Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows.
Identifieur interne : 000D34 ( Main/Exploration ); précédent : 000D33; suivant : 000D35Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows.
Auteurs : Lei Zhang ; Zhenxiang Xi ; Mingcheng Wang ; Xinyi Guo ; Tao MaSource :
- Ecology and evolution [ 2045-7758 ] ; 2018.
Abstract
Phylogenetic relationships and lineage diversification of the family Salicaceae sensu lato (s.l.) remain poorly understood. In this study, we examined phylogenetic relationships between 42 species from six genera based on the complete plastomes. Phylogenetic analyses of 77 protein coding genes of the plastomes produced good resolution of the interrelationships among most sampled species and the recovered clades. Of the sampled genera from the family, Flacourtia was identified as the most basal and the successive clades comprised both Itoa and Poliothyrsis, Idesia, two genera of the Salicaceae sensu stricto (s.s.) (Populus and Salix). Five major subclades were recovered within the Populus clade. These subclades and their interrelationships are largely inconsistent with morphological classifications and molecular phylogeny based on nuclear internal transcribed spacer sequence variations. Two major subclades were identified for the Salix clade. Molecular dating suggested that species diversification of the major subclades in the Populus and Salix clades occurred mainly within the recent Pliocene. In addition, we found that the rpl32 gene was lost and the rps7 gene evolved into a pseudogene multiple times in the sampled genera of the Salicaceae s.l. Compared with previous studies, our results provide a well-resolved phylogeny from the perspective of the plastomes.
DOI: 10.1002/ece3.4261
PubMed: 30250665
PubMed Central: PMC6145263
Affiliations:
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College of Life Sciences Sichuan University Chengdu Sichuan China.</wicri:noCountry></affiliation></author><author><name sortKey="Xi, Zhenxiang" sort="Xi, Zhenxiang" uniqKey="Xi Z" first="Zhenxiang" last="Xi">Zhenxiang Xi</name><affiliation><nlm:affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China.</nlm:affiliation><wicri:noCountry code="no comma">Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China.</wicri:noCountry></affiliation></author><author><name sortKey="Wang, Mingcheng" sort="Wang, Mingcheng" uniqKey="Wang M" first="Mingcheng" last="Wang">Mingcheng Wang</name><affiliation><nlm:affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China.</nlm:affiliation><wicri:noCountry code="no comma">Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China.</wicri:noCountry></affiliation></author><author><name sortKey="Guo, Xinyi" sort="Guo, Xinyi" uniqKey="Guo X" first="Xinyi" last="Guo">Xinyi Guo</name><affiliation><nlm:affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China.</nlm:affiliation><wicri:noCountry code="no comma">Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China.</wicri:noCountry></affiliation></author><author><name sortKey="Ma, Tao" sort="Ma, Tao" uniqKey="Ma T" first="Tao" last="Ma">Tao Ma</name><affiliation><nlm:affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China.</nlm:affiliation><wicri:noCountry code="no comma">Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China.</wicri:noCountry></affiliation></author></analytic><series><title level="j">Ecology and evolution</title><idno type="ISSN">2045-7758</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Phylogenetic relationships and lineage diversification of the family Salicaceae <i>sensu lato</i> (<i>s.l</i>.) remain poorly understood. In this study, we examined phylogenetic relationships between 42 species from six genera based on the complete plastomes. Phylogenetic analyses of 77 protein coding genes of the plastomes produced good resolution of the interrelationships among most sampled species and the recovered clades. Of the sampled genera from the family, <i>Flacourtia</i> was identified as the most basal and the successive clades comprised both <i>Itoa</i> and <i>Poliothyrsis</i>, <i>Idesia</i>, two genera of the Salicaceae <i>sensu stricto</i> (<i>s.s</i>.) (<i>Populus</i> and <i>Salix</i>). Five major subclades were recovered within the <i>Populus</i> clade. These subclades and their interrelationships are largely inconsistent with morphological classifications and molecular phylogeny based on nuclear internal transcribed spacer sequence variations. Two major subclades were identified for the <i>Salix</i> clade. Molecular dating suggested that species diversification of the major subclades in the <i>Populus</i> and <i>Salix</i> clades occurred mainly within the recent Pliocene. In addition, we found that the <i>rpl32</i> gene was lost and the <i>rps7</i> gene evolved into a pseudogene multiple times in the sampled genera of the Salicaceae <i>s.l</i>. Compared with previous studies, our results provide a well-resolved phylogeny from the perspective of the plastomes.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">30250665</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>01</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2045-7758</ISSN><JournalIssue CitedMedium="Print"><Volume>8</Volume><Issue>16</Issue><PubDate><Year>2018</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Ecology and evolution</Title><ISOAbbreviation>Ecol Evol</ISOAbbreviation></Journal><ArticleTitle>Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows.</ArticleTitle><Pagination><MedlinePgn>7817-7823</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/ece3.4261</ELocationID><Abstract><AbstractText>Phylogenetic relationships and lineage diversification of the family Salicaceae <i>sensu lato</i> (<i>s.l</i>.) remain poorly understood. In this study, we examined phylogenetic relationships between 42 species from six genera based on the complete plastomes. Phylogenetic analyses of 77 protein coding genes of the plastomes produced good resolution of the interrelationships among most sampled species and the recovered clades. Of the sampled genera from the family, <i>Flacourtia</i> was identified as the most basal and the successive clades comprised both <i>Itoa</i> and <i>Poliothyrsis</i>, <i>Idesia</i>, two genera of the Salicaceae <i>sensu stricto</i> (<i>s.s</i>.) (<i>Populus</i> and <i>Salix</i>). Five major subclades were recovered within the <i>Populus</i> clade. These subclades and their interrelationships are largely inconsistent with morphological classifications and molecular phylogeny based on nuclear internal transcribed spacer sequence variations. Two major subclades were identified for the <i>Salix</i> clade. Molecular dating suggested that species diversification of the major subclades in the <i>Populus</i> and <i>Salix</i> clades occurred mainly within the recent Pliocene. In addition, we found that the <i>rpl32</i> gene was lost and the <i>rps7</i> gene evolved into a pseudogene multiple times in the sampled genera of the Salicaceae <i>s.l</i>. Compared with previous studies, our results provide a well-resolved phylogeny from the perspective of the plastomes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Lei</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xi</LastName><ForeName>Zhenxiang</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Mingcheng</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Xinyi</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Tao</ForeName><Initials>T</Initials><Identifier Source="ORCID">0000-0002-7094-6868</Identifier><AffiliationInfo><Affiliation>Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>07</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Ecol Evol</MedlineTA><NlmUniqueID>101566408</NlmUniqueID><ISSNLinking>2045-7758</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Salicaceae sensu lato</Keyword><Keyword MajorTopicYN="N">chloroplast genome</Keyword><Keyword MajorTopicYN="N">gene loss</Keyword><Keyword MajorTopicYN="N">phylogenetic relationship</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>11</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2018</Year><Month>03</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>05</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>9</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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last="Guo">Xinyi Guo</name><name sortKey="Ma, Tao" sort="Ma, Tao" uniqKey="Ma T" first="Tao" last="Ma">Tao Ma</name><name sortKey="Wang, Mingcheng" sort="Wang, Mingcheng" uniqKey="Wang M" first="Mingcheng" last="Wang">Mingcheng Wang</name><name sortKey="Xi, Zhenxiang" sort="Xi, Zhenxiang" uniqKey="Xi Z" first="Zhenxiang" last="Xi">Zhenxiang Xi</name><name sortKey="Zhang, Lei" sort="Zhang, Lei" uniqKey="Zhang L" first="Lei" last="Zhang">Lei Zhang</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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