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Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon

BACKGROUND: High throughput next-generation sequencing technology has enabled the collection of genome-wide sequence data and revolutionized single nucleotide polymorphism (SNP) discovery in a broad range of species. When analyzed within a population genomics framework, SNP-based genotypic data may...

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Autores principales: Lemay, Matthew A, Donnelly, David J, Russello, Michael A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3653777/
https://www.ncbi.nlm.nih.gov/pubmed/23651561
http://dx.doi.org/10.1186/1471-2164-14-308
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author Lemay, Matthew A
Donnelly, David J
Russello, Michael A
author_facet Lemay, Matthew A
Donnelly, David J
Russello, Michael A
author_sort Lemay, Matthew A
collection PubMed
description BACKGROUND: High throughput next-generation sequencing technology has enabled the collection of genome-wide sequence data and revolutionized single nucleotide polymorphism (SNP) discovery in a broad range of species. When analyzed within a population genomics framework, SNP-based genotypic data may be used to investigate questions of evolutionary, ecological, and conservation significance in natural populations of non-model organisms. Kokanee salmon are recently diverged freshwater populations of sockeye salmon (Oncorhynchus nerka) that exhibit reproductive ecotypes (stream-spawning and shore-spawning) in lakes throughout western North America and northeast Asia. Current conservation and management strategies may treat these ecotypes as discrete stocks, however their recent divergence and low levels of gene flow make in-season genetic stock identification a challenge. The development of genome-wide SNP markers is an essential step towards fine-scale stock identification, and may enable a direct investigation of the genetic basis of ecotype divergence. RESULTS: We used pooled cDNA samples from both ecotypes of kokanee to generate 750 million base pairs of transcriptome sequence data. These raw data were assembled into 11,074 high coverage contigs from which we identified 32,699 novel single nucleotide polymorphisms. A subset of these putative SNPs was validated using high-resolution melt analysis and Sanger resequencing to genotype independent samples of kokanee and anadromous sockeye salmon. We also identified a number of contigs that were composed entirely of reads from a single ecotype, which may indicate regions of differential gene expression between the two reproductive ecotypes. In addition, we found some evidence for greater pathogen load among the kokanee sampled in stream-spawning habitats, suggesting a possible evolutionary advantage to shore-spawning that warrants further study. CONCLUSIONS: This study provides novel genomic resources to support population genetic and genomic studies of both kokanee and anadromous sockeye salmon, and has the potential to produce markers capable of fine-scale stock assessment. While this RNAseq approach was successful at identifying a large number of new SNP loci, we found that the frequency of alleles present in the pooled transcriptome data was not an accurate predictor of population allele frequencies.
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spelling pubmed-36537772013-05-15 Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon Lemay, Matthew A Donnelly, David J Russello, Michael A BMC Genomics Research Article BACKGROUND: High throughput next-generation sequencing technology has enabled the collection of genome-wide sequence data and revolutionized single nucleotide polymorphism (SNP) discovery in a broad range of species. When analyzed within a population genomics framework, SNP-based genotypic data may be used to investigate questions of evolutionary, ecological, and conservation significance in natural populations of non-model organisms. Kokanee salmon are recently diverged freshwater populations of sockeye salmon (Oncorhynchus nerka) that exhibit reproductive ecotypes (stream-spawning and shore-spawning) in lakes throughout western North America and northeast Asia. Current conservation and management strategies may treat these ecotypes as discrete stocks, however their recent divergence and low levels of gene flow make in-season genetic stock identification a challenge. The development of genome-wide SNP markers is an essential step towards fine-scale stock identification, and may enable a direct investigation of the genetic basis of ecotype divergence. RESULTS: We used pooled cDNA samples from both ecotypes of kokanee to generate 750 million base pairs of transcriptome sequence data. These raw data were assembled into 11,074 high coverage contigs from which we identified 32,699 novel single nucleotide polymorphisms. A subset of these putative SNPs was validated using high-resolution melt analysis and Sanger resequencing to genotype independent samples of kokanee and anadromous sockeye salmon. We also identified a number of contigs that were composed entirely of reads from a single ecotype, which may indicate regions of differential gene expression between the two reproductive ecotypes. In addition, we found some evidence for greater pathogen load among the kokanee sampled in stream-spawning habitats, suggesting a possible evolutionary advantage to shore-spawning that warrants further study. CONCLUSIONS: This study provides novel genomic resources to support population genetic and genomic studies of both kokanee and anadromous sockeye salmon, and has the potential to produce markers capable of fine-scale stock assessment. While this RNAseq approach was successful at identifying a large number of new SNP loci, we found that the frequency of alleles present in the pooled transcriptome data was not an accurate predictor of population allele frequencies. BioMed Central 2013-05-07 /pmc/articles/PMC3653777/ /pubmed/23651561 http://dx.doi.org/10.1186/1471-2164-14-308 Text en Copyright © 2013 Lemay et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Lemay, Matthew A
Donnelly, David J
Russello, Michael A
Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon
title Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon
title_full Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon
title_fullStr Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon
title_full_unstemmed Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon
title_short Transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon
title_sort transcriptome-wide comparison of sequence variation in divergent ecotypes of kokanee salmon
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3653777/
https://www.ncbi.nlm.nih.gov/pubmed/23651561
http://dx.doi.org/10.1186/1471-2164-14-308
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