Comparative analysis of the complete chloroplast genomes of seven Populus species: Insights into alternative female parents of Populus tomentosa.
Identifieur interne : 000A71 ( Main/Exploration ); précédent : 000A70; suivant : 000A72Comparative analysis of the complete chloroplast genomes of seven Populus species: Insights into alternative female parents of Populus tomentosa.
Auteurs : Dan Zong [République populaire de Chine] ; Peihua Gan [République populaire de Chine] ; Anpei Zhou [République populaire de Chine] ; Jinyu Li [République populaire de Chine] ; Zhongli Xie [République populaire de Chine] ; Anan Duan [République populaire de Chine] ; Chengzhong He [République populaire de Chine]Source :
- PloS one [ 1932-6203 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- Wicri :
- geographic : République populaire de Chine.
English descriptors
- KwdEn :
- MESH :
- geographic : China.
- classification : Populus.
- genetics : Chloroplasts, Genome, Chloroplast, Microsatellite Repeats, Populus.
- Evolution, Molecular, Genomics, Phylogeny.
Abstract
Populus tomentosa, of section Populus, is distributed mainly in northern China. This species has high resistance to many diseases and insects, and it plays key roles in shelterbelts and urban afforestation in northern China. It has long been suspected to be a hybrid, but its parents remain unknown. In the present study, we report four newly sequenced complete cp genomes from section Populus and comparative genomic analyses of these new sequences and three published cp genome sequences. The seven cp genomes ranged from 155,853 bp (P. tremula var. davidiana) to 156,746 bp (P. adenopoda) in length, and their gene orders, gene numbers and GC contents were similar. We analyzed SNPs, indels, SSRs and repeats among the seven cp genomes, and eight small inversions were detected in the ndhC-trnV, rbcL-accD, petA-psbJ, trnW-trnP, rpl16-rps3, trnL-ycf15, ycf15-trnL, and ndhF-trnL intergenic regions. Furthermore, seven divergent regions (trnH-psbA, matK, psbM-psbD, ndhC-trnV, ycf1, ndhF-ccsA and ccsA-ndhD) were found in more highly variable regions. The phylogenetic tree reveals that P. tomentosa is closely related to P. alba and P. alba var. pyramidalis. Hence, P. alba was involved in the formation of P. tomentosa.
DOI: 10.1371/journal.pone.0218455
PubMed: 31216332
PubMed Central: PMC6583991
Affiliations:
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University, Kunming, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation></author><author><name sortKey="Xie, Zhongli" sort="Xie, Zhongli" uniqKey="Xie Z" first="Zhongli" last="Xie">Zhongli Xie</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation></author><author><name sortKey="Duan, Anan" sort="Duan, Anan" uniqKey="Duan A" first="Anan" last="Duan">Anan Duan</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation></author><author><name sortKey="He, Chengzhong" sort="He, Chengzhong" uniqKey="He C" first="Chengzhong" last="He">Chengzhong He</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan</wicri:regionArea><wicri:noRegion>Yunnan</wicri:noRegion></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>China (MeSH)</term><term>Chloroplasts (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Genome, Chloroplast (genetics)</term><term>Genomics (MeSH)</term><term>Microsatellite Repeats (genetics)</term><term>Phylogeny (MeSH)</term><term>Populus (classification)</term><term>Populus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Chine (MeSH)</term><term>Chloroplastes (génétique)</term><term>Génome de chloroplaste (génétique)</term><term>Génomique (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Populus (classification)</term><term>Populus (génétique)</term><term>Répétitions microsatellites (génétique)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>China</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chloroplasts</term><term>Genome, Chloroplast</term><term>Microsatellite Repeats</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Chloroplastes</term><term>Génome de chloroplaste</term><term>Populus</term><term>Répétitions microsatellites</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Genomics</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Chine</term><term>Génomique</term><term>Phylogenèse</term><term>Populus</term><term>Évolution moléculaire</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>République populaire de Chine</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Populus tomentosa, of section Populus, is distributed mainly in northern China. This species has high resistance to many diseases and insects, and it plays key roles in shelterbelts and urban afforestation in northern China. It has long been suspected to be a hybrid, but its parents remain unknown. In the present study, we report four newly sequenced complete cp genomes from section Populus and comparative genomic analyses of these new sequences and three published cp genome sequences. The seven cp genomes ranged from 155,853 bp (P. tremula var. davidiana) to 156,746 bp (P. adenopoda) in length, and their gene orders, gene numbers and GC contents were similar. We analyzed SNPs, indels, SSRs and repeats among the seven cp genomes, and eight small inversions were detected in the ndhC-trnV, rbcL-accD, petA-psbJ, trnW-trnP, rpl16-rps3, trnL-ycf15, ycf15-trnL, and ndhF-trnL intergenic regions. Furthermore, seven divergent regions (trnH-psbA, matK, psbM-psbD, ndhC-trnV, ycf1, ndhF-ccsA and ccsA-ndhD) were found in more highly variable regions. The phylogenetic tree reveals that P. tomentosa is closely related to P. alba and P. alba var. pyramidalis. Hence, P. alba was involved in the formation of P. tomentosa.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31216332</PMID><DateCompleted><Year>2020</Year><Month>02</Month><Day>13</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>09</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>14</Volume><Issue>6</Issue><PubDate><Year>2019</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Comparative analysis of the complete chloroplast genomes of seven Populus species: Insights into alternative female parents of Populus tomentosa.</ArticleTitle><Pagination><MedlinePgn>e0218455</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0218455</ELocationID><Abstract><AbstractText>Populus tomentosa, of section Populus, is distributed mainly in northern China. This species has high resistance to many diseases and insects, and it plays key roles in shelterbelts and urban afforestation in northern China. It has long been suspected to be a hybrid, but its parents remain unknown. In the present study, we report four newly sequenced complete cp genomes from section Populus and comparative genomic analyses of these new sequences and three published cp genome sequences. The seven cp genomes ranged from 155,853 bp (P. tremula var. davidiana) to 156,746 bp (P. adenopoda) in length, and their gene orders, gene numbers and GC contents were similar. We analyzed SNPs, indels, SSRs and repeats among the seven cp genomes, and eight small inversions were detected in the ndhC-trnV, rbcL-accD, petA-psbJ, trnW-trnP, rpl16-rps3, trnL-ycf15, ycf15-trnL, and ndhF-trnL intergenic regions. Furthermore, seven divergent regions (trnH-psbA, matK, psbM-psbD, ndhC-trnV, ycf1, ndhF-ccsA and ccsA-ndhD) were found in more highly variable regions. The phylogenetic tree reveals that P. tomentosa is closely related to P. alba and P. alba var. pyramidalis. Hence, P. alba was involved in the formation of P. tomentosa.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zong</LastName><ForeName>Dan</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gan</LastName><ForeName>Peihua</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Anpei</ForeName><Initials>A</Initials><Identifier Source="ORCID">0000-0001-8162-367X</Identifier><AffiliationInfo><Affiliation>Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Jinyu</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xie</LastName><ForeName>Zhongli</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Duan</LastName><ForeName>Anan</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>He</LastName><ForeName>Chengzhong</ForeName><Initials>C</Initials><Identifier Source="ORCID">0000-0001-9487-8612</Identifier><AffiliationInfo><Affiliation>Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, Yunnan, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China.</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>2019</Year><Month>06</Month><Day>19</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002681" MajorTopicYN="N" Type="Geographic">China</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002736" MajorTopicYN="N">Chloroplasts</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054628" MajorTopicYN="N">Genome, Chloroplast</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="Y">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><CoiStatement>The authors have declared that no competing interests exist.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>12</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>06</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>6</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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sortKey="Li, Jinyu" sort="Li, Jinyu" uniqKey="Li J" first="Jinyu" last="Li">Jinyu Li</name><name sortKey="Xie, Zhongli" sort="Xie, Zhongli" uniqKey="Xie Z" first="Zhongli" last="Xie">Zhongli Xie</name><name sortKey="Xie, Zhongli" sort="Xie, Zhongli" uniqKey="Xie Z" first="Zhongli" last="Xie">Zhongli Xie</name><name sortKey="Zhou, Anpei" sort="Zhou, Anpei" uniqKey="Zhou A" first="Anpei" last="Zhou">Anpei Zhou</name><name sortKey="Zhou, Anpei" sort="Zhou, Anpei" uniqKey="Zhou A" first="Anpei" last="Zhou">Anpei Zhou</name><name sortKey="Zong, Dan" sort="Zong, Dan" uniqKey="Zong D" first="Dan" last="Zong">Dan Zong</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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