ArticleBMC genomics2018
De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 61 citations in OpenAlex.
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- Insights into aging mechanisms from comparative genomics in orange and silver roughies.Scientific reports · 2024Article
- A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus.Genetica · 2024Article
- Pseudo-chromosome-length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation.Science China. Life sciences · 2023Article
- The genome of a hadal sea cucumber reveals novel adaptive strategies to deep-sea environments.iScience · 2022Article
- Molecular Mechanisms of the Convergent Adaptation of Bathypelagic and Abyssopelagic Fishes.Genome biology and evolution · 2022Article
- Genetic diversity and connectivity of chemosynthetic cold seep mussels from the U.S. Atlantic margin.BMC ecology and evolution · 2022Article
- Comparative transcriptomic analysis ofiScience · 2022Article
- Trace Elemental Analysis of the Exoskeleton, Leg Muscle, and Gut of Three Hadal Amphipods.Biological trace element research · 2022Article
- Morphological and molecular evolution of hadal amphipod's eggs provides insights into embryogenesis under high hydrostatic pressure.Frontiers in cell and developmental biology · 2022Article
- Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea.PLoS genetics · 2021Article
- The thermal dependence and molecular basis of physiological color change inBiology open · 2021Article
- Transcriptomic Response toFrontiers in genetics · 2021Article
- Convergent Evolution and Structural Adaptation to the Deep Ocean in the Protein-Folding Chaperonin CCTα.Genome biology and evolution · 2020Article
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- Analysis of Natural Selection of Immune Genes inFrontiers in genetics · 2020Article
- Transcriptome of the Southern MuriquiFrontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundHigh hydrostatic pressure and low temperatures make the deep sea a harsh environment for life forms. Actin organization and microtubules assembly, which are essential for intracellular transport and cell motility, can be disrupted by high hydrostatic pressure. High hydrostatic pressure can also damage DNA. Nucleic acids exposed to low temperatures can form secondary structures that hinder genetic information processing. To study how deep-sea creatures adapt to such a hostile environment, one of the most straightforward ways is to sequence and compare their genes with those of their shallow-water relatives.
resultsWe captured an individual of the fish species Aldrovandia affinis, which is a typical deep-sea inhabitant, from the Okinawa Trough at a depth of 1550 m using a remotely operated vehicle (ROV). We sequenced its transcriptome and analyzed its molecular adaptation. We obtained 27,633 protein coding sequences using an Illumina platform and compared them with those of several shallow-water fish species. Analysis of 4918 single-copy orthologs identified 138 positively selected genes in A. affinis, including genes involved in microtubule regulation. Particularly, functional domains related to cold shock as well as DNA repair are exposed to positive selection pressure in both deep-sea fish and hadal amphipod.
conclusionsOverall, we have identified a set of positively selected genes related to cytoskeleton structures, DNA repair and genetic information processing, which shed light on molecular adaptation to the deep sea. These results suggest that amino acid substitutions of these positively selected genes may contribute crucially to the adaptation of deep-sea animals. Additionally, we provide a high-quality transcriptome of a deep-sea fish for future deep-sea studies.
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