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

Carruthers, M., Yurchenko, A. A., Augley, J. J., Adams, C. E. , Herzyk, P. and Elmer, K. R. (2018) De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species. BMC Genomics, 19, 32. (doi: 10.1186/s12864-017-4379-x) (PMID:29310597) (PMCID:PMC5759245)

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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 completeness and annotation statistics of our new assemblies to available related species. Conclusion: New, high-confidence protein-coding transcriptomes were generated for four ecologically and economically important species of salmonids. This offers a high quality pipeline for such complex genomes, represents a valuable contribution to the existing genomic resources for these species and provides robust tools for future investigation of gene expression and sequence evolution in these and other salmonid species.

Item Type:Articles
Additional Information:A correction to this article is available at
Glasgow Author(s) Enlighten ID:Carruthers, Madeleine and Augley, Dr Julian and Herzyk, Dr Pawel and Elmer, Professor Kathryn and Adams, Professor Colin and Yurchenko, Dr Andrey
Authors: Carruthers, M., Yurchenko, A. A., Augley, J. J., Adams, C. E., Herzyk, P., and Elmer, K. R.
College/School:College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
Journal Name:BMC Genomics
Publisher:Biomed Central
ISSN (Online):1471-2164
Copyright Holders:Copyright © 2018 The Authors
First Published:First published in BMC Genomics 19:32
Publisher Policy:Reproduced under a Creative Commons License
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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
621711The role of gene expression in phenotypic plasticity and adaptive divergence (ISSF Catalyst)Kathryn ElmerWellcome Trust (WELLCOTR)097821/Z/11/ZRI BIODIVERSITY ANIMAL HEALTH & COMPMED
612331GEN ECOL ADAPT: Adaptation genomics of trophic polymorphismKathryn ElmerEuropean Commission (EC)321999RI BIODIVERSITY ANIMAL HEALTH & COMPMED
5887510BBSRC Doctoral Training Partnership 2012George BaillieBiotechnology and Biological Sciences Research Council (BBSRC)BB/J013854/1MVLS COLLEGE SENIOR MANAGEMENT