Divergence of 3' ends as a driver of short interspersed nuclear element (SINE) evolution in the Salicaceae.
Identifieur interne : 000471 ( Main/Exploration ); précédent : 000470; suivant : 000472Divergence of 3' ends as a driver of short interspersed nuclear element (SINE) evolution in the Salicaceae.
Auteurs : Anja Kögler [Allemagne] ; Kathrin M. Seibt [Allemagne] ; Tony Heitkam [Allemagne] ; Kristin Morgenstern [Allemagne] ; Birgit Reiche [Allemagne] ; Marie Brückner [Allemagne] ; Heino Wolf [Allemagne] ; Doris Krabel [Allemagne] ; Thomas Schmidt [Allemagne]Source :
- The Plant journal : for cell and molecular biology [ 1365-313X ] ; 2020.
Abstract
Short interspersed nuclear elements (SINEs) are small, non-autonomous and heterogeneous retrotransposons that are widespread in plants. To explore the amplification dynamics and evolutionary history of SINE populations in representative deciduous tree species, we analyzed the genomes of the six following Salicaceae species: Populus deltoides, Populus euphratica, Populus tremula, Populus tremuloides, Populus trichocarpa, and Salix purpurea. We identified 11 Salicaceae SINE families (SaliS-I to SaliS-XI), comprising 27 077 full-length copies. Most of these families harbor segmental similarities, providing evidence for SINE emergence by reshuffling or heterodimerization. We observed two SINE groups, differing in phylogenetic distribution pattern, similarity and 3' end structure. These groups probably emerged during the 'salicoid duplication' (~65 million years ago) in the Salix-Populus progenitor and during the separation of the genus Salix (45-65 million years ago), respectively. In contrast to conserved 5' start motifs across species and SINE families, the 3' ends are highly variable in sequence and length. This extraordinary 3'-end variability results from mutations in the poly(A) tail, which were fixed by subsequent amplificational bursts. We show that the dissemination of newly evolved 3' ends is accomplished by a displacement of older motifs, leading to various 3'-end subpopulations within the SaliS families.
DOI: 10.1111/tpj.14721
PubMed: 32056333
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01735, Tharandt</wicri:regionArea><wicri:noRegion>01735, Tharandt</wicri:noRegion><orgName type="university">Université technique de Dresde</orgName><placeName><settlement type="city">Dresde</settlement><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Dresde</region></placeName></affiliation></author><author><name sortKey="Reiche, Birgit" sort="Reiche, Birgit" uniqKey="Reiche B" first="Birgit" last="Reiche">Birgit Reiche</name><affiliation wicri:level="4"><nlm:affiliation>Department of Forest Sciences, Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, 01735, Tharandt, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Forest Sciences, Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, 01735, Tharandt</wicri:regionArea><wicri:noRegion>01735, Tharandt</wicri:noRegion><orgName type="university">Université technique de 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xml:lang="fr">Allemagne</country><wicri:regionArea>Staatsbetrieb Sachsenforst, 01796, Pirna</wicri:regionArea><wicri:noRegion>01796, Pirna</wicri:noRegion><wicri:noRegion>01796, Pirna</wicri:noRegion><wicri:noRegion>Pirna</wicri:noRegion></affiliation></author><author><name sortKey="Krabel, Doris" sort="Krabel, Doris" uniqKey="Krabel D" first="Doris" last="Krabel">Doris Krabel</name><affiliation wicri:level="4"><nlm:affiliation>Department of Forest Sciences, Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, 01735, Tharandt, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Forest Sciences, Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, 01735, Tharandt</wicri:regionArea><wicri:noRegion>01735, Tharandt</wicri:noRegion><orgName type="university">Université technique de Dresde</orgName><placeName><settlement type="city">Dresde</settlement><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Dresde</region></placeName></affiliation></author><author><name sortKey="Schmidt, Thomas" sort="Schmidt, Thomas" uniqKey="Schmidt T" first="Thomas" last="Schmidt">Thomas Schmidt</name><affiliation wicri:level="4"><nlm:affiliation>Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01062, Dresden, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01062, Dresden</wicri:regionArea><wicri:noRegion>01062, Dresden</wicri:noRegion><orgName type="university">Université technique de Dresde</orgName><placeName><settlement type="city">Dresde</settlement><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Dresde</region></placeName></affiliation></author></analytic><series><title level="j">The Plant journal : for cell and molecular biology</title><idno type="eISSN">1365-313X</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">Short interspersed nuclear elements (SINEs) are small, non-autonomous and heterogeneous retrotransposons that are widespread in plants. To explore the amplification dynamics and evolutionary history of SINE populations in representative deciduous tree species, we analyzed the genomes of the six following Salicaceae species: Populus deltoides, Populus euphratica, Populus tremula, Populus tremuloides, Populus trichocarpa, and Salix purpurea. We identified 11 Salicaceae SINE families (SaliS-I to SaliS-XI), comprising 27 077 full-length copies. Most of these families harbor segmental similarities, providing evidence for SINE emergence by reshuffling or heterodimerization. We observed two SINE groups, differing in phylogenetic distribution pattern, similarity and 3' end structure. These groups probably emerged during the 'salicoid duplication' (~65 million years ago) in the Salix-Populus progenitor and during the separation of the genus Salix (45-65 million years ago), respectively. In contrast to conserved 5' start motifs across species and SINE families, the 3' ends are highly variable in sequence and length. This extraordinary 3'-end variability results from mutations in the poly(A) tail, which were fixed by subsequent amplificational bursts. We show that the dissemination of newly evolved 3' ends is accomplished by a displacement of older motifs, leading to various 3'-end subpopulations within the SaliS families.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32056333</PMID><DateRevised><Year>2020</Year><Month>08</Month><Day>17</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-313X</ISSN><JournalIssue CitedMedium="Internet"><Volume>103</Volume><Issue>1</Issue><PubDate><Year>2020</Year><Month>07</Month></PubDate></JournalIssue><Title>The Plant journal : for cell and molecular biology</Title><ISOAbbreviation>Plant J</ISOAbbreviation></Journal><ArticleTitle>Divergence of 3' ends as a driver of short interspersed nuclear element (SINE) evolution in the Salicaceae.</ArticleTitle><Pagination><MedlinePgn>443-458</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/tpj.14721</ELocationID><Abstract><AbstractText>Short interspersed nuclear elements (SINEs) are small, non-autonomous and heterogeneous retrotransposons that are widespread in plants. To explore the amplification dynamics and evolutionary history of SINE populations in representative deciduous tree species, we analyzed the genomes of the six following Salicaceae species: Populus deltoides, Populus euphratica, Populus tremula, Populus tremuloides, Populus trichocarpa, and Salix purpurea. We identified 11 Salicaceae SINE families (SaliS-I to SaliS-XI), comprising 27 077 full-length copies. Most of these families harbor segmental similarities, providing evidence for SINE emergence by reshuffling or heterodimerization. We observed two SINE groups, differing in phylogenetic distribution pattern, similarity and 3' end structure. These groups probably emerged during the 'salicoid duplication' (~65 million years ago) in the Salix-Populus progenitor and during the separation of the genus Salix (45-65 million years ago), respectively. In contrast to conserved 5' start motifs across species and SINE families, the 3' ends are highly variable in sequence and length. This extraordinary 3'-end variability results from mutations in the poly(A) tail, which were fixed by subsequent amplificational bursts. We show that the dissemination of newly evolved 3' ends is accomplished by a displacement of older motifs, leading to various 3'-end subpopulations within the SaliS families.</AbstractText><CopyrightInformation>© 2020 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kögler</LastName><ForeName>Anja</ForeName><Initials>A</Initials><Identifier Source="ORCID">0000-0003-4270-4762</Identifier><AffiliationInfo><Affiliation>Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01062, Dresden, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Seibt</LastName><ForeName>Kathrin M</ForeName><Initials>KM</Initials><Identifier Source="ORCID">0000-0002-5435-2381</Identifier><AffiliationInfo><Affiliation>Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01062, Dresden, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Heitkam</LastName><ForeName>Tony</ForeName><Initials>T</Initials><Identifier Source="ORCID">0000-0003-0168-8428</Identifier><AffiliationInfo><Affiliation>Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01062, Dresden, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Morgenstern</LastName><ForeName>Kristin</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Forest Sciences, Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, 01735, Tharandt, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Reiche</LastName><ForeName>Birgit</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Forest Sciences, Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, 01735, Tharandt, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Brückner</LastName><ForeName>Marie</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Staatsbetrieb Sachsenforst, 01796, Pirna, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wolf</LastName><ForeName>Heino</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Staatsbetrieb Sachsenforst, 01796, Pirna, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Krabel</LastName><ForeName>Doris</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Forest Sciences, Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, 01735, Tharandt, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schmidt</LastName><ForeName>Thomas</ForeName><Initials>T</Initials><Identifier Source="ORCID">0000-0001-7259-415X</Identifier><AffiliationInfo><Affiliation>Faculty of Biology, Institute of Botany, Technische Universität Dresden, 01062, Dresden, Germany.</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>2020</Year><Month>03</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Plant J</MedlineTA><NlmUniqueID>9207397</NlmUniqueID><ISSNLinking>0960-7412</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Salicaceae</Keyword><Keyword MajorTopicYN="Y">non-LTR retrotransposon</Keyword><Keyword MajorTopicYN="Y">poplar</Keyword><Keyword MajorTopicYN="Y">short interspersed nuclear elements (SINEs)</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>07</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>01</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>01</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>2</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>2</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32056333</ArticleId><ArticleId IdType="doi">10.1111/tpj.14721</ArticleId></ArticleIdList><ReferenceList><Title>References</Title><Reference><Citation>Argus, G.W. 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