MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes1
Identifieur interne : 000628 ( Ncbi/Merge ); précédent : 000627; suivant : 000629MarkerMiner 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
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<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>
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<author><name sortKey="Barbazuk, W Brad" sort="Barbazuk, W Brad" uniqKey="Barbazuk W" first="W. Brad" last="Barbazuk">W. Brad Barbazuk</name>
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<author><name sortKey="Soltis, Pamela S" sort="Soltis, Pamela S" uniqKey="Soltis P" first="Pamela S." last="Soltis">Pamela S. Soltis</name>
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<series><title level="j">Applications in Plant Sciences</title>
<idno type="eISSN">2168-0450</idno>
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<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>
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</TEI>
<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Appl Plant Sci</journal-id>
<journal-id journal-id-type="iso-abbrev">Appl Plant Sci</journal-id>
<journal-id journal-id-type="publisher-id">apps</journal-id>
<journal-title-group><journal-title>Applications in Plant Sciences</journal-title>
</journal-title-group>
<issn pub-type="epub">2168-0450</issn>
<publisher><publisher-name>Botanical Society of America</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25909041</article-id>
<article-id pub-id-type="pmc">4406834</article-id>
<article-id pub-id-type="publisher-id">apps1400115</article-id>
<article-id pub-id-type="doi">10.3732/apps.1400115</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Software Note</subject>
</subj-group>
</article-categories>
<title-group><article-title>MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes<xref ref-type="author-notes" rid="fn1"><sup>1</sup>
</xref>
</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Chamala</surname>
<given-names>Srikar</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>12</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>García</surname>
<given-names>Nicolás</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
<xref ref-type="aff" rid="aff4"><sup>4</sup>
</xref>
<xref ref-type="author-notes" rid="fn2">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Godden</surname>
<given-names>Grant T.</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
<xref ref-type="aff" rid="aff5"><sup>5</sup>
</xref>
<xref ref-type="author-notes" rid="fn2">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Krishnakumar</surname>
<given-names>Vivek</given-names>
</name>
<xref ref-type="aff" rid="aff6"><sup>6</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Jordon-Thaden</surname>
<given-names>Ingrid E.</given-names>
</name>
<xref ref-type="aff" rid="aff7"><sup>7</sup>
</xref>
<xref ref-type="aff" rid="aff8"><sup>8</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>De Smet</surname>
<given-names>Riet</given-names>
</name>
<xref ref-type="aff" rid="aff9"><sup>9</sup>
</xref>
<xref ref-type="aff" rid="aff10"><sup>10</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Barbazuk</surname>
<given-names>W. Brad</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff11"><sup>11</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Soltis</surname>
<given-names>Douglas E.</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
<xref ref-type="aff" rid="aff11"><sup>11</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Soltis</surname>
<given-names>Pamela S.</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
<xref ref-type="aff" rid="aff11"><sup>11</sup>
</xref>
</contrib>
<aff id="aff2"><label>2</label>
Department of Biology, University of Florida, Gainesville, Florida, USA</aff>
<aff id="aff3"><label>3</label>
Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</aff>
<aff id="aff4"><label>4</label>
Facultad de Ciencias Forestales y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile</aff>
<aff id="aff5"><label>5</label>
Rancho Santa Ana Botanic Garden, Claremont, California, USA</aff>
<aff id="aff6"><label>6</label>
Plant Genomics, J. Craig Venter Institute, Rockville, Maryland, USA</aff>
<aff id="aff7"><label>7</label>
Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA</aff>
<aff id="aff8"><label>8</label>
Jepson and University Herbaria, University of California, Berkeley, Berkeley, California, USA</aff>
<aff id="aff9"><label>9</label>
Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium</aff>
<aff id="aff10"><label>10</label>
Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium</aff>
<aff id="aff11"><label>11</label>
Genetics Institute, University of Florida, Gainesville, Florida, USA</aff>
</contrib-group>
<author-notes><fn id="fn1"><label>1</label>
<p>The authors thank all oneKP contributors, especially Gane Ka-Shu Wong, and BGI. Funding for S.C. was provided by the National Science Foundation (NSF; grant IOS-0922742 [P.S.S., D.E.S., W.B.B.]). Research funding for N.G. and G.T.G. was provided in part by NSF Doctoral Dissertation Improvement grants DEB-1310839 (P.S.S. and N.G.) and DEB-1210671 (P.S.S. and G.T.G.), respectively. The salary of I.J.T. was provided by the David Burpee Endowment and Chris Martine (Bucknell University).</p>
</fn>
<fn id="fn2"><label>*</label>
<p>Authors are listed alphabetically by surname and contributed equally.</p>
</fn>
<corresp id="cor1"><label>12</label>
Author for correspondence: <email>srikarchamala@gmail.com</email>
</corresp>
</author-notes>
<pub-date pub-type="collection"><month>4</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="epub"><day>6</day>
<month>4</month>
<year>2015</year>
</pub-date>
<volume>3</volume>
<issue>4</issue>
<elocation-id>apps.1400115</elocation-id>
<history><date date-type="received"><day>4</day>
<month>12</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>25</day>
<month>2</month>
<year>2015</year>
</date>
</history>
<permissions><copyright-statement>© 2015 Chamala et al. Published by the Botanical Society of America</copyright-statement>
<copyright-year>2015</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/"><license-p>This work is licensed under a Creative Commons Attribution License (CC-BY-NC-SA).</license-p>
</license>
</permissions>
<abstract><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>
</abstract>
<kwd-group><kwd>data mining</kwd>
<kwd>introns</kwd>
<kwd>marker development</kwd>
<kwd>next-generation sequencing</kwd>
<kwd>phylogenetics</kwd>
<kwd>single-copy nuclear genes</kwd>
<kwd>transcriptomes</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Belgique</li>
<li>Chili</li>
<li>États-Unis</li>
</country>
<region><li>Californie</li>
<li>Floride</li>
<li>Maryland</li>
<li>Pennsylvanie</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="Barbazuk, W Brad" sort="Barbazuk, W Brad" uniqKey="Barbazuk W" first="W. Brad" last="Barbazuk">W. 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>
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