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

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...

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Main Authors:	Madeleine Carruthers, Andrey A. Yurchenko, Julian J. Augley, Colin E. Adams, Pawel Herzyk, Kathryn R. Elmer
Format:	Article
Language:	English
Published:	BioMed Central 2018-01-01
Series:	BMC Genomics
Subjects:	Salmonids Transcriptome RNA-seq Annotation BLAST Gene Ontology (GO) analysis
Online Access:	http://link.springer.com/article/10.1186/s12864-017-4379-x

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spelling	doaj-art-9992c88da8c04edfa3a008ae3ba954c92018-08-16T00:49:32ZengBioMed CentralBMC Genomics1471-21642018-01-0119111710.1186/s12864-017-4379-xDe novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish speciesMadeleine Carruthers0Andrey A. Yurchenko1Julian J. Augley2Colin E. Adams3Pawel Herzyk4Kathryn R. Elmer5Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of GlasgowInstitute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of GlasgowGlasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of GlasgowInstitute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of GlasgowGlasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of GlasgowInstitute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of GlasgowAbstract 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.http://link.springer.com/article/10.1186/s12864-017-4379-xSalmonidsTranscriptomeRNA-seqAnnotationBLASTGene Ontology (GO) analysis
institution	Open Data Bank
collection	Open Access Journals
building	Directory of Open Access Journals
language	English
format	Article
author	Madeleine Carruthers Andrey A. Yurchenko Julian J. Augley Colin E. Adams Pawel Herzyk Kathryn R. Elmer
spellingShingle	Madeleine Carruthers Andrey A. Yurchenko Julian J. Augley Colin E. Adams Pawel Herzyk Kathryn R. Elmer De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species BMC Genomics Salmonids Transcriptome RNA-seq Annotation BLAST Gene Ontology (GO) analysis
author_facet	Madeleine Carruthers Andrey A. Yurchenko Julian J. Augley Colin E. Adams Pawel Herzyk Kathryn R. Elmer
author_sort	Madeleine Carruthers
title	De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species
title_short	De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species
title_full	De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species
title_fullStr	De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species
title_full_unstemmed	De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species
title_sort	de novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species
publisher	BioMed Central
series	BMC Genomics
issn	1471-2164
publishDate	2018-01-01
description	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 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.
topic	Salmonids Transcriptome RNA-seq Annotation BLAST Gene Ontology (GO) analysis
url	http://link.springer.com/article/10.1186/s12864-017-4379-x
_version_	1612696522075406336

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

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