The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights

Changwei Shao*, Shuai Sun, Kaiqiang Liu, Jiahao Wang, Shuo Li, Qun Liu, Bruce E. Deagle, Inge Seim, Alberto Biscontin, Qian Wang, Xin Liu, So Kawaguchi, Yalin Liu, Simon Jarman, Yue Wang, Hong Yan Wang, Guodong Huang, Jiang Hu, Bo Feng, Cristiano De PittàShanshan Liu, Rui Wang, Kailong Ma, Yiping Ying, Gabrielle Sales, Tao Sun, Xinliang Wang, Yaolei Zhang, Yunxia Zhao, Shanshan Pan, Xiancai Hao, Yang Wang, Jiakun Xu, Bowen Yue, Yanxu Sun, He Zhang, Mengyang Xu, Yuyan Liu, Xiaodong Jia, Jiancheng Zhu, Shufang Liu, Jue Ruan, Guojie Zhang, Huanming Yang, Xun Xu, Jun Wang, Xianyong Zhao, Bettina Meyer, Guangyi Fan

*Corresponding author af dette arbejde

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

33 Citationer (Scopus)
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Abstract

Antarctic krill (Euphausia superba) is Earth’s most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.
OriginalsprogEngelsk
TidsskriftCell
Vol/bind186
Udgave nummer6
Sider (fra-til)1279-1294.e19
Antal sider36
ISSN0092-8674
DOI
StatusUdgivet - 2023

Bibliografisk note

Funding Information:
This study was supported by the National Key R&D Program of China ( 2022YFD2400100 , 2022YFC2807500 ); the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao) (No. 2022QNLM030004 ); the Central Public-interest Scientific Institution Basal Research Fund, CAFS (NO. 2019QY01 ); the Major Science and Technology Innovation Project of Shandong Province ( 2018SDKJ0302 ); the AoShan Talents Cultivation Program Supported by Qingdao National Laboratory for Marine Science and Technology ( 2017ASTCP-ES06 ); the Taishan Scholars Program (NO. tstp20221149 to C.S.); the National Ten-Thousands Talents Special Support Program to C.S.; the Central Public-interest Scientific Institution Basal Research Fund , CAFS (No. 2020TD19 ); the Specially-Appointed Professor Program of Jiangsu Province to I.S.; the Jiangsu Foreign Expert Bureau to I.S.; and the Helmholtz Earth and Environment Research Program "Changing Earth - Sustaining our Future", Topic 6, Subtopic 6.2 to B.M. We appreciate the support from the supercomputing center of Qingdao National Laboratory for Marine Science and Technology. We also appreciate the technical support from China National GeneBank for the library construction and sequencing in Hi-C and whole-genome short reads.

Funding Information:
This study was supported by the National Key R&D Program of China (2022YFD2400100, 2022YFC2807500); the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao) (No. 2022QNLM030004); the Central Public-interest Scientific Institution Basal Research Fund, CAFS (NO.2019QY01); the Major Science and Technology Innovation Project of Shandong Province (2018SDKJ0302); the AoShan Talents Cultivation Program Supported by Qingdao National Laboratory for Marine Science and Technology (2017ASTCP-ES06); the Taishan Scholars Program (NO.tstp20221149 to C.S.); the National Ten-Thousands Talents Special Support Program to C.S.; the Central Public-interest Scientific Institution Basal Research Fund, CAFS (No.2020TD19); the Specially-Appointed Professor Program of Jiangsu Province to I.S.; the Jiangsu Foreign Expert Bureau to I.S.; and the Helmholtz Earth and Environment Research Program "Changing Earth - Sustaining our Future", Topic 6, Subtopic 6.2 to B.M. We appreciate the support from the supercomputing center of Qingdao National Laboratory for Marine Science and Technology. We also appreciate the technical support from China National GeneBank for the library construction and sequencing in Hi-C and whole-genome short reads. C.S. initiated the Antarctic krill genome project. C.S. G.F. and B.M. conceived the study and coordinated the work. C.S. G.F. S.S. K.L. Jiahao Wang, Shuo Li, I.S. X.L. S.J. B.E.D. G.Z. and H.Y. wrote the manuscript with contributions from all other authors. C.S. X.Z. G.F. B.E.D. Yang Wang, S.K. Y.Y. and Shanshan Liu. coordinated and performed sample collection and sequencing. K.L. J.H. Shuo Li, Q.L. Jiahao Wang, T.S. and J.R. performed genome assembly into contigs and genome correction and transcript alignment. Jiahao Wang, K.L. S.S. S.P. and H.Z. performed repeat analysis. Shuo Li, K.L. G.H. B.F. R.W. K.M. X.J. and X.H. undertook transcriptome and genome annotation analysis. S.L. A.B. C.D.P. G.S. Yaolei Zhang, K.L. B.F. J.X. X.Z. Jun Wang, and B.M. conducted comparative genomics analysis. Y.S. B.Y. Q.W. and H.-Y.W. performed the isolation of RNA and DNA and the validation of SNPs by PCR and Sanger sequencing. S.S. B.E.D. S.J. Yaolei Zhang, M.X. Yalin Liu, Yuyan Liu, J.Z. X.W. Shufang Liu; Yue Wang, and X.X. conducted population analysis. The authors declare no competing interests.

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