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Nat Ecol Evol. 2018 Nov;2(11):1761-1771. doi: 10.1038/s41559-018-0673-5. Epub 2018 Oct 8.

Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates.

Author information

1
Phyloinformatics Unit, RIKEN Center for Life Science Technologies (CLST), Kobe, Japan.
2
Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.
3
Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, Japan.
4
The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan.
5
Deutsche Forschungsgemeinschaft (DFG) Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany.
6
Graduate School of Science and Technology, Kwansei Gakuin University, Sanda, Japan.
7
Okinawa Churashima Research Center, Okinawa Churashima Foundation, Okinawa, Japan.
8
Okinawa Churaumi Aquarium, Okinawa, Japan.
9
Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan.
10
Aix-Marseille Université, IBDM, CNRS, Marseille, France.
11
Osaka Aquarium Kaiyukan, Osaka, Japan.
12
Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.
13
Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa, Japan.
14
Phyloinformatics Unit, RIKEN Center for Life Science Technologies (CLST), Kobe, Japan. shigehiro.kuraku@riken.jp.
15
Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan. shigehiro.kuraku@riken.jp.

Abstract

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.

PMID:
30297745
DOI:
10.1038/s41559-018-0673-5

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