Transcriptomics and Comparative Analysis of Three Antarctic Notothenioid Fishes

Abstract

For the past 10 to 13 million years, Antarctic notothenioid fish have undergone extraordinary periods of evolution and have adapted to a cold and highly oxygenated Antarctic marine environment. While these species are considered an attractive model with which to study physiology and evolutionary adaptation, they are poorly characterized at the molecular level, and sequence information is lacking. The transcriptomes of the Antarctic fishes Notothenia coriiceps, Chaenocephalus aceratus, and Pleuragramma antarcticum were obtained by 454 FLX Titanium sequencing of a normalized cDNA library. More than 1,900,000 reads were assembled in a total of 71,539 contigs. Overall, 40% of the contigs were annotated based on similarity to known protein or nucleotide sequences, and more than 50% of the predicted transcripts were validated as full-length or putative full-length cDNAs. These three Antarctic fishes shared 663 genes expressed in the brain and 1,557 genes expressed in the liver. In addition, these cold-adapted fish expressed more Ub-conjugated proteins compared to temperate fish; Ub-conjugated proteins are involved in maintaining proteins in their native state in the cold and thermally stable Antarctic environments. Our transcriptome analysis of Antarctic notothenioid fish provides an archive for future studies in molecular mechanisms of fundamental genetic questions, and can be used in evolution studies comparing other fish.

De Novo Assembly and Analysis of the Testes Transcriptome from the Menhaden, Bervoortia tyrannus

“…By merging the Blast2GO annotations with the InterProScan results, 70,919 contigs out of 254,446 (27.87%) were assigned at least one GO term (Table 3). These results are comparable to other annotation efforts in non-model fish studies that utilized the de novo assembly approach [9,13,47,50]. Again, it should be taken into consideration that the limited number of publically available fish genomes inhibits the overall successful rate of annotating non-model fish [49].…”

“…Based on a phylogenetic tree analysis with the eleven publically available fish genomes on Ensembl, it was determined that zebrafish along with Mexican tetra were the closest related genera to menhaden. The BLASTX alignments for the menhaden against the zebrafish (42.56%) and Mexican tetra (41.34%) yielded analogous results with other non-model fish de novo transcriptome assembly studies signifying that the assemblies are reliable [9,12,13,47,48]. The low number of hits for both zebrafish and Mexican tetra could be due the presence of menhaden-specific contigs, as menhaden belong to separate clades in the phylogenetic tree ( Figure 2).…”

“…In this study, the percentage of matches for the menhaden was 46.23%. This percentage is comparable to other non-model fish de novo assemblies, further establishing the credibility of the assemblies [9,12,13,47,50]. It should be noted that the number of matches is affected by the amount of available sequence data, and there is a limited number of publically available fish genomes to contribute to the overall success of the annotation [49].…”

De novo Assembly, Characterization and Functional Annotation of Southern Hake (Merluccius australis) Transcriptome

“…Of these, approximately 75% (2401) of the unigenes had significant BLAST matches with fish species, such as Nile tilapia, zebrafish, Atlantic salmon and spotted green pufferfish, among others ( Table 3). The remaining 7143 (69.26%) unigenes resulted in non-significant hits, a result similar to other studies of non-model fish species (Shin et al, 2012;Qian et al, 2014). Normally this happens either due to incomplete gene information on non-model species in public database or because sequences of non-coding RNAs among the unigenes are included (Hou et al, 2011).…”

Head Kidney Transcriptome Analysis and Characterization for the Sub-Antarctic Notothenioid Fish Eleginops maclovinus

“…Genetic analyses of Antarctic fish are possible due to an availability of cDNA sequence libraries for various species, including Dissostichus mawsoni (Nototheniidae) [6], Harpagifer antarcticus (Harpagiferidae) [7], Chionodraco hamatus (Channichthyidae) [8], Trematomus bernacchii [9,10], Pagothenia borchgrevinki [11], Chaenocephalus aceratus (Channichthyidae), Notothenia coriiceps, and Pleuragramma antarcticum (Nototheniidae) [12,13]. To date, relatively little sequence information is available for E. maclovinus [2], despite the physiological characteristics that consider it an eurythermic, euryhaline and stenobatic species [14], with a hermaphrodite type of reproduction (unique among the notothenioids) [15] and with a relevant participation in the transmission of diseases that affect aquaculture as the Piscirickettsiosis [16].…”