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

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.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4720-z) contains supplementary material, which is available to authorized users.

Convergent evolution and structural adaptation to the deep ocean in the protein folding chaperonin CCTα

“…Furthermore, an additional ribosomal protein was positively selected in Ophiodermatidae and two transcription factors were positively selected in Amphiuridae. Previous studies have shown that several genes involved in genetic information processing such as protein folding, transcription or translation (including ribosomal proteins) were positively selected in the hadal (>6000m depth) amphipod Hirondella gigas (Lan et al 2017), in the bathyal (200-3000m depth) fish Aldrovandia affinis (Lan et al 2018) and in the bathyal barnacle Glyptelasma gigas (Gan et al 2020). Taken together, these and previous results indicate that adaptations in protein biogenesis are essential to deep-sea life.…”

“…Patterns of positive selection have been investigated to uncover genes underlying adaptation to specific environments, including the deep-sea, in non-model species Lan et al 2018;Oliver et al 2010;Sun et al 2017;Zhang et al 2017;Weber et al 2017). Although valuable, these studies typically focus on a single or few shallow-deep transitions in a limited number of species, and thus lack the comparative power to separate confounding effects.…”

Host–Symbiont Interactions in Deep-Sea Chemosymbiotic Vesicomyid Clams: Insights From Transcriptome Sequencing

“…But for the second calculation, the reads of each tissue were separately mapped to the clean transcripts with an open reading frame to quantify the gene-level abundance of each gene in each tissue. In detail, to remove the assembly error, the transcripts with a TPM value below 0.1 were eliminated as in our previous studies (Lan et al, 2017(Lan et al, , 2018. The isoforms with the highest TPM value were retained to predict genes.…”

“…Therefore, the default pairwise similarity threshold of PosiGene (Sahm et al, 2017a) was applied to remove alignment errors, such as orthologs that were pseudo or poorly aligned, and nominal P-values were directly used to identify positively selected genes (Fletcher and Yang, 2010;Sahm et al, 2017b). If the genes had a P-value below 0.05 and amino acid sites with a bayes empirical bayes (BEB) probability above 0.9, they were regarded as the positively selected genes (Lan et al, 2017(Lan et al, , 2018Sun et al, 2017). For the positive selection analysis of symbionts, the settings of PosiGene was -target_species = symbiont Candidatus Vesicomyosocius okutanii, -anchor species = symbiont Candidatus Vesicomyosocius okutanii, -min_seq_num = 3, -min_omega = 0, -min_site_signifance = 0.9.…”

Comparative transcriptomic analysis of deep- and shallow-water barnacle species (Cirripedia, Poecilasmatidae) provides insights into deep-sea adaptation of sessile crustaceans

“…Conditions on the deep-sea floor are poorly known but generally are considered too harsh for the survival of most organisms, e.g., high hydrostatic pressure, darkness, hypoxia, low temperature, and limited food availability [1][2][3][4][5]. However, a macrofauna consisting of a growing range of newly discovered animals adapted to deep-sea habitats has been reported, including crustaceans [6][7][8], polychaetes [9,10], fishes [11,12], and mollusks [13,14]. Various mechanisms have adapted them for survival in deep-sea environments: e.g., squat lobsters and mussels have developed chemoautotrophic systems of symbiotic bacteria for inhabiting hydrothermal vents and cold seeps in the seafloor [15][16][17]; and snailfish have evolved special morphological and physiological characters to survive and thrive in the hadal zone [12].…”