Chromosome-level genome assemblies of deep-sea eels shed light on the adaptation to the deep-sea environments

It is relatively poorly understood how vertebrates can survive and thrive in deep-sea environments (depths below 3,000 m that are characterized by high hydrostatic pressures, low temperatures, and sparse food resources). In this study, we compared the genomes of two deep-sea eels (Ilyophis sp1 and Ilyophis sp2 living below 3,000 m) against those of shallow-water closely related eels and other teleosts to examine the genetic bases of their adaptations to the deep-sea. Phylogenetic analyses showed that these two deep-sea eels diverged from European eels ~111.9 million years ago (Mya) and likely evolved into two separate groups ~3.59 Mya. Comparative genomic analyses reveal that: (1) the positively selected cytoskeleton gene TUBGCP3 and the expanded family MLC1 may improve the cytoskeleton stability under high pressure; (2) the changes in protein sequences of Acox1 may enhance cell membrane fluidity and maintain transport activity under high pressure; (3) functional mutation of the translation gene HARS in deep-sea eels may change its translation ability to resist the influence of low temperature on translation-related enzymes; and (4) energy metabolism under a food-limited environment may be increased by expanded and positively selected gene enrichment in AMPK and mTOR signaling pathways. Our results provide insights into the underlying genetic basis and molecular evolution of deep-sea vertebrates.