A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae.
Identifieur interne : 000585 ( Main/Exploration ); précédent : 000584; suivant : 000586A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae.
Auteurs : Brian J. Sanderson ; Stephen P. Difazio ; Quentin C B. Cronk ; Tao Ma ; Matthew S. OlsonSource :
- Applications in plant sciences [ 2168-0450 ] ; 2020.
Abstract
Premise
The family Salicaceae has proved taxonomically challenging, especially in the genus
Methods
We used the wealth of sequence data in the family to design sequence capture probes to target regions of 300-1200 bp of exonic regions of 972 genes.
Results
We recovered sequence data for nearly all of the targeted genes in three species of
Conclusions
Our sequence capture array has extremely high capture efficiency within the genera
DOI: 10.1002/aps3.11394
PubMed: 33163293
PubMed Central: PMC7598885
Affiliations:
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Sanderson</name><affiliation><nlm:affiliation>Department of Biological Sciences Texas Tech University Lubbock Texas 79409-3131 USA.</nlm:affiliation><wicri:noCountry code="no comma">Department of Biological Sciences Texas Tech University Lubbock Texas 79409-3131 USA.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Department of Biology West Virginia University Morgantown West Virginia 26506 USA.</nlm:affiliation><wicri:noCountry code="no comma">Department of Biology West Virginia University Morgantown West Virginia 26506 USA.</wicri:noCountry></affiliation></author><author><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name><affiliation><nlm:affiliation>Department of Biology West Virginia University Morgantown West Virginia 26506 USA.</nlm:affiliation><wicri:noCountry code="no comma">Department of Biology West Virginia University Morgantown West Virginia 26506 USA.</wicri:noCountry></affiliation></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><affiliation><nlm:affiliation>Department of Botany University of British Columbia Vancouver British Columbia V6T 1Z4 Canada.</nlm:affiliation><wicri:noCountry code="no comma">Department of Botany University of British Columbia Vancouver British Columbia V6T 1Z4 Canada.</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 610065 People's Republic of 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 610065 People's Republic of China.</wicri:noCountry></affiliation></author><author><name sortKey="Olson, Matthew S" sort="Olson, Matthew S" uniqKey="Olson M" first="Matthew S" last="Olson">Matthew S. Olson</name><affiliation><nlm:affiliation>Department of Biological Sciences Texas Tech University Lubbock Texas 79409-3131 USA.</nlm:affiliation><wicri:noCountry code="no comma">Department of Biological Sciences Texas Tech University Lubbock Texas 79409-3131 USA.</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:33163293</idno><idno type="pmid">33163293</idno><idno type="doi">10.1002/aps3.11394</idno><idno type="pmc">PMC7598885</idno><idno type="wicri:Area/Main/Corpus">000018</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000018</idno><idno type="wicri:Area/Main/Curation">000018</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000018</idno><idno type="wicri:Area/Main/Exploration">000018</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae.</title><author><name sortKey="Sanderson, Brian J" sort="Sanderson, Brian J" uniqKey="Sanderson B" first="Brian J" last="Sanderson">Brian J. Sanderson</name><affiliation><nlm:affiliation>Department of Biological Sciences Texas Tech University Lubbock Texas 79409-3131 USA.</nlm:affiliation><wicri:noCountry code="no comma">Department of Biological Sciences Texas Tech University Lubbock Texas 79409-3131 USA.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Department of Biology West Virginia University Morgantown West Virginia 26506 USA.</nlm:affiliation><wicri:noCountry code="no comma">Department of Biology West Virginia University Morgantown West Virginia 26506 USA.</wicri:noCountry></affiliation></author><author><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name><affiliation><nlm:affiliation>Department of Biology West Virginia University Morgantown West Virginia 26506 USA.</nlm:affiliation><wicri:noCountry code="no comma">Department of Biology West Virginia University Morgantown West Virginia 26506 USA.</wicri:noCountry></affiliation></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><affiliation><nlm:affiliation>Department of Botany University of British Columbia Vancouver British Columbia V6T 1Z4 Canada.</nlm:affiliation><wicri:noCountry code="no comma">Department of Botany University of British Columbia Vancouver British Columbia V6T 1Z4 Canada.</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 610065 People's Republic of 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 610065 People's Republic of China.</wicri:noCountry></affiliation></author><author><name sortKey="Olson, Matthew S" sort="Olson, Matthew S" uniqKey="Olson M" first="Matthew S" last="Olson">Matthew S. Olson</name><affiliation><nlm:affiliation>Department of Biological Sciences Texas Tech University Lubbock Texas 79409-3131 USA.</nlm:affiliation><wicri:noCountry code="no comma">Department of Biological Sciences Texas Tech University Lubbock Texas 79409-3131 USA.</wicri:noCountry></affiliation></author></analytic><series><title level="j">Applications in plant sciences</title><idno type="ISSN">2168-0450</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"><p><b>Premise</b></p><p>The family Salicaceae has proved taxonomically challenging, especially in the genus </p></div><div type="abstract" xml:lang="en"><p><b>Methods</b></p><p>We used the wealth of sequence data in the family to design sequence capture probes to target regions of 300-1200 bp of exonic regions of 972 genes.</p></div><div type="abstract" xml:lang="en"><p><b>Results</b></p><p>We recovered sequence data for nearly all of the targeted genes in three species of </p></div><div type="abstract" xml:lang="en"><p><b>Conclusions</b></p><p>Our sequence capture array has extremely high capture efficiency within the genera </p></div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">33163293</PMID><DateRevised><Year>2020</Year><Month>11</Month><Day>12</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2168-0450</ISSN><JournalIssue CitedMedium="Print"><Volume>8</Volume><Issue>10</Issue><PubDate><Year>2020</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Applications in plant sciences</Title><ISOAbbreviation>Appl Plant Sci</ISOAbbreviation></Journal><ArticleTitle>A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae.</ArticleTitle><Pagination><MedlinePgn>e11394</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/aps3.11394</ELocationID><Abstract><AbstractText Label="Premise" NlmCategory="UNASSIGNED">The family Salicaceae has proved taxonomically challenging, especially in the genus <i>Salix</i>, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections of the genus.</AbstractText><AbstractText Label="Methods" NlmCategory="UNASSIGNED">We used the wealth of sequence data in the family to design sequence capture probes to target regions of 300-1200 bp of exonic regions of 972 genes.</AbstractText><AbstractText Label="Results" NlmCategory="UNASSIGNED">We recovered sequence data for nearly all of the targeted genes in three species of <i>Populus</i> and three species of <i>Salix</i>. We present a species tree, discuss concordance among gene trees, and present population genomic summary statistics for these loci.</AbstractText><AbstractText Label="Conclusions" NlmCategory="UNASSIGNED">Our sequence capture array has extremely high capture efficiency within the genera <i>Populus</i> and <i>Salix</i>, resulting in abundant phylogenetic information. Additionally, these loci show promise for population genomic studies.</AbstractText><CopyrightInformation>© 2020 Sanderson et al. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sanderson</LastName><ForeName>Brian J</ForeName><Initials>BJ</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-0310-0440</Identifier><AffiliationInfo><Affiliation>Department of Biological Sciences Texas Tech University Lubbock Texas 79409-3131 USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biology West Virginia University Morgantown West Virginia 26506 USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>DiFazio</LastName><ForeName>Stephen P</ForeName><Initials>SP</Initials><Identifier Source="ORCID">https://orcid.org/0000-0003-4077-1590</Identifier><AffiliationInfo><Affiliation>Department of Biology West Virginia University Morgantown West Virginia 26506 USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cronk</LastName><ForeName>Quentin C B</ForeName><Initials>QCB</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-4027-7368</Identifier><AffiliationInfo><Affiliation>Department of Botany University of British Columbia Vancouver British Columbia V6T 1Z4 Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Tao</ForeName><Initials>T</Initials><Identifier Source="ORCID">https://orcid.org/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 610065 People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Olson</LastName><ForeName>Matthew S</ForeName><Initials>MS</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-0798-145X</Identifier><AffiliationInfo><Affiliation>Department of Biological Sciences Texas Tech University Lubbock Texas 79409-3131 USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>10</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Appl Plant Sci</MedlineTA><NlmUniqueID>101590473</NlmUniqueID><ISSNLinking>2168-0450</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus</Keyword><Keyword MajorTopicYN="N">Salicaceae</Keyword><Keyword MajorTopicYN="N">Salix</Keyword><Keyword MajorTopicYN="N">phylogenetics</Keyword><Keyword MajorTopicYN="N">targeted sequence capture</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>05</Month><Day>08</Day></PubMedPubDate><PubMedPubDate 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Cronk</name><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name><name sortKey="Ma, Tao" sort="Ma, Tao" uniqKey="Ma T" first="Tao" last="Ma">Tao Ma</name><name sortKey="Olson, Matthew S" sort="Olson, Matthew S" uniqKey="Olson M" first="Matthew S" last="Olson">Matthew S. Olson</name><name sortKey="Sanderson, Brian J" sort="Sanderson, Brian J" uniqKey="Sanderson B" first="Brian J" last="Sanderson">Brian J. Sanderson</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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