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

Abstract

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.

Keywords: Cold shock; Cytoskeleton; High hydrostatic pressure; Microtubule; Positive selection.

Fig. 1

Photograph of an individual of the deep-sea fish Aldrovandia affinis. Aldrovandia affinis being captured from the Sakai hydrothermal vent field of the Okinawa Trough (21°31.4749’ N, 126°59.021′ E) at a depth of 1550 m by the remotely operated vehicle Kaiko (Dive Number #676)

Fig. 2

Gene ontology distribution for the cellular component, molecular function and biological process of Aldrovandia affinis

Fig. 3

Maximum-likelihood phylogenetic tree for Aldrovandia affinis and shallow-water fish. The shallow-water fish species include the cave fish Astyanax mexicanus, the cod fish Gadus morhua, the spotted gar Lepisosteus oculatus, the medaka fish Oryzias latipes, the tetraodon fish Tetraodon nigroviridis, the platy fish Xiphophorus maculatus and the coelacanth Latimeria chalumnae (class Sarcopterygii; serving as the outgroup). This tree was constructed based on the substitution model of PROGAMMA + GTR with 100 bootstraps

Fig. 4

Gene families shared by Aldrovandia affinis, Astyanax mexicanus, Gadus morhua and Xiphophorus maculatus

Fig. 5

Partial alignment of positively selected genes. Double asterisks indicate that the amino acids in Aldrovandia affinis have a BEB posterior probability higher than 95% and a single asterisk indicates that the sites have a posterior probability between 90% and 95%. (Aa: Aldrovandia affinis; Am: Astyanax mexicanus; Gm: Gadus morhua and Xm: Xiphophorus maculatus)