Liver transcriptome resources of four commercially exploited teleost species

Abstract

The generation of omic resources is central to develop adequate management strategies for species with economic value. Here, we provide high-coverage RNA-seq datasets of liver tissue (containing between 80,2 and 88,4 million of paired-end reads) from four wildtype teleost species with high commercial value: Trachurus trachurus (TTR; Atlantic horse mackerel), Scomber scombrus (SSC; Atlantic mackerel), Trisopterus luscus (TLU; pout), and Micromesistius poutassou (MPO; blue whiting). A comprehensive assembly pipeline, using de novo single and multi-kmer assembly approaches, produced 64 single high-quality liver transcriptomes - 16 per species. The final assemblies, with N50 values ranging from 2,543-3,700 bp and BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness values between 81.8-86.5% of the Actinopterygii gene set, were subjected to open reading frame (ORF) prediction and functional annotation. Our study provides the first transcriptomic resources for these species and offers valuable tools to evaluate both neutral and selected genetic variation among populations, and to identify candidate genes for environmental adaptation assisting in the investigation of the effects of global changes in fisheries.

Fig. 1

Schematic overview of the study. (a) Geographic coordinates of sampling, photographs of the collected specimens, taxonomy classification and fishery relevance. (b) Experimental setup used to perform RNA extraction and sequencing. (c) Bioinformatics workflow used to post-sequencing dataset analyses.

Fig. 2

Quality FastQC report of post-processing RNA-seq datasets (after Centrifuge (version 1.0.3-beta) cleaning stage). For each species, it is presented the R1 and R2 FastQC reports. (a) Trachurus trachurus; (b) Scomber scombrus; (c) Trisopterus luscu; (d) Micromesistius poutassou.