Pseudo-chromosome–length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation

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,Pac Bio,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 m TOR signaling pathways.