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

Abstract

Southern hake (Merluccius australis) is an ecological and economically important demersal fish in Chile and Argentina. Notwithstanding, genetic resource for genetic or ecological studies on this species are scarce. Consequently, here we present transcriptome sequencing results (RNA-Seq) for spleen and liver tissues with the 454 FLX titanium platform. The de novo transcriptome assembly generated 10,314 unigenes, with an average length of 510 bp, N50 of 572 bp and 3171 annotated sequences. A specific Gadiform BLAST search, with focus on immune genes, showed 186 (56%) genes homologous to those of Atlantic cod. A total of 2302 microsatellites were detected in 1687 unigenes and 741 presented adequate flanking sequences for primer design. In total, these potential molecular markers and transcriptome characterization represent an important resource for genetic and ecological studies on southern hake.

De novo Assembly and Characterization of Patagonian Toothfish Transcriptome and Develop of EST-SSR Markers for Population Genetics

“…Although currently there are several bioinformatics packages that can perform de novo assembly, Trinity package (Grabherr et al, 2011) and superTranscript options were selected, because this produces the best assemblies based on the quality of the assemblies [e.g., fewer transcripts, N50 increased and larger size of transcripts (Amin et al, 2014;Li et al, 2018)]. The metrics of the Patagonian toothfish assembled de novo transcriptome, such as the N50, were similar to those obtained for other transcriptomes encoding non-model fish species (Pérez-Portela et al, 2016;Reyes et al, 2016;Krabbenhoft and Turner, 2018). Moreover, we determined coverage of 78.92% of essential eukaryotic genes (BUSCO) and 83.26% of conserved domain arrangements (DOGMA) and showed that 88.08% of the reads were mapped to the reference transcriptome.…”