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The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next‐generation sequencing

Identifieur interne : 001263 ( Istex/Corpus ); précédent : 001262; suivant : 001264

The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next‐generation sequencing

Auteurs : Julie Jeukens ; Sébastien Renaut ; Jérôme St-Cyr ; Arne W. Nolte ; Louis Bernatchez

Source :

RBID : ISTEX:ED617AF2E1C5CE6C891D3CCF8FF62732F0A14BCC

English descriptors

Abstract

Gene expression divergence is one of the mechanisms thought to be involved in the emergence of incipient species. Next‐generation sequencing has become an extremely valuable tool for the study of this process by allowing whole transcriptome sequencing, or RNA‐Seq. We have conducted a 454 GS‐FLX pyrosequencing experiment to refine our understanding of adaptive divergence between dwarf and normal lake whitefish species (Coregonus clupeaformis spp.). The objectives were to: (i) investigate transcriptomic divergence as measured by liver RNA‐Seq; (ii) test the correlation between divergence in expression and sequence polymorphism; and (iii) investigate the extent of allelic imbalance. We also compared the results of RNA‐seq with those of a previous microarray study performed on the same fish. Following de novo assembly, results showed that normal whitefish overexpressed more contigs associated with protein synthesis while dwarf fish overexpressed more contigs related to energy metabolism, immunity and DNA replication and repair. Moreover, 63 SNPs showed significant allelic imbalance, and this phenomenon prevailed in the recently diverged dwarf whitefish. Results also showed an absence of correlation between gene expression divergence as measured by RNA‐Seq and either polymorphism rate or sequence divergence between normal and dwarf whitefish. This study reiterates an important role for gene expression divergence, and provides evidence for allele‐specific expression divergence as well as evolutionary decoupling of regulatory and coding sequences in the adaptive divergence of normal and dwarf whitefish. It also demonstrates how next‐generation sequencing can lead to a more comprehensive understanding of transcriptomic divergence in a young species pair.

Url:
DOI: 10.1111/j.1365-294X.2010.04934.x

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ISTEX:ED617AF2E1C5CE6C891D3CCF8FF62732F0A14BCC

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<correspondenceTo>Julie Jeukens, Fax: 1 418 656 7176; E‐mail:
<email>julie.jeukens.1@ulaval.ca</email>
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<unparsedEditorialHistory>Received 7 June 2010; revision received 18 August 2010; accepted 29 August 2010</unparsedEditorialHistory>
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<titleGroup>
<title type="main">The transcriptomics of sympatric dwarf and normal lake whitefish (
<i>Coregonus clupeaformis</i>
spp., Salmonidae) divergence as revealed by next‐generation sequencing</title>
<title type="shortAuthors">J. JEUKENS
<i>ET AL.</i>
</title>
<title type="short">TRANSCRIPTOMIC DIVERGENCE IN LAKE WHITEFISH</title>
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<keyword xml:id="k1">454 sequencing</keyword>
<keyword xml:id="k2">adaptive divergence</keyword>
<keyword xml:id="k3">allelic imbalance</keyword>
<keyword xml:id="k4">Coregonus</keyword>
<keyword xml:id="k5">gene expression</keyword>
<keyword xml:id="k6">RNA‐Seq</keyword>
<keyword xml:id="k7">speciation</keyword>
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<p>
<b>Table S1</b>
Functional gene categories</p>
<p>
<b>Table S2</b>
<i>De novo</i>
contigs from RNA‐Seq of the whitefish liver transcriptome</p>
<p>
<b>Table S3</b>
Representation of functional gene categories in the whitefish liver transcriptome</p>
<p>
<b>Table S4</b>
Candidate genes for allelic imbalance (AI)</p>
<p>
<b>Fig. S1</b>
Scatter plot of gene expression divergence measured by RNA‐Seq and microarray.</p>
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<p>Gene expression divergence is one of the mechanisms thought to be involved in the emergence of incipient species. Next‐generation sequencing has become an extremely valuable tool for the study of this process by allowing whole transcriptome sequencing, or RNA‐Seq. We have conducted a 454 GS‐FLX pyrosequencing experiment to refine our understanding of adaptive divergence between dwarf and normal lake whitefish species (
<i>Coregonus clupeaformis</i>
spp.). The objectives were to: (i) investigate transcriptomic divergence as measured by liver RNA‐Seq; (ii) test the correlation between divergence in expression and sequence polymorphism; and (iii) investigate the extent of allelic imbalance. We also compared the results of RNA‐seq with those of a previous microarray study performed on the same fish. Following
<i>de novo</i>
assembly, results showed that normal whitefish overexpressed more contigs associated with protein synthesis while dwarf fish overexpressed more contigs related to energy metabolism, immunity and DNA replication and repair. Moreover, 63 SNPs showed significant allelic imbalance, and this phenomenon prevailed in the recently diverged dwarf whitefish. Results also showed an absence of correlation between gene expression divergence as measured by RNA‐Seq and either polymorphism rate or sequence divergence between normal and dwarf whitefish. This study reiterates an important role for gene expression divergence, and provides evidence for allele‐specific expression divergence as well as evolutionary decoupling of regulatory and coding sequences in the adaptive divergence of normal and dwarf whitefish. It also demonstrates how next‐generation sequencing can lead to a more comprehensive understanding of transcriptomic divergence in a young species pair.</p>
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<title>The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next‐generation sequencing</title>
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<title>TRANSCRIPTOMIC DIVERGENCE IN LAKE WHITEFISH</title>
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<title>The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next‐generation sequencing</title>
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<namePart type="given">JULIE</namePart>
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<affiliation>Institut de Biologie Intégrative et des Systèmes (IBIS), Québec‐Océan, Université Laval, 1030 av. de la médecine, Québec, QC, G1V 0A6, Canada</affiliation>
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<name type="personal">
<namePart type="given">ARNE W.</namePart>
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<roleTerm type="text">author</roleTerm>
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<abstract lang="en">Gene expression divergence is one of the mechanisms thought to be involved in the emergence of incipient species. Next‐generation sequencing has become an extremely valuable tool for the study of this process by allowing whole transcriptome sequencing, or RNA‐Seq. We have conducted a 454 GS‐FLX pyrosequencing experiment to refine our understanding of adaptive divergence between dwarf and normal lake whitefish species (Coregonus clupeaformis spp.). The objectives were to: (i) investigate transcriptomic divergence as measured by liver RNA‐Seq; (ii) test the correlation between divergence in expression and sequence polymorphism; and (iii) investigate the extent of allelic imbalance. We also compared the results of RNA‐seq with those of a previous microarray study performed on the same fish. Following de novo assembly, results showed that normal whitefish overexpressed more contigs associated with protein synthesis while dwarf fish overexpressed more contigs related to energy metabolism, immunity and DNA replication and repair. Moreover, 63 SNPs showed significant allelic imbalance, and this phenomenon prevailed in the recently diverged dwarf whitefish. Results also showed an absence of correlation between gene expression divergence as measured by RNA‐Seq and either polymorphism rate or sequence divergence between normal and dwarf whitefish. This study reiterates an important role for gene expression divergence, and provides evidence for allele‐specific expression divergence as well as evolutionary decoupling of regulatory and coding sequences in the adaptive divergence of normal and dwarf whitefish. It also demonstrates how next‐generation sequencing can lead to a more comprehensive understanding of transcriptomic divergence in a young species pair.</abstract>
<subject lang="en">
<genre>keywords</genre>
<topic>454 sequencing</topic>
<topic>adaptive divergence</topic>
<topic>allelic imbalance</topic>
<topic>Coregonus</topic>
<topic>gene expression</topic>
<topic>RNA‐Seq</topic>
<topic>speciation</topic>
<topic>transcriptome</topic>
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<title>Molecular Ecology</title>
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<genre type="journal">journal</genre>
<note type="content"> Table S1 Functional gene categories Table S2 De novo contigs from RNA‐Seq of the whitefish liver transcriptome Table S3 Representation of functional gene categories in the whitefish liver transcriptome Table S4 Candidate genes for allelic imbalance (AI) Fig. S1 Scatter plot of gene expression divergence measured by RNA‐Seq and microarray. Table S1 Functional gene categories Table S2 De novo contigs from RNA‐Seq of the whitefish liver transcriptome Table S3 Representation of functional gene categories in the whitefish liver transcriptome Table S4 Candidate genes for allelic imbalance (AI) Fig. S1 Scatter plot of gene expression divergence measured by RNA‐Seq and microarray. Table S1 Functional gene categories Table S2 De novo contigs from RNA‐Seq of the whitefish liver transcriptome Table S3 Representation of functional gene categories in the whitefish liver transcriptome Table S4 Candidate genes for allelic imbalance (AI) Fig. S1 Scatter plot of gene expression divergence measured by RNA‐Seq and microarray. Table S1 Functional gene categories Table S2 De novo contigs from RNA‐Seq of the whitefish liver transcriptome Table S3 Representation of functional gene categories in the whitefish liver transcriptome Table S4 Candidate genes for allelic imbalance (AI) Fig. S1 Scatter plot of gene expression divergence measured by RNA‐Seq and microarray. Table S1 Functional gene categories Table S2 De novo contigs from RNA‐Seq of the whitefish liver transcriptome Table S3 Representation of functional gene categories in the whitefish liver transcriptome Table S4 Candidate genes for allelic imbalance (AI) Fig. S1 Scatter plot of gene expression divergence measured by RNA‐Seq and microarray.Supporting Info Item: Supporting info item - Supporting info item - </note>
<identifier type="ISSN">0962-1083</identifier>
<identifier type="eISSN">1365-294X</identifier>
<identifier type="DOI">10.1111/(ISSN)1365-294X</identifier>
<identifier type="PublisherID">MEC</identifier>
<part>
<date>2010</date>
<detail type="volume">
<caption>vol.</caption>
<number>19</number>
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<caption>no.</caption>
<number>24</number>
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