Chromosome-level genome assembly of hadal snailfish reveals mechanisms of deep-sea adaptation in vertebrates

Reviewer #1 (Public Review):

This manuscript provides an important case study for in-depth research on the adaptability of vertebrates in deep-sea environments. Through analysis of the genomic data of the hadal snailfish, the authors found that this species may have entered and fully adapted to extreme environments only in the last few million years. Additionally, the study revealed the adaptive features of hadal snailfish in terms of perceptions, circadian rhythms and metabolisms, and the role of ferritin in high-hydrostatic pressure adaptation. Besides, the reads mapping method used to identify events such as gene loss and duplication avoids false positives caused by genome assembly and annotation. This ensures the reliability of the results presented in this manuscript. Overall, these findings provide important clues for a better understanding of deep-sea ecosystems and vertebrate evolution.

Reviewer #2 (Public Review):

This paper presents improved, chromosome level assemblies of the hadal snailfish and Tanaka's snailfish. This is an extension and update of previous work from the group on the hadal snailfish genome. The chromosomal assemblies allow comparisons of genome architecture between a shallow water snailfish and the hadal snailfish to aid inference on timing of colonization of trenches and genomic changes that may have been adaptive for that move.

The comparisons in genomic architecture are compelling: genes present in Tanaka's snailfish that are lost in hadal snailfish that involve whole regions of the genome that no longer map even though adjacent regions do map between the species and across a large evolutionary distance to stickleback. Or genes that are duplicated in hadal snailfish but only appear as single copy in other fishes. The paper focuses on genes in the eye, in hearing, in circadian rhythms, and in ROS scavaging. These are all functions that could play a role in adapting to the hadal environment.

The genomic comparisons all seem sound. Stylistically I would prefer if the authors could introduce the gene product and protein function every time they introduce a gene locus. They introduce a gene and general function, but don't usually note what the protein encoded by the gene is and what it's specific function is.

I found the paper generally well written, and the data compelling and creatively displayed. There is room for improvement in places where additional details could be added (e.g. the choice to show expression data as TPMs) and the writing could be clarified.