De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish

Yi Lan, Jin Sun, Ting Xu, Chong Chen, Renmao Tian, Jianwen QIU, Pei Yuan Qian*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

32 Citations (Scopus)


Background: High 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. Results: We 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. Conclusions: Overall, 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.

Original languageEnglish
Article number394
JournalBMC Genomics
Issue number1
Publication statusPublished - 24 May 2018

Scopus Subject Areas

  • Biotechnology
  • Genetics

User-Defined Keywords

  • Cold shock
  • Cytoskeleton
  • High hydrostatic pressure
  • Microtubule
  • Positive selection


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