In 2019, Dr. He Shunping's team from the Deep-Sea Institute of the Chinese Academy of Sciences published a groundbreaking study in the prestigious journal Nature Ecology & Evolution, revealing the genetic basis for extreme environmental adaptation in hadal snailfish (Pseudoliparis swirei). This paper garnered significant international attention and stimulated discussion. Recently, the team, in collaboration with Professor Wang Kun's group from Northwestern Polytechnical University, published another study in the top-tier journal eLife titled "Chromosome-level genome assembly of hadal snailfish reveals mechanisms of deep-sea adaptation in vertebrates." The study provides new insights into the unique adaptation mechanisms of Pseudoliparis swirei, the deepest-living vertebrate known, which inhabits hadal zones between 6,000 and 8,000 meters deep. Through comparative genomics and transcriptomics, the study uncovered the species’ unique adaptations to extreme environments.

The team optimized the genome assembly of Pseudoliparis swirei from the Mariana Trench using ONT long-read sequencing, BGI short-read sequencing, and Hi-C technology, producing a high-quality chromosome-level genome assembly. The genome spans 626.44 Mb and includes 24 chromosomes. The updated assembly filled in 1.26 Mb of previously missing sequences, significantly improving the continuity and completeness of the genome. By analyzing nuclear and mitochondrial genomes across different trench populations, the study revealed that Pseudoliparis swirei diverged from its shallow-water relative, Tanaka's snailfish, approximately 18 million years ago, and from other deep-sea relatives (living at ~1,000 meters) around 9.9 million years ago—coinciding with the formation of the Mariana Trench. The findings suggest that the ancestors of Pseudoliparis swirei initially adapted to ~1,000-meter depths around 9.9 million years ago before gradually colonizing deeper environments. Phylogenetic analyses indicate that they dispersed across Pacific trenches within a few million years.

Fig. 1 Sampling information of hadal snailfish, and phylogenetic relationships and

population structure of resequenced individuals.

The study also explored adaptations to darkness during evolution. Compared to Tanaka's snailfish, Pseudoliparis swirei lost multiple photoreceptor-related genes, and photoreceptor expression varied significantly across depths, indicating reduced reliance on vision. Additionally, genes associated with circadian rhythms were either lost or pseudogenized, suggesting the persistence of a biological clock independent of light regulation.

Fig. 2 Alterations in vision-related genes in hadal snailfish

Fig. 3 Adaptive alterations in hearing-related genes in hadal snailfish

In the absence of light, hearing appears crucial for survival. The team found an increased copy number of the hearing-related gene cldnj, essential for otolith formation, with transcriptomic data showing significantly elevated expression of hearing-related proteins.

Fig. 4 Adaptive changes in the dark environment of hadal snailfish.

Notably, the ferritin-encoding gene fthl27 underwent tandem duplication in the Pseudoliparis swirei genome, resulting in 14 copies. Cellular experiments demonstrated that overexpression of fthl27 significantly reduced intracellular ROS levels and enhanced cell viability, improving resistance to oxidative stress under high hydrostatic pressure. This likely represents a key factor in the snailfish's adaptation to extreme pressure.

Fig. 5 High hydrostatic pressure adaptation of molecules and cells in hadal snailfish.

Overall, this study provides valuable insights into the evolution and adaptation mechanisms of deep-sea fish, enhancing our understanding of how life adapts to extreme environments and offering reference value for the conservation and management of deep-sea biological resources.

Dr. Shunping He from IDSSE of the Chinese Academy of Sciences and Professor Kun Wang from Northwestern Polytechnical University are co-corresponding authors, and Dr. Han Xu from IDSSE is a co-first author of this study.