Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa.
Identifieur interne : 000125 ( Main/Exploration ); précédent : 000124; suivant : 000126Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa.
Auteurs : Ran Zhou [États-Unis] ; David Macaya-Sanz [États-Unis] ; Jeremy Schmutz [États-Unis] ; Jerry W. Jenkins [États-Unis] ; Gerald A. Tuskan [États-Unis] ; Stephen P. Difazio [États-Unis]Source :
- Genes [ 2073-4425 ] ; 2020.
Abstract
The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present in the SDRs help provide clues about how SDRs are established and how they evolve in the absence of recombination. Several Populus species have been reported with a male heterogametic configuration of sex (XX/XY system) mapped on chromosome 19, but the exact location of the SDR has been inconsistent among species, and thus far, none of these SDRs has been fully assembled in a genomic context. Here we identify the Y-SDR from a Y-linked contig directly from a long-read PacBio assembly of a Populus trichocarpa male individual. We also identified homologous gene sequences in the SDR of P. trichocarpa and the SDR of the W chromosome in Salix purpurea. We show that inverted repeats (IRs) found in the Y-SDR and the W-SDR are lineage-specific. We hypothesize that, although the two IRs are derived from the same orthologous gene within each species, they likely have independent evolutionary histories. Furthermore, the truncated inverted repeats in P. trichocarpa may code for small RNAs that target the homologous gene for RNA-directed DNA methylation. These findings support the hypothesis that diverse sex-determining systems may be achieved through similar evolutionary pathways, thereby providing a possible mechanism to explain the lability of sex-determination systems in plants in general.
DOI: 10.3390/genes11080843
PubMed: 32722098
PubMed Central: PMC7465354
Affiliations:
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Difazio</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, West Virginia University, Morgantown, WV 26506-6057</wicri:regionArea><placeName><region type="state">Virginie-Occidentale</region></placeName></affiliation></author></analytic><series><title level="j">Genes</title><idno type="eISSN">2073-4425</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present in the SDRs help provide clues about how SDRs are established and how they evolve in the absence of recombination. Several <i>Populus</i> species have been reported with a male heterogametic configuration of sex (XX/XY system) mapped on chromosome 19, but the exact location of the SDR has been inconsistent among species, and thus far, none of these SDRs has been fully assembled in a genomic context. Here we identify the Y-SDR from a Y-linked contig directly from a long-read PacBio assembly of a <i>Populus trichocarpa</i> male individual. We also identified homologous gene sequences in the SDR of <i>P. trichocarpa</i> and the SDR of the W chromosome in <i>Salix purpurea</i>. We show that inverted repeats (IRs) found in the Y-SDR and the W-SDR are lineage-specific. We hypothesize that, although the two IRs are derived from the same orthologous gene within each species, they likely have independent evolutionary histories. Furthermore, the truncated inverted repeats in <i>P. trichocarpa</i> may code for small RNAs that target the homologous gene for RNA-directed DNA methylation. These findings support the hypothesis that diverse sex-determining systems may be achieved through similar evolutionary pathways, thereby providing a possible mechanism to explain the lability of sex-determination systems in plants in general.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">32722098</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>05</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2073-4425</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><Issue>8</Issue><PubDate><Year>2020</Year><Month>Jul</Month><Day>24</Day></PubDate></JournalIssue><Title>Genes</Title><ISOAbbreviation>Genes (Basel)</ISOAbbreviation></Journal><ArticleTitle>Sequencing and Analysis of the Sex Determination Region of <i>Populus trichocarpa</i>.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E843</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/genes11080843</ELocationID><Abstract><AbstractText>The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present in the SDRs help provide clues about how SDRs are established and how they evolve in the absence of recombination. Several <i>Populus</i> species have been reported with a male heterogametic configuration of sex (XX/XY system) mapped on chromosome 19, but the exact location of the SDR has been inconsistent among species, and thus far, none of these SDRs has been fully assembled in a genomic context. Here we identify the Y-SDR from a Y-linked contig directly from a long-read PacBio assembly of a <i>Populus trichocarpa</i> male individual. We also identified homologous gene sequences in the SDR of <i>P. trichocarpa</i> and the SDR of the W chromosome in <i>Salix purpurea</i>. We show that inverted repeats (IRs) found in the Y-SDR and the W-SDR are lineage-specific. We hypothesize that, although the two IRs are derived from the same orthologous gene within each species, they likely have independent evolutionary histories. Furthermore, the truncated inverted repeats in <i>P. trichocarpa</i> may code for small RNAs that target the homologous gene for RNA-directed DNA methylation. These findings support the hypothesis that diverse sex-determining systems may be achieved through similar evolutionary pathways, thereby providing a possible mechanism to explain the lability of sex-determination systems in plants in general.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Ran</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Macaya-Sanz</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schmutz</LastName><ForeName>Jeremy</ForeName><Initials>J</Initials><Identifier Source="ORCID">0000-0001-8062-9172</Identifier><AffiliationInfo><Affiliation>HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jenkins</LastName><ForeName>Jerry W</ForeName><Initials>JW</Initials><AffiliationInfo><Affiliation>HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tuskan</LastName><ForeName>Gerald A</ForeName><Initials>GA</Initials><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>DiFazio</LastName><ForeName>Stephen P</ForeName><Initials>SP</Initials><Identifier Source="ORCID">0000-0003-4077-1590</Identifier><AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>1542509</GrantID><Agency>National Science Foundation</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>07</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Genes (Basel)</MedlineTA><NlmUniqueID>101551097</NlmUniqueID><ISSNLinking>2073-4425</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus</Keyword><Keyword MajorTopicYN="N">cytokinin response regulator</Keyword><Keyword MajorTopicYN="N">genome</Keyword><Keyword MajorTopicYN="N">inverted repeats</Keyword><Keyword MajorTopicYN="N">sex</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>07</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>07</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>07</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>7</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>7</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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Difazio</name><name sortKey="Jenkins, Jerry W" sort="Jenkins, Jerry W" uniqKey="Jenkins J" first="Jerry W" last="Jenkins">Jerry W. Jenkins</name><name sortKey="Macaya Sanz, David" sort="Macaya Sanz, David" uniqKey="Macaya Sanz D" first="David" last="Macaya-Sanz">David Macaya-Sanz</name><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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