TY - JOUR
T1 - Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates
AU - Hara, Yuichiro
AU - Yamaguchi, Kazuaki
AU - Onimaru, Koh
AU - Kadota, Mitsutaka
AU - Koyanagi, Mitsumasa
AU - Keeley, Sean D.
AU - Tatsumi, Kaori
AU - Tanaka, Kaori
AU - Motone, Fumio
AU - Kageyama, Yuka
AU - Nozu, Ryo
AU - Adachi, Noritaka
AU - Nishimura, Osamu
AU - Nakagawa, Reiko
AU - Tanegashima, Chiharu
AU - Kiyatake, Itsuki
AU - Matsumoto, Rui
AU - Murakumo, Kiyomi
AU - Nishida, Kiyonori
AU - Terakita, Akihisa
AU - Kuratani, Shigeru
AU - Sato, Keiichi
AU - Hyodo, Susumu
AU - Kuraku, Shigehiro
N1 - Funding Information:
We thank J. Donald for critical reading of the manuscript, K. Shirato, K. Yamamoto, S. Shibuya and members of the Evolutionary Morphology Laboratory, RIKEN for rearing catsharks, M. Andrabi for assistance in sequence data analysis, K. Tanimoto, H. Kiyonari, T. Yoshikuni, T. Ito, Y. Miyagawa and S. Sodeyama for providing materials. Our gratitude extends to K. Muguruma, Y. Murakami, F. Sugahara, J. Pascual-Anaya, R. Kusakabe, S. Higuchi, Y. Yamaguchi, W. Takagi, H. Kaiya, Y. Ishihama, S. Miyake, T. Kaku, T. Tanaka, D. Sipp, M. Tan, A. D. M. Dove, T. D. Read, D. Lagman, D. Ocampo Daza, D. Larhammar, Y. Uno and S. Mazan for insightful discussion. This study was supported by RIKEN and JSPS KAKENHI Grant Numbers 26650110, 26291065 and 17H03868 to S.Kuraku and S.H. and 17K07426 to S.Kuraku.
Publisher Copyright:
© 2018, The Author(s), under exclusive licence to Springer Nature Limited.
PY - 2018/11/1
Y1 - 2018/11/1
N2 - Modern cartilaginous fishes are divided into elasmobranchs (sharks, rays and skates) and chimaeras, and the lack of established whole-genome sequences for the former has prevented our understanding of early vertebrate evolution and the unique phenotypes of elasmobranchs. Here we present de novo whole-genome assemblies of brownbanded bamboo shark and cloudy catshark and an improved assembly of the whale shark genome. These relatively large genomes (3.8–6.7 Gbp) contain sparse distributions of coding genes and regulatory elements and exhibit reduced molecular evolutionary rates. Our thorough genome annotation revealed Hox C genes previously hypothesized to have been lost, as well as distinct gene repertories of opsins and olfactory receptors that would be associated with adaptation to unique underwater niches. We also show the early establishment of the genetic machinery governing mammalian homoeostasis and reproduction at the jawed vertebrate ancestor. This study, supported by genomic, transcriptomic and epigenomic resources, provides a foundation for the comprehensive, molecular exploration of phenotypes unique to sharks and insights into the evolutionary origins of vertebrates.
AB - Modern cartilaginous fishes are divided into elasmobranchs (sharks, rays and skates) and chimaeras, and the lack of established whole-genome sequences for the former has prevented our understanding of early vertebrate evolution and the unique phenotypes of elasmobranchs. Here we present de novo whole-genome assemblies of brownbanded bamboo shark and cloudy catshark and an improved assembly of the whale shark genome. These relatively large genomes (3.8–6.7 Gbp) contain sparse distributions of coding genes and regulatory elements and exhibit reduced molecular evolutionary rates. Our thorough genome annotation revealed Hox C genes previously hypothesized to have been lost, as well as distinct gene repertories of opsins and olfactory receptors that would be associated with adaptation to unique underwater niches. We also show the early establishment of the genetic machinery governing mammalian homoeostasis and reproduction at the jawed vertebrate ancestor. This study, supported by genomic, transcriptomic and epigenomic resources, provides a foundation for the comprehensive, molecular exploration of phenotypes unique to sharks and insights into the evolutionary origins of vertebrates.
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U2 - 10.1038/s41559-018-0673-5
DO - 10.1038/s41559-018-0673-5
M3 - Article
C2 - 30297745
AN - SCOPUS:85054580135
VL - 2
SP - 1761
EP - 1771
JO - Nature Ecology and Evolution
JF - Nature Ecology and Evolution
SN - 2397-334X
IS - 11
ER -