Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae).
Identifieur interne : 001F64 ( Main/Exploration ); précédent : 001F63; suivant : 001F65Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae).
Auteurs : Daisie I. Huang [Canada] ; Charles A. Hefer ; Natalia Kolosova ; Carl J. Douglas ; Quentin C B. CronkSource :
- The New phytologist [ 1469-8137 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
- Wicri :
- geographic : Canada, États-Unis.
English descriptors
- KwdEn :
- MESH :
- geographic : Canada, United States.
- genetics : Populus.
- Base Sequence, Demography, Gene Expression Regulation, Plant, Molecular Sequence Data, Phylogeny, Sequence Alignment, Species Specificity.
Abstract
As molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance - the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees - are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6-7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a 'ghost lineage' of a now-extinct North American poplar.
DOI: 10.1111/nph.12956
PubMed: 25078531
Affiliations:
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Huang</name><affiliation wicri:level="4"><nlm:affiliation>Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada; Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada; Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Hefer, Charles A" sort="Hefer, Charles A" uniqKey="Hefer C" first="Charles A" last="Hefer">Charles A. Hefer</name></author><author><name sortKey="Kolosova, Natalia" sort="Kolosova, Natalia" uniqKey="Kolosova N" first="Natalia" last="Kolosova">Natalia Kolosova</name></author><author><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name></author><author><name sortKey="Cronk, Quentin C B" sort="Cronk, Quentin C B" uniqKey="Cronk Q" first="Quentin C B" last="Cronk">Quentin C B. 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Huang</name><affiliation wicri:level="4"><nlm:affiliation>Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada; Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada; Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Hefer, Charles A" sort="Hefer, Charles A" uniqKey="Hefer C" first="Charles A" last="Hefer">Charles A. Hefer</name></author><author><name sortKey="Kolosova, Natalia" sort="Kolosova, Natalia" uniqKey="Kolosova N" first="Natalia" last="Kolosova">Natalia Kolosova</name></author><author><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name></author><author><name sortKey="Cronk, Quentin C B" sort="Cronk, Quentin C B" uniqKey="Cronk Q" first="Quentin C B" last="Cronk">Quentin C B. Cronk</name></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Canada (MeSH)</term><term>Demography (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Phylogeny (MeSH)</term><term>Populus (genetics)</term><term>Sequence Alignment (MeSH)</term><term>Species Specificity (MeSH)</term><term>United States (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences (MeSH)</term><term>Canada (MeSH)</term><term>Données de séquences moléculaires (MeSH)</term><term>Démographie (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Populus (génétique)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Spécificité d'espèce (MeSH)</term><term>Séquence nucléotidique (MeSH)</term><term>États-Unis (MeSH)</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Canada</term><term>United States</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Demography</term><term>Gene Expression Regulation, Plant</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Sequence Alignment</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Canada</term><term>Données de séquences moléculaires</term><term>Démographie</term><term>Phylogenèse</term><term>Régulation de l'expression des gènes végétaux</term><term>Spécificité d'espèce</term><term>Séquence nucléotidique</term><term>États-Unis</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Canada</term><term>États-Unis</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">As molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance - the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees - are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6-7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a 'ghost lineage' of a now-extinct North American poplar.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25078531</PMID><DateCompleted><Year>2015</Year><Month>06</Month><Day>01</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-8137</ISSN><JournalIssue CitedMedium="Internet"><Volume>204</Volume><Issue>3</Issue><PubDate><Year>2014</Year><Month>Nov</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae).</ArticleTitle><Pagination><MedlinePgn>693-703</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.12956</ELocationID><Abstract><AbstractText>As molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance - the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees - are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6-7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a 'ghost lineage' of a now-extinct North American poplar.</AbstractText><CopyrightInformation>© 2014 The Authors. 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Cronk</name><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name><name sortKey="Hefer, Charles A" sort="Hefer, Charles A" uniqKey="Hefer C" first="Charles A" last="Hefer">Charles A. Hefer</name><name sortKey="Kolosova, Natalia" sort="Kolosova, Natalia" uniqKey="Kolosova N" first="Natalia" last="Kolosova">Natalia Kolosova</name></noCountry><country name="Canada"><region name="Colombie-Britannique "><name sortKey="Huang, Daisie I" sort="Huang, Daisie I" uniqKey="Huang D" first="Daisie I" last="Huang">Daisie I. Huang</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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