De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

• Published in: BMC Genomics
• Main Authors: Madeleine Carruthers, Andrey A. Yurchenko, Julian J. Augley, Colin E. Adams, Pawel Herzyk, Kathryn R. Elmer
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2018
• Subjects: Salmonids; Transcriptome; RNA-seq; Annotation; BLAST; Gene Ontology (GO) analysis; Biotechnology; TP248.13-248.65; Genetics; QH426-470; Arctic; Arctic charr; Atlantic salmon; Salmo salar; Salvelinus alpinus
• Online Access: https://doi.org/10.1186/s12864-017-4379-x; https://doaj.org/article/9992c88da8c04edfa3a008ae3ba954c9

Abstract Background Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are of major interest in fisheries, aquaculture, and conservation research. Improving understanding of the genetic mechanisms underlying traits in these species would significantly progress research in these fields. Here we generate high quality de novo transcriptomes for four salmonid species: Atlantic salmon (Salmo salar), brown trout (Salmo trutta), Arctic charr (Salvelinus alpinus), and European whitefish (Coregonus lavaretus). All species except Atlantic salmon have no reference genome publicly available and few if any genomic studies to date. Results We used paired-end RNA-seq on Illumina to generate high coverage sequencing of multiple individuals, yielding between 180 and 210 M reads per species. After initial assembly, strict filtering was used to remove duplicated, redundant, and low confidence transcripts. The final assemblies consisted of 36,505 protein-coding transcripts for Atlantic salmon, 35,736 for brown trout, 33,126 for Arctic charr, and 33,697 for European whitefish and are made publicly available. Assembly completeness was assessed using three approaches, all of which supported high quality of the assemblies: 1) ~78% of Actinopterygian single-copy orthologs were successfully captured in our assemblies, 2) orthogroup inference identified high overlap in the protein sequences present across all four species (40% shared across all four and 84% shared by at least two), and 3) comparison with the published Atlantic salmon genome suggests that our assemblies represent well covered (~98%) protein-coding transcriptomes. Thorough comparison of the generated assemblies found that 84-90% of transcripts in each assembly were orthologous with at least one of the other three species. We also identified 34-37% of transcripts in each assembly as paralogs. We further compare ...