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Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus).

Identifieur interne : 001B64 ( Main/Exploration ); précédent : 001B63; suivant : 001B65

Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus).

Auteurs : A. Geraldes [Canada] ; C A Hefer [Canada] ; A. Capron [Canada] ; N. Kolosova [Canada] ; F. Martinez-Nu Ez [Canada] ; R Y Soolanayakanahally [Canada] ; B. Stanton [États-Unis] ; R D Guy [Canada] ; S D Mansfield [Canada] ; C J Douglas [Canada] ; Q C B. Cronk [Canada]

Source :

RBID : pubmed:25728270

Descripteurs français

English descriptors

Abstract

All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of 'turnover' of sex-determination regions in animals. We performed whole-genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ~100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex-associated SNPs revealed this to be an XY sex-determining system. Estimated divergence times of X and Y haplotype sequences (6-7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.

DOI: 10.1111/mec.13126
PubMed: 25728270


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<div type="abstract" xml:lang="en">All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of 'turnover' of sex-determination regions in animals. We performed whole-genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ~100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex-associated SNPs revealed this to be an XY sex-determining system. Estimated divergence times of X and Y haplotype sequences (6-7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past. </div>
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<ELocationID EIdType="doi" ValidYN="Y">10.1111/mec.13126</ELocationID>
<Abstract>
<AbstractText>All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of 'turnover' of sex-determination regions in animals. We performed whole-genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ~100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex-associated SNPs revealed this to be an XY sex-determining system. Estimated divergence times of X and Y haplotype sequences (6-7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past. </AbstractText>
<CopyrightInformation>© 2015 John Wiley & Sons Ltd.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Geraldes</LastName>
<ForeName>A</ForeName>
<Initials>A</Initials>
<AffiliationInfo>
<Affiliation>Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Hefer</LastName>
<ForeName>C A</ForeName>
<Initials>CA</Initials>
<AffiliationInfo>
<Affiliation>Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Capron</LastName>
<ForeName>A</ForeName>
<Initials>A</Initials>
<AffiliationInfo>
<Affiliation>Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Kolosova</LastName>
<ForeName>N</ForeName>
<Initials>N</Initials>
<AffiliationInfo>
<Affiliation>Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Martinez-Nuñez</LastName>
<ForeName>F</ForeName>
<Initials>F</Initials>
<AffiliationInfo>
<Affiliation>Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Soolanayakanahally</LastName>
<ForeName>R Y</ForeName>
<Initials>RY</Initials>
<AffiliationInfo>
<Affiliation>Agroforestry Development Centre, Agriculture and Agri-Food Canada, Indian Head, SK, S0G 2K0, Canada.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Stanton</LastName>
<ForeName>B</ForeName>
<Initials>B</Initials>
<AffiliationInfo>
<Affiliation>Greenwood Resources, Portland, OR, 97201, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Guy</LastName>
<ForeName>R D</ForeName>
<Initials>RD</Initials>
<AffiliationInfo>
<Affiliation>Department of Forest and Conservation Sciences, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Mansfield</LastName>
<ForeName>S D</ForeName>
<Initials>SD</Initials>
<AffiliationInfo>
<Affiliation>Department of Wood Science, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Douglas</LastName>
<ForeName>C J</ForeName>
<Initials>CJ</Initials>
<AffiliationInfo>
<Affiliation>Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Cronk</LastName>
<ForeName>Q C B</ForeName>
<Initials>QC</Initials>
<AffiliationInfo>
<Affiliation>Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList>
<PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic">
<Year>2015</Year>
<Month>04</Month>
<Day>02</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo>
<Country>England</Country>
<MedlineTA>Mol Ecol</MedlineTA>
<NlmUniqueID>9214478</NlmUniqueID>
<ISSNLinking>0962-1083</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<CommentsCorrectionsList>
<CommentsCorrections RefType="CommentIn">
<RefSource>Mol Ecol. 2015 Jul;24(13):3217-9</RefSource>
<PMID Version="1">26113024</PMID>
</CommentsCorrections>
</CommentsCorrectionsList>
<MeshHeadingList>
<MeshHeading>
<DescriptorName UI="D032461" MajorTopicYN="Y">Chromosomes, Plant</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D005787" MajorTopicYN="N">Gene Frequency</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D056726" MajorTopicYN="N">Genetic Association Studies</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D056426" MajorTopicYN="N">Genetic Loci</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D015810" MajorTopicYN="N">Linkage Disequilibrium</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D012730" MajorTopicYN="Y">Sex Chromosomes</DescriptorName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM">
<Keyword MajorTopicYN="N">SNP</Keyword>
<Keyword MajorTopicYN="N">XY sex-determining system</Keyword>
<Keyword MajorTopicYN="N">gender</Keyword>
<Keyword MajorTopicYN="N">genomewide association studies</Keyword>
<Keyword MajorTopicYN="N">methylation</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="received">
<Year>2014</Year>
<Month>12</Month>
<Day>12</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised">
<Year>2015</Year>
<Month>02</Month>
<Day>15</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted">
<Year>2015</Year>
<Month>02</Month>
<Day>19</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez">
<Year>2015</Year>
<Month>3</Month>
<Day>3</Day>
<Hour>6</Hour>
<Minute>0</Minute>
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<PubMedPubDate PubStatus="pubmed">
<Year>2015</Year>
<Month>3</Month>
<Day>3</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>2015</Year>
<Month>9</Month>
<Day>29</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">25728270</ArticleId>
<ArticleId IdType="doi">10.1111/mec.13126</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
<affiliations>
<list>
<country>
<li>Canada</li>
<li>États-Unis</li>
</country>
<region>
<li>Colombie-Britannique </li>
</region>
<settlement>
<li>Vancouver</li>
</settlement>
<orgName>
<li>Université de la Colombie-Britannique</li>
</orgName>
</list>
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<country name="Canada">
<region name="Colombie-Britannique ">
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<name sortKey="Capron, A" sort="Capron, A" uniqKey="Capron A" first="A" last="Capron">A. Capron</name>
<name sortKey="Cronk, Q C B" sort="Cronk, Q C B" uniqKey="Cronk Q" first="Q C B" last="Cronk">Q C B. Cronk</name>
<name sortKey="Douglas, C J" sort="Douglas, C J" uniqKey="Douglas C" first="C J" last="Douglas">C J Douglas</name>
<name sortKey="Guy, R D" sort="Guy, R D" uniqKey="Guy R" first="R D" last="Guy">R D Guy</name>
<name sortKey="Hefer, C A" sort="Hefer, C A" uniqKey="Hefer C" first="C A" last="Hefer">C A Hefer</name>
<name sortKey="Kolosova, N" sort="Kolosova, N" uniqKey="Kolosova N" first="N" last="Kolosova">N. Kolosova</name>
<name sortKey="Mansfield, S D" sort="Mansfield, S D" uniqKey="Mansfield S" first="S D" last="Mansfield">S D Mansfield</name>
<name sortKey="Martinez Nu Ez, F" sort="Martinez Nu Ez, F" uniqKey="Martinez Nu Ez F" first="F" last="Martinez-Nu Ez">F. Martinez-Nu Ez</name>
<name sortKey="Soolanayakanahally, R Y" sort="Soolanayakanahally, R Y" uniqKey="Soolanayakanahally R" first="R Y" last="Soolanayakanahally">R Y Soolanayakanahally</name>
</country>
<country name="États-Unis">
<noRegion>
<name sortKey="Stanton, B" sort="Stanton, B" uniqKey="Stanton B" first="B" last="Stanton">B. Stanton</name>
</noRegion>
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</record>

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