1
|
Li W, Song J, Tu H, Jiang S, Pan B, Li J, Zhao Y, Chen L, Xu Q. Genome sequencing of Coryphaenoides yaquinae reveals convergent and lineage-specific molecular evolution in deep-sea adaptation. Mol Ecol Resour 2024:e13989. [PMID: 38946220 DOI: 10.1111/1755-0998.13989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/30/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
Abyssal (3501-6500 m) and hadal (>6500 m) fauna evolve under harsh abiotic stresses, characterized by high hydrostatic pressure, darkness and food shortage, providing unique opportunities to investigate mechanisms underlying environmental adaptation. Genomes of several hadal species have recently been reported. However, the genetic adaptation of deep sea species across a broad spectrum of ocean depths has yet to be thoroughly investigated, due to the challenges imposed by collecting the deep sea species. To elucidate the correlation between genetic innovation and vertical distribution, we generated a chromosome-level genome assembly of the macrourids Coryphaenoides yaquinae, which is widely distributed in the abyssal/hadal zone ranging from 3655 to 7259 m in depth. Genomic comparisons among shallow, abyssal and hadal-living species identified idiosyncratic and convergent genetic alterations underlying the extraordinary adaptations of deep-sea species including light perception, circadian regulation, hydrostatic pressure and hunger tolerance. The deep-sea fishes (Coryphaenoides Sp. and Pseudoliparis swirei) venturing into various ocean depths independently have undergone convergent amino acid substitutions in multiple proteins such as rhodopsin 1, pancreatic and duodenal homeobox 1 and melanocortin 4 receptor which are known or verified in zebrafish to be related with vision adaptation and energy expenditure. Convergent evolution events were also identified in heat shock protein 90 beta family member 1 and valosin-containing protein genes known to be related to hydrostatic pressure adaptation specifically in fishes found around the hadal range. The uncovering of the molecular convergence among the deep-sea species shed new light on the common genetic innovations required for deep-sea adaptation by the fishes.
Collapse
Affiliation(s)
- Wenhao Li
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Jie Song
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Huaming Tu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Shouwen Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Binbin Pan
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jiazhen Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Yongpeng Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Liangbiao Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Qianghua Xu
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| |
Collapse
|
2
|
Xu W, Zhu C, Gao X, Wu B, Xu H, Hu M, Zeng H, Gan X, Feng C, Zheng J, Bo J, He LS, Qiu Q, Wang W, He S, Wang K. Chromosome-level genome assembly of hadal snailfish reveals mechanisms of deep-sea adaptation in vertebrates. eLife 2023; 12:RP87198. [PMID: 38134226 PMCID: PMC10746142 DOI: 10.7554/elife.87198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023] Open
Abstract
As the deepest vertebrate in the ocean, the hadal snailfish (Pseudoliparis swirei), which lives at a depth of 6,000-8,000 m, is a representative case for studying adaptation to extreme environments. Despite some preliminary studies on this species in recent years, including their loss of pigmentation, visual and skeletal calcification genes, and the role of trimethylamine N-oxide in adaptation to high-hydrostatic pressure, it is still unknown how they evolved and why they are among the few vertebrate species that have successfully adapted to the deep-sea environment. Using genomic data from different trenches, we found that the hadal snailfish may have entered and fully adapted to such extreme environments only in the last few million years. Meanwhile, phylogenetic relationships show that they spread into different trenches in the Pacific Ocean within a million years. Comparative genomic analysis has also revealed that the genes associated with perception, circadian rhythms, and metabolism have been extensively modified in the hadal snailfish to adapt to its unique environment. More importantly, the tandem duplication of a gene encoding ferritin significantly increased their tolerance to reactive oxygen species, which may be one of the important factors in their adaptation to high-hydrostatic pressure.
Collapse
Affiliation(s)
- Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical UniversityXi'anChina
| | - Chenglong Zhu
- School of Ecology and Environment, Northwestern Polytechnical UniversityXi'anChina
| | - Xueli Gao
- School of Ecology and Environment, Northwestern Polytechnical UniversityXi'anChina
| | - Baosheng Wu
- School of Ecology and Environment, Northwestern Polytechnical UniversityXi'anChina
| | - Han Xu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of SciencesSanyaChina
| | - Mingliang Hu
- School of Ecology and Environment, Northwestern Polytechnical UniversityXi'anChina
| | - Honghui Zeng
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of SciencesWuhanChina
| | - Xiaoni Gan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of SciencesWuhanChina
| | - Chenguang Feng
- School of Ecology and Environment, Northwestern Polytechnical UniversityXi'anChina
| | - Jiangmin Zheng
- School of Ecology and Environment, Northwestern Polytechnical UniversityXi'anChina
| | - Jing Bo
- Institute of Deep-Sea Science and Engineering, Chinese Academy of SciencesSanyaChina
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of SciencesSanyaChina
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical UniversityXi'anChina
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical UniversityXi'anChina
| | - Shunping He
- School of Ecology and Environment, Northwestern Polytechnical UniversityXi'anChina
- Institute of Deep-Sea Science and Engineering, Chinese Academy of SciencesSanyaChina
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of SciencesWuhanChina
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical UniversityXi'anChina
| |
Collapse
|