Abstract
High hydrostatic pressure, low temperature, and scarce food supply are the major factors that limit the survival of vertebrates in extreme deep-sea environments. Here, we constructed a high-quality genome of the deep-sea Muddy arrowtooth eel (MAE, Ilyophis brunneus, captured below a depth of 3,500 m) by using Illumina, PacBio, and Hi-C sequencing. We compare it against those of shallow-water eel and other outgroups to explore the genetic basis that underlies the adaptive evolution to deep-sea biomes. The MAE genome was estimated to be 1.47 Gb and assembled into 14 pseudo-chromosomes. Phylogenetic analyses indicated that MAE diverged from its closely related shallow-sea species, European eel, ∼111.9 Mya and experienced a rapid evolution. The genome evolutionary analyses primarily revealed the following: (i) under high hydrostatic pressure, the positively selected gene TUBGCP3 and the expanded family MLC1 may improve the cytoskeleton stability; ACOX1 may enhance the fluidity of cell membrane and maintain transport activity; the expansion of ABCC12 gene family may enhance the integrity of DNA; (ii) positively selected HARS likely maintain the transcription ability at low temperatures; and (iii) energy metabolism under a food-limited environment may be increased by expanded and positively selected genes in AMPK and mTOR signaling pathways.
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Raw sequence reads are deposited at NCBI under the project accession number PRJNA792465. The genome assembly files are under accession numbers JAKUDJ000000000.
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Acknowledgements
This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB42000000, XDB06010105), the National Key Research and Development Program of China (2018YFC0309800), the National Natural Science Foundation of China (41876179), and the Major scientific and technological projects of Hainan Province (2019PT03) to S.P.H.
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Chen, J., Zeng, H., Lv, W. et al. Pseudo-chromosome—length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation. Sci. China Life Sci. 66, 1379–1391 (2023). https://doi.org/10.1007/s11427-022-2251-8
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DOI: https://doi.org/10.1007/s11427-022-2251-8