MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.
Identifieur interne : 000029 ( PubMed/Checkpoint ); précédent : 000028; suivant : 000030MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.
Auteurs : Srikar Chamala [États-Unis] ; Nicolás García [Chili] ; Grant T. Godden [États-Unis] ; Vivek Krishnakumar [États-Unis] ; Ingrid E. Jordon-Thaden [États-Unis] ; Riet De Smet [Belgique] ; W Brad Barbazuk [États-Unis] ; Douglas E. Soltis [États-Unis] ; Pamela S. Soltis [États-Unis]Source :
- Applications in plant sciences ; 2015.
Abstract
Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited.
DOI: 10.3732/apps.1400115
PubMed: 25909041
Affiliations:
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Soltis</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author><author><name sortKey="Soltis, Pamela S" sort="Soltis, Pamela S" uniqKey="Soltis P" first="Pamela S" last="Soltis">Pamela S. Soltis</name><affiliation wicri:level="2"><nlm:affiliation>Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25909041</idno><idno type="pmid">25909041</idno><idno type="doi">10.3732/apps.1400115</idno><idno type="wicri:Area/PubMed/Corpus">000035</idno><idno type="wicri:Area/PubMed/Curation">000035</idno><idno type="wicri:Area/PubMed/Checkpoint">000035</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.</title><author><name sortKey="Chamala, Srikar" sort="Chamala, Srikar" uniqKey="Chamala S" first="Srikar" last="Chamala">Srikar Chamala</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of Florida, Gainesville, Florida, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author><author><name sortKey="Garcia, Nicolas" sort="Garcia, Nicolas" uniqKey="Garcia N" first="Nicolás" last="García">Nicolás García</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Facultad de Ciencias Forestales y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile.</nlm:affiliation><country xml:lang="fr">Chili</country><wicri:regionArea>Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Facultad de Ciencias Forestales y Conservación de la Naturaleza, Universidad de Chile, Santiago</wicri:regionArea><wicri:noRegion>Santiago</wicri:noRegion></affiliation></author><author><name sortKey="Godden, Grant T" sort="Godden, Grant T" uniqKey="Godden G" first="Grant T" last="Godden">Grant T. Godden</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Rancho Santa Ana Botanic Garden, Claremont, California, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Rancho Santa Ana Botanic Garden, Claremont, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Krishnakumar, Vivek" sort="Krishnakumar, Vivek" uniqKey="Krishnakumar V" first="Vivek" last="Krishnakumar">Vivek Krishnakumar</name><affiliation wicri:level="2"><nlm:affiliation>Plant Genomics, J. Craig Venter Institute, Rockville, Maryland, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Plant Genomics, J. Craig Venter Institute, Rockville, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Jordon Thaden, Ingrid E" sort="Jordon Thaden, Ingrid E" uniqKey="Jordon Thaden I" first="Ingrid E" last="Jordon-Thaden">Ingrid E. Jordon-Thaden</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA ; Jepson and University Herbaria, University of California, Berkeley, Berkeley, California, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA ; Jepson and University Herbaria, University of California, Berkeley, Berkeley, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="De Smet, Riet" sort="De Smet, Riet" uniqKey="De Smet R" first="Riet" last="De Smet">Riet De Smet</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium ; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium ; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent</wicri:regionArea><wicri:noRegion>9052 Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Barbazuk, W Brad" sort="Barbazuk, W Brad" uniqKey="Barbazuk W" first="W Brad" last="Barbazuk">W Brad Barbazuk</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author><author><name sortKey="Soltis, Douglas E" sort="Soltis, Douglas E" uniqKey="Soltis D" first="Douglas E" last="Soltis">Douglas E. Soltis</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author><author><name sortKey="Soltis, Pamela S" sort="Soltis, Pamela S" uniqKey="Soltis P" first="Pamela S" last="Soltis">Pamela S. Soltis</name><affiliation wicri:level="2"><nlm:affiliation>Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author></analytic><series><title level="j">Applications in plant sciences</title><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">25909041</PMID><DateCreated><Year>2015</Year><Month>4</Month><Day>24</Day></DateCreated><DateCompleted><Year>2015</Year><Month>04</Month><Day>24</Day></DateCompleted><DateRevised><Year>2015</Year><Month>4</Month><Day>27</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><JournalIssue CitedMedium="Print"><Volume>3</Volume><Issue>4</Issue><PubDate><Year>2015</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Applications in plant sciences</Title><ISOAbbreviation>Appl Plant Sci</ISOAbbreviation></Journal><ArticleTitle>MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.3732/apps.1400115</ELocationID><ELocationID EIdType="pii" ValidYN="Y">apps.1400115</ELocationID><Abstract><AbstractText Label="PREMISE OF THE STUDY" NlmCategory="OBJECTIVE">Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited.</AbstractText><AbstractText Label="METHODS AND RESULTS" NlmCategory="RESULTS">We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chamala</LastName><ForeName>Srikar</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biology, University of Florida, Gainesville, Florida, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>García</LastName><ForeName>Nicolás</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Facultad de Ciencias Forestales y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Godden</LastName><ForeName>Grant T</ForeName><Initials>GT</Initials><AffiliationInfo><Affiliation>Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Rancho Santa Ana Botanic Garden, Claremont, California, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Krishnakumar</LastName><ForeName>Vivek</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Plant Genomics, J. Craig Venter Institute, Rockville, Maryland, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jordon-Thaden</LastName><ForeName>Ingrid E</ForeName><Initials>IE</Initials><AffiliationInfo><Affiliation>Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA ; Jepson and University Herbaria, University of California, Berkeley, Berkeley, California, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>De Smet</LastName><ForeName>Riet</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium ; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Barbazuk</LastName><ForeName>W Brad</ForeName><Initials>WB</Initials><AffiliationInfo><Affiliation>Department of Biology, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Soltis</LastName><ForeName>Douglas E</ForeName><Initials>DE</Initials><AffiliationInfo><Affiliation>Department of Biology, University of Florida, Gainesville, Florida, USA ; Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Soltis</LastName><ForeName>Pamela S</ForeName><Initials>PS</Initials><AffiliationInfo><Affiliation>Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Genetics Institute, University of Florida, Gainesville, Florida, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>ENG</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>Apr</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Appl Plant Sci</MedlineTA><NlmUniqueID>101590473</NlmUniqueID><ISSNLinking>2168-0450</ISSNLinking></MedlineJournalInfo><OtherID Source="NLM">PMC4406834</OtherID><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">data mining</Keyword><Keyword MajorTopicYN="N">introns</Keyword><Keyword MajorTopicYN="N">marker development</Keyword><Keyword MajorTopicYN="N">next-generation sequencing</Keyword><Keyword MajorTopicYN="N">phylogenetics</Keyword><Keyword MajorTopicYN="N">single-copy nuclear genes</Keyword><Keyword MajorTopicYN="N">transcriptomes</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>12</Month><Day>4</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>2</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>4</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>4</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>4</Month><Day>25</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25909041</ArticleId><ArticleId IdType="doi">10.3732/apps.1400115</ArticleId><ArticleId IdType="pii">apps1400115</ArticleId><ArticleId IdType="pmc">PMC4406834</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Belgique</li><li>Chili</li><li>États-Unis</li></country><region><li>Californie</li><li>Floride</li><li>Maryland</li></region></list><tree><country name="États-Unis"><region name="Floride"><name sortKey="Chamala, Srikar" sort="Chamala, Srikar" uniqKey="Chamala S" first="Srikar" last="Chamala">Srikar Chamala</name></region><name sortKey="Barbazuk, W Brad" sort="Barbazuk, W Brad" uniqKey="Barbazuk W" first="W Brad" last="Barbazuk">W Brad Barbazuk</name><name sortKey="Godden, Grant T" sort="Godden, Grant T" uniqKey="Godden G" first="Grant T" last="Godden">Grant T. Godden</name><name sortKey="Jordon Thaden, Ingrid E" sort="Jordon Thaden, Ingrid E" uniqKey="Jordon Thaden I" first="Ingrid E" last="Jordon-Thaden">Ingrid E. Jordon-Thaden</name><name sortKey="Krishnakumar, Vivek" sort="Krishnakumar, Vivek" uniqKey="Krishnakumar V" first="Vivek" last="Krishnakumar">Vivek Krishnakumar</name><name sortKey="Soltis, Douglas E" sort="Soltis, Douglas E" uniqKey="Soltis D" first="Douglas E" last="Soltis">Douglas E. Soltis</name><name sortKey="Soltis, Pamela S" sort="Soltis, Pamela S" uniqKey="Soltis P" first="Pamela S" last="Soltis">Pamela S. Soltis</name></country><country name="Chili"><noRegion><name sortKey="Garcia, Nicolas" sort="Garcia, Nicolas" uniqKey="Garcia N" first="Nicolás" last="García">Nicolás García</name></noRegion></country><country name="Belgique"><noRegion><name sortKey="De Smet, Riet" sort="De Smet, Riet" uniqKey="De Smet R" first="Riet" last="De Smet">Riet De Smet</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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