MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes1
Identifieur interne : 000096 ( Main/Exploration ); précédent : 000095; suivant : 000097MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes1
Auteurs : Srikar Chamala [États-Unis] ; Nicolás García [États-Unis, 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 [ 2168-0450 ] ; 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.
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.
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.
Url:
DOI: 10.3732/apps.1400115
PubMed: 25909041
PubMed Central: 4406834
Affiliations:
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Soltis</name><affiliation wicri:level="2"><nlm:aff id="aff3">Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Florida Museum of Natural History, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff11">Genetics Institute, University of Florida, Gainesville, Florida, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genetics Institute, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25909041</idno><idno type="pmc">4406834</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406834</idno><idno type="RBID">PMC:4406834</idno><idno type="doi">10.3732/apps.1400115</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000477</idno><idno type="wicri:Area/Pmc/Curation">000477</idno><idno type="wicri:Area/Pmc/Checkpoint">000089</idno><idno type="wicri:Area/Ncbi/Merge">000628</idno><idno type="wicri:Area/Ncbi/Curation">000628</idno><idno type="wicri:Area/Ncbi/Checkpoint">000628</idno><idno type="wicri:Area/Main/Merge">000096</idno><idno type="wicri:Area/Main/Curation">000096</idno><idno type="wicri:Area/Main/Exploration">000096</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes<xref ref-type="author-notes" rid="fn1"><sup>1</sup></xref></title><author><name sortKey="Chamala, Srikar" sort="Chamala, Srikar" uniqKey="Chamala S" first="Srikar" last="Chamala">Srikar Chamala</name><affiliation wicri:level="2"><nlm:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff><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="2"><nlm:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff><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><affiliation wicri:level="2"><nlm:aff id="aff3">Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Florida Museum of Natural History, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4">Facultad de Ciencias Forestales y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile</nlm:aff><country xml:lang="fr">Chili</country><wicri:regionArea>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:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff><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><affiliation wicri:level="2"><nlm:aff id="aff3">Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Florida Museum of Natural History, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff5">Rancho Santa Ana Botanic Garden, Claremont, California, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>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:aff id="aff6">Plant Genomics, J. Craig Venter Institute, Rockville, Maryland, USA</nlm:aff><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:aff id="aff7">Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, Bucknell University, Lewisburg, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff8">Jepson and University Herbaria, University of California, Berkeley, Berkeley, California, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>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:aff id="aff9">Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent</wicri:regionArea><wicri:noRegion>9052 Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff10">Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>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:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff><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><affiliation wicri:level="2"><nlm:aff id="aff11">Genetics Institute, University of Florida, Gainesville, Florida, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>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:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff><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><affiliation wicri:level="2"><nlm:aff id="aff3">Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Florida Museum of Natural History, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff11">Genetics Institute, University of Florida, Gainesville, Florida, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>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:aff id="aff3">Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Florida Museum of Natural History, University of Florida, Gainesville, Florida</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff11">Genetics Institute, University of Florida, Gainesville, Florida, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>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><idno type="eISSN">2168-0450</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Premise of the study:</title><p>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.</p></sec><sec><title>Methods and Results:</title><p>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.</p></sec><sec><title>Conclusions:</title><p>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.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Altschul, S F" uniqKey="Altschul S">S. F. Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W. Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W. Miller</name></author><author><name sortKey="Myers, E W" uniqKey="Myers E">E. W. Myers</name></author><author><name sortKey="Lipman, D J" uniqKey="Lipman D">D. J. Lipman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, S F" uniqKey="Altschul S">S. F. Altschul</name></author><author><name sortKey="Madden, T L" uniqKey="Madden T">T. L. Madden</name></author><author><name sortKey="Sch Ffer, A A" uniqKey="Sch Ffer A">A. A. 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Brad Barbazuk</name><name sortKey="Garcia, Nicolas" sort="Garcia, Nicolas" uniqKey="Garcia N" first="Nicolás" last="García">Nicolás García</name><name sortKey="Garcia, Nicolas" sort="Garcia, Nicolas" uniqKey="Garcia N" first="Nicolás" last="García">Nicolás García</name><name sortKey="Godden, Grant T" sort="Godden, Grant T" uniqKey="Godden G" first="Grant T." last="Godden">Grant T. Godden</name><name sortKey="Godden, Grant T" sort="Godden, Grant T" uniqKey="Godden G" first="Grant T." last="Godden">Grant T. Godden</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="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, Douglas E" sort="Soltis, Douglas E" uniqKey="Soltis D" first="Douglas E." last="Soltis">Douglas E. Soltis</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><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><name sortKey="De Smet, Riet" sort="De Smet, Riet" uniqKey="De Smet R" first="Riet" last="De Smet">Riet De Smet</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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