology and molecular phylogenetics. Genesis, 2002. 34: 175-183.

Book Chapters

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Tereza Manousaki, Huan Qiu, Miyuki Noro, Falk Hildebrand, Axel Meyer, Shigehiro Kuraku. “Molecular Evolution in the Lamprey Genomes and Its Relevance to the Timing of Whole Genome Duplications.” Chapter 2 in the book “Jawless fishes of the World”, Cambridge Scholars Publishing 2016.

Hiroshi Nagashima, Shigehiro Kuraku, Katsuhisa Uchida, Yoshie Kawashima-Ohya, Yuichi Narita, and Shigeru Kuratani. “Origin of the turtle body plan - The folding theory to illustrate turtle-specific developmental repatterning.” In D, Brinkman (Ed.), Eugene S. Gaffney Festschrift volume. Dordrecht, Springer. 2012.

Shigehiro Kuraku and Axel Meyer. “Detection and phylogenetic assessment of conserved synteny derived from whole genome duplications” in Volume 'Evolutionary Genomics: statistical and computational methods' in Series 'Methods in Molecular Biology'. Maria Anisimova, Ed. Springer. 2012.

Shigehiro Kuraku and Axel Meyer. “Whole Genome Duplications and the Radiation of Vertebrates” in Evolution after Gene Duplication. Pp. 299 - 311. Katharina Dittmar and David Liberles, Eds. Wiley-Blackwell, NY. 2010.

Shigehiro Kuraku*, Kinya G. Ota, Shigeru Kuratani. “Jawless Fishes (Cyclostomata)” in The Timetree of Life. S. Blair Hedges and Sudhir Kumar, Eds. Pp315-319. Oxford University Press. 2009.

Shigehiro Kuraku*, Yoko Takio, Shigeru Kuratani. Hox genes and emerging body plans. “Frontiers of development, differentiation, and regeneration 2005” Experimental Medicine Vol. 23-No.1 (Japanese only)

Translation into Japanese

Chapter 9 of “Evolution” by Nicholas H. Barton et al. (2009). Edited by Takashi Miyata. MEDSi International.

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(given in English)

Oral Presentations Osamu Nishimura, Yuichiro Hara, & Shigehiro Kuraku gVolante: for more standardized completeness assessment of genome/transcriptome assemblies Global Biodiversity Genomics Conference 2017 in Smithsonian National Museum of Natural History, Washington DC, USA, February 21-23, 2017. Shigehiro Kuraku (Invited) Can modern genomics help sustainable aquarium exhibition? International Satellite Symposium 2016‘The Synergy of Aquariums and Zoological Science in the 21st Century’in Okinawa Churaumi Aquarium, Okinawa, Japan, November 19, 2016. Shigehiro Kuraku (Invited) What did we learn from the genomes of two lamprey species, Petromyzon marinus and Lethenteron camtschaticum? The 22nd International Congress of Zoology in Okinawa Institute of Science and Technology Graduate University, and Okinawa Convention Center, Okinawa, Japan, November 14-19, 2016 Shigehiro Kuraku (Invited) Finally, it is time for multi-omics of cyclostomes and chondrichthyans. AORI Symposium ‘Adaptation to Marine Environments ~Contributions of advanced technologies and comparative approaches to the understanding of adaptation strategies in marine organisms~’ Atmosphere and Ocean Research Institute, University of Tokyo, in Kashiwa, Japan, September 15-16, 2016. Shigehiro Kuraku (Invited) Revisiting the origin of vertebrate endocrine system with genome informatics. International Symposium on the Pituitary Gland and Related Systems (ISPGRS) 2016 Hawaii Imin International Conference Center, Univ. Hawaii, USA, September 1-5, 2016. Shigehiro Kuraku (Invited) Vanishing phylogenetic signals?: revisiting molecular phylogenies of cyclostome genes. Symposium on Palaeontological and molecular approaches to early vertebrate evolution, in Uppsala, Sweden, May 12-13, 2015. Shigehiro Kuraku Sequence informatics for evolution-aware molecular zoology. CDB Symposium ‘Time in Development’ in Kobe, Japan March 23-25, 2015. Shigehiro Kuraku (Invited) Revealing cryptic pan-vertebrate gene repertoire in developmental phylome The fifth meeting of the European Society for Evolutionary Developmental Biology, in Vienna, Austria, July 22-25, 2014. Shigehiro Kuraku (Invited) Phylogenetics in Evo-Devo: genomic dissection of vertebrate novelty and diversity Commemorable Symposium for International Prize for Biology 2013 'Influences and Impacts of Evolutionary Biology'. Fukuoka, Japan. November 21-22, 2013. Shigehiro Kuraku (Invited) Diverse Vertebrate Genomic Architecture Elucidated by Wide Taxon Sampling and Modern Sequencing Technologies The 24th CDB Meeting ‘Genomics and Epigenomics with Deep Sequencing’ at RIKEN CDB

Curriculum vitae – Shigehiro Kuraku 13

in Kobe, Japan. June 13-14, 2013. Shigehiro Kuraku (Invited) Evolving regulatory gene repertoire Commemorable Symposium for International Prize for Biology 2011 'Genomic Regulation of Development' in Kyoto, Japan. November 30-December 1, 2011. Shigehiro Kuraku (Invited) Navigating evolution-aware life science: our ancestral genome, 500 million years ago Young Researchers Conference on Evolutionary Genomics in Tokyo, Japan. August 1-2, 2011. Tereza Manousaki, Axel Meyer, Shigehiro Kuraku Reasons why dating the two-round whole genome duplications is so difficult Society for Molecular Biology and Evolution (SMBE) in Kyoto, Japan. July 26-28, 2011. Shigehiro Kuraku (Invited) Unveiling hidden paralogy in cyclostome developmental programs Evo-Devo: where are we and where do we go? Symposium organized by Fondation des Treilles. Tourtour, France. April 26-29, 2011. Shigehiro Kuraku (Invited) Unsolved problems about whole genome duplications in early vertebrate evolution Leopoldina Symposium 'Modern approaches to ecology and evolution: Genomics of speciation, species differences and adaptations'. Hegne, Germany. August 3-5, 2010 Tereza Manousaki, Huan Qiu, Falk Hildebrand, Axel Meyer, and Shigehiro Kuraku* What are cyclostomes, genomically speaking? The 3rd meeting of European Society for Evolutionary Developmental Biology. Paris, France. July 6–9, 2010 Shigehiro Kuraku (Invited) ’Post-2R’ cyclostomes: molecular phylogenetic view of the vertebrate ancestor Annual meeting of the Society of Integrative and Comparative Biology (SICB). Seattle, USA. Jan. 3-7, 2010 Shigehiro Kuraku (Invited) Vertebrate phylome: bioinformatics or informatic biology? The 4th Global COE International Symposium joint with the 19th Hot Spring Harbor Symposium of Medical Institute of Bioregulation “Molecular Evolution and Bioinformatics”. Kyushu Univ. Fukuoka, Japan. Nov 1-2, 2009 Shigehiro Kuraku Phylogenomic Evo-Devo: orthology/paralogy revisited The 2nd meeting of European Society for Evolutionary Developmental Biology. Ghent, Belgium. July 29 - August 1, 2008 Shigehiro Kuraku (Invited) Cyclostome Phylogenomics The 15th CDB Meeting - Advances in Cyclostome Research: Body plan and developmental programs before the jawed vertebrates. RIKEN CDB, Kobe, Japan. Jan. 24-25, 2008

Shigehiro Kuraku, Kinya, Ota, Rie Kusakabe, and Shigeru Kuratani Pre-2R or post-2R?: phylogeny and expression patterns of Dlx genes in cyclostomes. The first and founding meeting of European Society for Evolutionary Developmental Biology. Prague, Czech Republic. Aug. 16-19, 2006

14 Curriculum vitae – Shigehiro Kuraku

Shigehiro Kuraku and Shigeru Kuratani Detecting gene losses: a search for developmental genes missing only in mammals. Genomes, Evolution & Bioinformatics 2006 (Society of molecular biology and evolution) Arizona State University, USA. 2006. May 24-28, 2006 Shigehiro Kuraku, Ryo Usuda, Hiroshi Nagashima and Shigeru Kuratani Identification of carapacial ridge-specific gene expressions and gene co-option in turtle evolution International Society for Developmental Biologists (ISDB) Congress, Sydney, Australia. Sep. 3-7, 2005 Shigehiro Kuraku, Ryo Usuda, Shigeru Kuratani Identification of gene co-option involved in turtle shell evolution. Genome & Evolution 2004 (Annual Meeting for Society of Molecular Biology and Evolution), Pennsylvania State Univ., USA. Jun. 17-20, 2004

Poster Presentations (Only those presented by myself)

Osamu Nishimura, Yuichiro Hara, and Shigehiro Kuraku. gVolante: multi-faceted evaluation of de novo genome assemblies. Plant & Animal Genome XXVI, Town & Country Hotel, USA. January 13-17,2018．

Shigehiro Kuraku Expanded homolog space in vertebrate genomes: insights from cyclostomes and cartilaginous fishes Society of Molecular Biology and Evolution (SMBE) annual meeting, Vienna, Austria. July 13-17, 2015. Shigehiro Kuraku, Osamu Nishimura and Kazutaka Katoh aLeaves: a Web Server to Help Explore Protein-coding Landscape Across Diverse Animal Genomes CDB Symposium 2013 ‘The Making of a Vertebrate’ at RIKEN CDB in Kobe, Japan. March 4-6, 2013. Nathalie Feiner, Axel Meyer, Shigehiro Kuraku Non-conservation of developmental ‘toolkitʼ genes Society for Molecular Biology and Evolution (SMBE) in Kyoto, Japan. July 26-28, 2011.

Shigehiro Kuraku Half a billion years of human genome evolution illuminated by non-human genomes EMBO Meeting 2010, Barcelona, Spain. September 4-7, 2010 Tereza Manousaki, Huan Qiu, Falk Hildebrand, Axel Meyer and Shigehiro Kuraku* Molecular evolution in early vertebrate genomes Society of Molecular Biology and Evolution (SMBE) annual meeting, Lyon, France. July 4-8, 2010 Shigehiro Kuraku Phylogenetics of developmental genes in vertebrates: formulae and exceptions German Society of Developmental Biology (GfE) meeting, Hannover, Germany. March 25-28, 2009

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Shigehiro Kuraku Timing of two-round (2R) genome duplications in early vertebrates Society of Molecular Biology and Evolution (SMBE) annual meeting, Barcelona, Spain. June 5-8, 2008

Shigehiro Kuraku Potential reasons why molecular phylogenies of cyclostome genes are not clear-cut The 15th CDB Meeting - Advances in Cyclostome Research: Body plan and developmental programs before the jawed vertebrates. RIKEN CDB, Kobe, Japan. Jan. 24-25, 2008

Shigehiro Kuraku and Shigeru Kuratani Evolution of gene repertoire: Formulae and exceptions 4th CDB Symposium, Kobe, Japan. April 11, 2006

Shigehiro Kuraku, Junko Ishijima, Shigeru Kuratani and Yoichi Matsuda Chromosome size-dependent GC-compartmentalization in sauropsids estimated by cDNA sequencing and gene mapping in Chinese soft-shelled turtle Pelodiscus sinensis Society of Molecular Biology and Evolution (SMBE), Aotea Center, Auckland, New Zealand. Jun. 18-23, 2005

Shigehiro Kuraku, Shigeru Kuratani. Detection of developmental constraint and its breakage at the molecular level 3rd CDB Symposium, Kobe, Japan. April 11, 2005

Shigehiro Kuraku, Ryo Usuda, Shigeru Kuratani An evolutionary developmental attempt to elucidate how turtle acquired the shell 5th Internaltional Workshop on Advanced Genomics, Yokohama, Japan. Jun. 26-7, 2003

Shigehiro Kuraku, Ryo Usuda, Shigeru Kuratani Searching for molecular mechanisms that evolved turtle shell 1st CDB Symposium, Kobe, Japan. Mar. 23, 2003

Shigehiro Kuraku, Kazutaka Katoh, Takashi Miyata Evolution of the nuclear receptor family by gene duplication Symposium on Evolutionary Genomics, Atami, Japan. Nov. 4, 2001

(Summary) More detailed information is available upon request Invited Oral Presentations Annual meeting of Society of Chromosome Research of Japan in 2006 Annual meeting of Zoological Society of Japan in 2004 and 2013 Annual meeting of the Japan Society for Comparative Endocrinology in 2013 Annual meetings of Japanese Society of Developmental Biologists in 2012 and 2013 Annual meeting of Molecular Biology Society of Japan in 2003 Annual meeting of Society of Evolutionary Studies Japan in 2016 Annual Meeting of the Genetics Society of Japan in 2017

16 Curriculum vitae – Shigehiro Kuraku

Contributed Oral Presentations Annual meetings of Genetics Society of Japan in 1998, 1999, 2000, 2001 and 2005 Annual meetings of Japanese Society of Developmental Biologists in 2003 and 2006 Annual meeting of Zoological Society of Japan in 2013 Annual meeting of Society of Evolutionary Studies Japan in 2001 Biennial meetings of Japanese Society of Elasmobranch Studies in 2012 and 2016 Contributed Poster Presentations Annual meetings of Society of Evolutionary Studies Japan in 2000, 2003 and 2014 Annual meetings of Molecular Biology Society of Japan in 1999, 2000, 2002, 2005 and 2013 Annual meeting of Zoological Society of Japan in 2005

(given in English)

- Invited Seminar for SciLifeLab at Karolinska Institute, Sweden ‘Asymmetric evolution of paralogs in vertebrate genomes’ in September 6, 2017. - The Svedberg seminar and JSPS seminar series for SciLifeLab, Uppsala University, Sweden ‘Vertebrate Genome Evolution’ in September 4, 2017. - Invited seminar for School for Life Environmental Sciences, Deakin University, Australia ‘Genomic Characterization of Cyclostomes and Chondrichthyans’ on March 9, 2017. - Invited Seminar for Department of Zoology, University of Oxford ‘Assessing homolog space of vertebrates: molecular phylogenetics for controlling modern sequencing’ in May 2015. - Invited seminar at Hamada Lab in Graduate School of Frontier Biosciences of Osaka Univ. ‘Loss of developmental regulatory genes in mammalian evolution: molecular phylogenetics for developmental biology’, April 2014. - Invited seminar at National Institute for Basic Biology ‘Vertebrate phylome for ‘next-generation’ comparative zoology’ in Okazaki, Feb 2014. - Invited Marine Genomics Seminar at Okinawa Institute of Science and Technology, Japan. ‘Challenges in analyzing emerging non-model vertebrates.’ June 12, 2012. - Department seminar at Department of Zoology and Biodiversity, Charles University, Prague, Czech Republic. ‘Vertebrate palaeogenomics - our genome and fish genome’. March 21, 2011 - Invited seminar at Zurich Colloquium for Computational Molecular Evolution in ETH Zurich, titled 'Early vertebrate phylome as a basis to understand evolution of model vertebrate genomes'. June 14, 2010 - Invited seminar at Swiss Federal Institute of Aquatic Science and Technology (EAWAG) in Switzerland, titled ‘Our inner fish genome: what were gained and lost during the 500-million-year evolution?’ March 22, 2010 - Invited seminar at Biological Station Roscoff, in France, titled ‘Vertebrate phylome: connecting taxonomy, evolutionary genomics and developmental biology’. February 18, 2010 - Department Seminar at Department of Biology, University of Konstanz, Germany. ‘Evolution of gene repertoires and animal body plans: lessons from turtles and cyclostomes’. November 22, 2007

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Contribution to editorial services for academic journals - Faculty of F1000Prime (former Faculty1000) (since April 2013) - Associate Editor for the journal BMC Evolutionary Biology (since April 2014) - Associate Editor for the journal Scientific Data (since June 2016) - A number of ad hoc contributions as reviewers for academic journals (see Publons Profile) Contribution to graduate program administration - Principal investigator at the graduate school, International Max-Planck Research School (IMPRS) Organismal Biology (2010-2012) - Principal investigator at the graduate school, Konstanz Research School Chemical Biology (KoRS-CB) (2009-2012) Contribution to academic societies - Editorial staff of the Society of Evolutionary Studies, Japan (since 2010-2017)

18 Curriculum vitae – Shigehiro Kuraku

Teaching experience Jun. 2001 – Jan. 2002 Position: Teaching Assistant (during doctoral study) Department of Biophysics, Graduate School of Science, Kyoto University Practical course: Phylogenetics Computing Course Apr. 2007 – Feb. 2012 Position: Assistant Professor Department of Biology, University of Konstanz

Regular lectures/courses [hours per year] - Vertiefungskurs 2007-2011 ‘Molecular Evolutionary Biology’ (Practical experiment course) [70] - Lecture ‘Evolutionary Biology’ 2007/08- [10] - Anatomy course ‘Animal Body Plan’ 2007/08-2011/12 [20] - Course ‘Computational Life Science’ 2008/09 and 2011/12 [6] (for PhD students in Graduate School KoRS-CB) - Lecture ‘Evolutionary Organismal Biology’ 2010 [2] - IMPRS (International Max Planck Research School) Organismal Biology Course ‘Molecular Evolution’ – 2010/11 [2]

Direct supervision of students 3 PhD students, 3 diploma students, 1 master student, 6 pre-diploma technical assistants, 3 bachelor students

Invited lecture - ‘Vertebrate Morphology’ Course (BIO262) at University of Zurich Title: Vertebrate evolutionary genomics: a reference for morphological studies. February 29, 2008 - Reviews in Computational Biology (263-5151-00L) at ETH Zurich. Title: Gene prediction in animal genomes. May 16, 2011

Sep. 2013 - Position: Adjunct Associate Professor Department of Bioscience, Kwansei Gakuin University

Regular course [hours per year] - Molecular Evolution and Genome Informatics in 2013, 2014 and 2015 [20]

Direct supervision of students 2 undergraduate students (2014 & 2015), 2 master students (2015 & 2016) Jul. 2014 - Position: Adjunct Associate Professor Organization for Advanced Science and Technology, Kobe University

Lecture - Advanced Integrative Science Lecture Series in 2014, 2015 and

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2017 [1.5] Regular course - Biology Experiment Course 2016 and 2017 [7] Apr. 2017 – 2022 Position: Lecturer (scheduled） Open University of Japan（日本放送大学）放送授業「生物の進化と多様化の科学」において、第 10 章「動物の発生と進化」と第 11 章「ゲノムの進化と生物の多様化」を担当

Activities for career development and education

Presentations (in Japanese) 「ドイツで見た桜‐キャリアを創っていくということ」at the annual meeting of the Japanese Society of Developmental Biologists. May 29, 2012.

「そこでしか得られないもの―ゲノムと世界を見渡して」at the IGER program meeting of Nagoya University held at RIKEN CDB in January 2014.

Participation in pedagogic workshops

'Introduction to the German Higher Education System and Sources of Financial Support' Organized by Academic Staff Development Office, University of Konstanz. October 21, 2010.

'Planning a scientific career for postdocs' Lecturer: Dr. Beate Scholz Organized by Academic Staff Development Office, University of Konstanz. December 8, 2010.

Workshop ‘ゲノムの樹いきものつなぎ’ in RIKEN Kobe Campus Open House in 2015 and 2016.

Seminar at RIKEN Yokohama Campus Open House ‘What distinguishes humans from other animals? - evolution of life viewed through the lens of genomics’（「結局わたしたちとどう違うの？ゲノムからみる生命の進化」）in Yokohama, Japan. September 10, 2016.

Seminar at Sumoto High School in Awaji, Hyogo, titled ‘DNA で探る生命の進化’ and the Workshop ‘ゲノムの樹いきものつなぎ’ January 24, 2017.