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

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

doi:10.1016/j.cell.2023.02.005

Cited by 46 publications

(47 citation statements)

References 156 publications

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“…S8A-B; table S11), including those related to chitin, cuticular metabolism, regulation of the molting cycle, which are important processes for growth and reproduction in crustaceans. This is notable as renewal of the exoskeleton is unusually frequent and plastic in euphausiids (10,33), and similar expansions were independently detected in the Antarctic krill genome (26). Moreover, we detected expansions of the opsin gene repertoire, which encodes the light-sensitive receptors in ommatidia.…”

Section: Expansion Of Cuticular and Opsin Gene Familiessupporting

confidence: 75%

“…S7, table S10). Compared to the Antarctic krill (26), genes are ~2.5× longer in the Northern krill, consistent with lineage-specific proliferation of retrotransposable elements in its highly repeated introns (fig. S6B).…”

Section: Expansion Of Cuticular and Opsin Gene Familiessupporting

confidence: 56%

“…Using a custom transposable element (TE) library, we find that about 74% of the Northern krill genome is repetitive (Fig. 1C; table S5), similar to the recently characterized Antarctic krill genome (72-92%) (26). While we are unable to classify all TEs, retrotransposons (LINEs+LTRs) outweigh DNA-transposons 4:1, similarly to the American lobster or black tiger shrimp (29,30).…”

Section: A Highly Repeated Genomesupporting

confidence: 52%

“…While we are unable to classify all TEs, retrotransposons (LINEs+LTRs) outweigh DNA-transposons 4:1, similarly to the American lobster or black tiger shrimp (29,30). This differs from the repeatome of the Antarctic krill, which appears to be dominated by DNA-transposons (26), and hints at divergent genome composition and evolution among krill. Furthermore, TE divergence in the Northern krill is comparably unimodal, not indicating multiple bursts of proliferation as seen in the Antarctic krill.…”

Section: A Highly Repeated Genomementioning

confidence: 66%

“…In particular, we lack insight into adaptation in euphausiids, due to their large and repetitive genomes ranging between 11-48 Gb (4-16× the human genome), which have hindered genetic analysis until now (25). The recently published Antarctic krill genome represented a major step forward but revealed extensive genetic homogeneity and limited adaptive variation in that circumpolar and panmictic species (26).…”

mentioning

confidence: 99%

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Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins

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Krill is a vital food source for many marine animals but also strongly impacted by climate change. Genetic adaptation could support populations, but remains uncharacterized. We assembled the 19 Gb Northern krill genome and compared genome-scale variation among 74 specimens from the colder Atlantic Ocean and warmer Mediterranean Sea. The genome is dominated by methylated transposable elements and contains many duplicated genes implied in molting and vision. Analysis of 760 million SNPs indicates extensive homogenizing gene-flow among populations. Nevertheless, we detect extreme divergence across hundreds of genes, governing ecophysiological functions like photoreception, circadian regulation, reproduction and thermal tolerance. Such standing variation may be essential for resilience in zooplankton, necessitating insight into adaptive variation to forecast their roles in future marine ecosystems and support ocean conservation.

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Section: Expansion Of Cuticular and Opsin Gene Familiessupporting

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

Cited by 46 publications

References 156 publications

Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins

Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins

Exploring the enigma: history, present, and future of long non-coding RNAs in cancer

Genome variations in sea cucumbers: Insights from genome survey sequencing and comparative analysis of mitochondrial genomes

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