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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">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><nlm:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation></author><author><name sortKey="Garcia, Nicolas" sort="Garcia, Nicolas" uniqKey="Garcia N" first="Nicolás" last="García">Nicolás García</name><affiliation><nlm:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff4">Facultad de Ciencias Forestales y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile</nlm:aff></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><nlm:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff5">Rancho Santa Ana Botanic Garden, Claremont, California, USA</nlm:aff></affiliation></author><author><name sortKey="Krishnakumar, Vivek" sort="Krishnakumar, Vivek" uniqKey="Krishnakumar V" first="Vivek" last="Krishnakumar">Vivek Krishnakumar</name><affiliation><nlm:aff id="aff6">Plant Genomics, J. Craig Venter Institute, Rockville, Maryland, USA</nlm:aff></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><nlm:aff id="aff7">Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff8">Jepson and University Herbaria, University of California, Berkeley, Berkeley, California, USA</nlm:aff></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><nlm:aff id="aff9">Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium</nlm:aff></affiliation><affiliation><nlm:aff id="aff10">Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium</nlm:aff></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><nlm:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff11">Genetics Institute, University of Florida, Gainesville, Florida, USA</nlm:aff></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><nlm:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff11">Genetics Institute, University of Florida, Gainesville, Florida, USA</nlm:aff></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><nlm:aff id="aff3">Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff11">Genetics Institute, University of Florida, Gainesville, Florida, USA</nlm:aff></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></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><nlm:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation></author><author><name sortKey="Garcia, Nicolas" sort="Garcia, Nicolas" uniqKey="Garcia N" first="Nicolás" last="García">Nicolás García</name><affiliation><nlm:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff4">Facultad de Ciencias Forestales y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile</nlm:aff></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><nlm:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff5">Rancho Santa Ana Botanic Garden, Claremont, California, USA</nlm:aff></affiliation></author><author><name sortKey="Krishnakumar, Vivek" sort="Krishnakumar, Vivek" uniqKey="Krishnakumar V" first="Vivek" last="Krishnakumar">Vivek Krishnakumar</name><affiliation><nlm:aff id="aff6">Plant Genomics, J. Craig Venter Institute, Rockville, Maryland, USA</nlm:aff></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><nlm:aff id="aff7">Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff8">Jepson and University Herbaria, University of California, Berkeley, Berkeley, California, USA</nlm:aff></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><nlm:aff id="aff9">Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium</nlm:aff></affiliation><affiliation><nlm:aff id="aff10">Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium</nlm:aff></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><nlm:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff11">Genetics Institute, University of Florida, Gainesville, Florida, USA</nlm:aff></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><nlm:aff id="aff2">Department of Biology, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff11">Genetics Institute, University of Florida, Gainesville, Florida, USA</nlm:aff></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><nlm:aff id="aff3">Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA</nlm:aff></affiliation><affiliation><nlm:aff id="aff11">Genetics Institute, University of Florida, Gainesville, Florida, USA</nlm:aff></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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<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><body><p>The availability of next-generation sequencing (NGS) technologies and improved computational tools has revolutionized the field of plant molecular systematics (reviewed in <xref rid="bib6" ref-type="bibr">Cronn et al., 2012</xref>; <xref rid="bib16" ref-type="bibr">McCormack et al., 2013</xref>; <xref rid="bib20" ref-type="bibr">Soltis et al., 2013</xref>). Access to genome-scale data presents exciting opportunities for researchers to develop hundreds or potentially thousands of informative, taxon-specific loci from nuclear genomes—large, multilocus data sets that can potentially resolve relationships at any phylogenetic scale (e.g., <xref rid="bib9" ref-type="bibr">Godden et al., 2012</xref>).</p><p>Recently, there has been much interest in developing single-copy nuclear (SCN) loci from new or existing NGS resources such as transcriptomes (i.e., sequences representing the expressed portion of the genome; see <xref rid="bib4" ref-type="bibr">Bräutigam and Gowik, 2010</xref>; <xref rid="bib23" ref-type="bibr">Strickler et al., 2012</xref>) or genome skimming data (i.e., low-coverage genome sequencing; see <xref rid="bib22" ref-type="bibr">Straub et al., 2012</xref>), and a few pioneering studies have reported great success in developing large sets of orthologous SCN loci with elaborately designed bioinformatic pipelines (e.g., <xref rid="bib21" ref-type="bibr">Straub et al., 2011</xref>; <xref rid="bib19" ref-type="bibr">Rothfels et al., 2013</xref>; <xref rid="bib26" ref-type="bibr">Weitemier et al., 2014</xref>; <xref rid="bib24" ref-type="bibr">Tonnabel et al., 2014</xref>; <xref rid="bib18" ref-type="bibr">Pillon et al., 2014</xref>). Nevertheless, SCN locus discovery from NGS data remains a complex process for many researchers with limited bioinformatics training and access to computational resources. To address these challenges, we developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow to aid plant researchers in the discovery of putative orthologous SCN loci and to facilitate downstream marker development activities such as primer or probe design with user-friendly output.</p><sec sec-type="methods"><title>METHODS AND RESULTS</title><sec><title>Overall design of the application</title><p>Transcriptome sequencing is a useful approach for acquiring new data for phylogenetic marker development, and it might offer some advantages over genome skimming approaches. For example, the high output of NGS platforms, coupled with the reduced representation afforded by transcriptome sequencing, permits multiplexing of more samples from a clade of interest. This provides a more comprehensive a priori survey of phylogenetic utility across both gene space and the clade of interest than genome skimming on a fixed budget. Moreover, researchers may find that expressed sequence tags (ESTs) or de novo transcriptome assemblies already exist for many groups of angiosperms (e.g., transcriptomes available through the 1000 Plants [oneKP] project; see <ext-link ext-link-type="uri" xlink:href="www.onekp.com">www.onekp.com</ext-link> for more information), and use of these existing data resources can eliminate or reduce the overall costs and time investment for some marker discovery projects.</p><p>MarkerMiner is a novel, command line–based computational workflow that identifies putative orthologous SCN loci present in two or more user-provided angiosperm transcriptome assemblies and outputs detailed tabular results and sequence alignments for downstream assessment of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development for targeted sequencing (see <xref ref-type="fig" rid="fig1">Figs. 1</xref>–<xref ref-type="fig" rid="fig3">3</xref>) . The tool features a user-configurable command line interface that is backed by a computational pipeline, and its job submission graphical user interface is accessible to researchers with limited bioinformatics training. Moreover, MarkerMiner is freely available via the iPlant cloud computing infrastructure (<ext-link ext-link-type="uri" xlink:href="http://www.iplantcollaborative.org/ci/atmosphere">http://www.iplantcollaborative.org/ci/atmosphere</ext-link>; <xref rid="bib10" ref-type="bibr">Goff et al., 2011</xref> [also available at <ext-link ext-link-type="uri" xlink:href="https://bitbucket.org/srikarchamala/markerminer">https://bitbucket.org/srikarchamala/markerminer</ext-link>]), providing a working solution for researchers with limited or no access to high-performance computing resources.</p><fig id="fig1" position="float"><label>Fig. 1.</label><caption><p>Filtering steps performed by MarkerMiner 1.0 to identify single-copy nuclear genes from angiosperm transcriptome assembly input. Best (primary) alignments are identified with a star, and secondary alignments are identified with a diamond.</p></caption><graphic xlink:href="apps.1400115fig1"></graphic></fig><fig id="fig2" position="float"><label>Fig. 2.</label><caption><p>Additional data processing and output steps performed by MarkerMiner 1.0.</p></caption><graphic xlink:href="apps.1400115fig2"></graphic></fig><fig id="fig3" position="float"><label>Fig. 3.</label><caption><p>Alignment output produced by MarkerMiner 1.0, including multiple sequence alignments and reference CDS profile alignments for single-copy nuclear loci. The alignment output is useful for assessing the phylogenetic utility of individual loci, predicting putative intron sizes and locations, and developing primers or probes for targeted sequencing.</p></caption><graphic xlink:href="apps.1400115fig3"></graphic></fig><p>MarkerMiner’s fully automated workflow (<xref ref-type="fig" rid="fig1">Figs. 1</xref> and <xref ref-type="fig" rid="fig2">2</xref>) is implemented in Python and makes use of specific open-source bioinformatic software to perform the following data filtering and processing steps: transcript length filtering, putative ortholog filtering, putative SCN locus filtering, secondary transcript reporting, transcript clustering and reorientation, DNA multiple sequence alignments, and DNA profile alignments with protein-coding reference sequences (CDS) containing masked introns. The tool offers convenient functions with regard to user-specified filtering parameters and reference CDS, and these are described in more detail below.</p></sec><sec><title>Filtering transcriptomes using minimum length parameters</title><p>As a first step, MarkerMiner filters each user-provided transcriptome assembly using a minimum length parameter. By default, the application removes transcripts less than 900 bp. However, users have the flexibility to specify an alternative length parameter based on their individual preferences and research needs. Decreasing the default length parameter (e.g., <900 bp) will facilitate retention of larger numbers of transcripts for downstream filtering steps. In contrast, increasing the default length parameter (e.g., >900 bp) may result in discovery of fewer orthologs between sampled taxa.</p></sec><sec><title>Filtering putative ortholog pairs with reciprocal BLAST queries</title><p>MarkerMiner employs independent reciprocal BLAST (<xref rid="bib1" ref-type="bibr">Altschul et al., 1990</xref>, <xref rid="bib2" ref-type="bibr">1997</xref>) queries on each filtered transcriptome assembly to identify putative orthologs. By default, the application uses the <italic>Arabidopsis thaliana</italic> (L.) Heynh. proteome from the PLAZA 2.5 database (<xref rid="bib25" ref-type="bibr">Van Bel et al., 2012</xref>) as a reference. However, we offer the flexibility to use one of 15 additional reference options (see <xref ref-type="boxed-text" rid="Box1">Box 1</xref>), and MarkerMiner is updated periodically as new references become available. Under the default settings, the filtered transcripts from each assembly are aligned against <italic>Arabidopsis</italic> proteins with NCBI-BLASTX using <italic>E</italic>-value 0.01 and, conversely, the <italic>Arabidopsis</italic> proteins are aligned against the filtered transcripts from each assembly with TBLASTN using <italic>E</italic>-value 0.01. The reciprocal top hits from each of the BLAST analyses are retained if they meet the following criteria, respectively: a minimum of 70% of the transcript length is aligned with a reference protein with at least 70% sequence similarity (BLASTX), and a minimum of 80% of the protein length is aligned to a transcript with at least 70% sequence similarity (TBLASTN). These stringency criteria for parsing BLAST output are default parameters, but users have the option to specify alternative criteria.</p></sec><sec><title>Filtering putative single-copy nuclear genes</title><p><xref rid="bib7" ref-type="bibr">De Smet et al. (2013)</xref> reported a carefully curated list of SCN genes as part of a gene family analysis that included 17 genomes broadly distributed across angiosperm phylogeny (i.e., five monocots and 12 eudicots). Of the SCN genes identified by the study, 177 were “strictly single-copy” in all 17 genomes, and 2809 were “mostly single-copy” (i.e., single-copy in most of the genomes, with duplicates detected in at least one to as many as three other genomes) (<xref rid="bib7" ref-type="bibr">De Smet et al., 2013</xref>). As the evolution of these SCN genes is largely uninfluenced by gene duplication, their sequence evolution is expected to act in concordance with species evolution, making them an invaluable resource in mining for SCN loci from transcriptomes.</p><p>MarkerMiner employs a user-specified SCN gene reference set curated by <xref rid="bib7" ref-type="bibr">DeSmet et al. (2013)</xref> as a final data filter. Putative ortholog pairs whose transcripts have top reciprocal BLAST hits against SCN reference proteins are retained and classified as putative single-copy ortholog pairs.</p></sec><sec><title>Secondary transcript reporting</title><p>There may be cases in which a single-copy protein has more than one transcript passing the BLAST filtering criteria. However, as previously indicated, only the transcript with the top scoring alignment is reported by MarkerMiner as a putatively orthologous single-copy transcript. For some researchers, information about additional transcripts with lower scores (which also align uniquely to a single-copy protein) may be of particular interest. These “secondary transcripts” may represent splice isoforms, putative paralogs, or partially assembled transcripts, although their characterization is difficult in the absence of a reference genome.</p><boxed-text id="Box1" position="float"><sec><label>Box 1.</label><title>Reference options available in MarkerMiner 1.0. The default option is indicated with an asterisk (*). Reference genomes and their corresponding annotations were downloaded from the PLAZA 2.5 database (<xref rid="bib25" ref-type="bibr">Van Bel et al., 2012</xref>).</title><p><italic>Arabidopsis lyrata</italic> (L.) O’Kane & Al-Shehbaz</p><p><italic>Arabidopsis thaliana</italic> L.*</p><p><italic>Brachypodium distachyon</italic> (L.) P. Beauv.</p><p><italic>Carica papaya</italic> L.</p><p><italic>Fragaria vesca</italic> L.</p><p><italic>Glycine max</italic> (L.) Merr.</p><p><italic>Malus</italic><italic>domestica</italic> Borkh.</p><p><italic>Manihot esculenta</italic> Crantz</p><p><italic>Medicago truncatula</italic> Gaertn.</p><p><italic>Oryza sativa</italic> L.</p><p><italic>Populus trichocarpa</italic> Torr. & A. Gray</p><p><italic>Ricinus communis</italic> L.</p><p><italic>Sorghum bicolor</italic> (L.) Moench</p><p><italic>Theobroma cacao</italic> L.</p><p><italic>Vitis vinifera</italic> L.</p><p><italic>Zea mays</italic> L.</p></sec></boxed-text><p>MarkerMiner provides additional information about secondary transcripts via additional output. Users can use these tabular results to guide decisions about which loci to pursue for downstream marker development or to investigate further the duplication status of secondary transcripts for particular genes of interest.</p></sec><sec><title>Clustering, reorientation, and alignment of single-copy transcripts and output</title><p>After the transcripts corresponding to SCN loci are filtered from all assemblies, MarkerMiner clusters transcripts by reference protein ID (<xref ref-type="fig" rid="fig2">Fig. 2</xref>). The transcripts within each of the resulting SCN gene clusters (or orthogroup sets) are reverse-complemented as necessary to ensure identical sequence orientation prior to multiple sequence alignment; the corresponding DNA reference sequence of <italic>A. thaliana</italic> (or an alternative, user-specified reference) is used to reorient sequences. Next, MarkerMiner outputs a detailed tabular report that includes the following details for each SCN locus detected: a reference gene ID, a single-copy classification (e.g., “strictly” or “mostly”) according to <xref rid="bib7" ref-type="bibr">De Smet at al. (2013)</xref>, a gene functional description, the number of putative orthologs detected across all assemblies, and a scaffold ID for each of the transcriptome assemblies included in the analysis (<xref ref-type="fig" rid="fig2">Fig. 2</xref>; see also the user manual [available at <ext-link ext-link-type="uri" xlink:href="https://bitbucket.org/srikarchamala/markerminer">https://bitbucket.org/srikarchamala/markerminer</ext-link>], for example). All gene functional descriptions reported to users by MarkerMiner correspond to the TAIR10 <italic>Arabidopsis</italic> genome release (<xref rid="bib14" ref-type="bibr">Lamesch et al., 2012</xref>).</p><p>MarkerMiner outputs two types of alignments to aid researchers with downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development. First, a multiple sequence alignment is performed for each gene cluster with MAFFT (<xref rid="bib11" ref-type="bibr">Katoh et al., 2002</xref>, <xref rid="bib12" ref-type="bibr">2009</xref>) using −quiet and −auto parameters, and alignment files are reported in FASTA format (<xref ref-type="fig" rid="fig2">Figs. 2</xref> and <xref ref-type="fig" rid="fig3">3</xref>). Users can edit these alignments, assess phylogenetic utility among detected loci, infer preliminary phylogenies (if appropriate), or proceed with downstream development of individual loci for phylogenetic applications (<xref ref-type="fig" rid="fig2">Figs. 2</xref> and <xref ref-type="fig" rid="fig3">3</xref>). Second, MarkerMiner aligns the user-specified reference CDS with intronic regions masked with the character ‘N’ to their respective MAFFT multiple sequence alignments (<xref ref-type="fig" rid="fig3">Fig. 3</xref>) by using MAFFT’s ‘−add’ functionality (<xref rid="bib13" ref-type="bibr">Katoh and Frith, 2012</xref>); the intron coordinates correspond to data extracted from the PLAZA 2.5 database.</p><p>MarkerMiner provides all alignment output in FASTA format. The alignments can be useful for prediction of putative intron-exon boundaries and approximate intron size, which will facilitate design of primers or probes for amplification or capture of complete or partial intronic regions. For example, intronic regions can be recovered completely using exon-anchored primer pairs and PCR amplification (<xref rid="bib15" ref-type="bibr">Lemmon and Lemmon, 2013</xref>; <xref rid="bib18" ref-type="bibr">Pillon et al., 2014</xref>). Alternatively, intronic regions can also be recovered with hybrid enrichment approaches (e.g., sequence capture; see <xref rid="bib15" ref-type="bibr">Lemmon and Lemmon, 2013</xref>), whereby probes are designed in the flanking exonic regions of targeted introns (e.g., close to the intron-exon junction). These probes will facilitate capture of partial or complete intronic regions along with their exonic counterparts during a hybridization step, followed by PCR enrichment and sequencing on NGS platforms. With current sequencing technologies capable of generating read lengths up to 2 × 300 bp (Illumina MiSeq; see <ext-link ext-link-type="uri" xlink:href="http://www.illumina.com/systems/sequencing.html">http://www.illumina.com/systems/sequencing.html</ext-link>), sequencing of flanking intronic regions captured or amplified by exonic probes or primers is becoming straightforward. The use of MarkerMiner to develop intronic markers will therefore enable greater use of intron regions for phylogenetic applications.</p><p>Many of the SCN loci identified by <xref rid="bib7" ref-type="bibr">De Smet et al. (2013)</xref> correspond to “housekeeping” genes. Due to their wide conservation across eukaryotes, the exonic regions of these genes may offer limited utility at shallow phylogenetic scales (<xref rid="bib5" ref-type="bibr">Calonje et al., 2009</xref>). Fast-evolving intronic regions may represent more desirable choices for phylogenetic studies of closely related, recently derived, and rapidly diverging angiosperm lineages (see <xref rid="bib9" ref-type="bibr">Godden et al., 2012</xref>). MarkerMiner’s intron-exon boundary predictions are based on a user-specified reference CDS; the accuracy of intron-exon boundaries and intron sizes will depend on the level of divergence between the user-specified reference and the taxa under study.</p></sec><sec><title>Accessibility and high-performance computing</title><p>MarkerMiner is open-source and is made freely accessible to the research community for use in a local computing environment as well as via the iPlant Collaborative Atmosphere cloud-computing infrastructure (<ext-link ext-link-type="uri" xlink:href="http://www.iplantcollaborative.org/ci/atmosphere">http://www.iplantcollaborative.org/ci/atmosphere</ext-link>; <xref rid="bib10" ref-type="bibr">Goff et al., 2011</xref> [also available at <ext-link ext-link-type="uri" xlink:href="https://bitbucket.org/srikarchamala/markerminer">https://bitbucket.org/srikarchamala/markerminer</ext-link>]). Dedicated instances based on a preconfigured MarkerMiner machine image can be requisitioned on iPlant for an analysis and terminated once the workflow is completed. Apart from providing command-line access, each instance also exposes a lightweight Web application with a graphical user interface that can be used to configure and invoke the workflow with the desired input files and job parameters. A user manual for the web application and instructions to access an example data set are provided at <ext-link ext-link-type="uri" xlink:href="https://bitbucket.org/srikarchamala/markerminer">https://bitbucket.org/srikarchamala/markerminer</ext-link>.</p></sec><sec><title>Tests of MarkerMiner using oneKP transcriptomes</title><p>We evaluated the performance of MarkerMiner and tested its efficacy for SCN locus discovery with four data sets comprising transcriptome assemblies from the oneKP project: Lamiales (<italic>n</italic> = 77), Amaryllidaceae s.l. (<italic>n</italic> = 7), <italic>Draba</italic> L. (<italic>n</italic> = 6), and <italic>Solanum</italic> L. (<italic>n</italic> = 6) (see <xref ref-type="app" rid="app1">Appendix 1</xref> for a list of samples). The selected data sets represent groups broadly distributed across angiosperm phylogeny (e.g., asterids, rosids, and monocots sensu <xref rid="bib3" ref-type="bibr">APG III [2009]</xref>) and actual marker development projects (or test cases) focused on resolving relationships at different phylogenetic scales (e.g., interfamilial [Lamiales], intrafamilial [Amaryllidaceae s.l.], and intrageneric [<italic>Draba</italic> and <italic>Solanum</italic>]).</p><p>The total number of distinct, putative SCN loci detected by MarkerMiner (<xref ref-type="fig" rid="fig4">Fig. 4A</xref>) for each clade ranged from 666 (<italic>Draba</italic>) to 1993 (Lamiales) (mean = 1217, median = 1106, standard deviation = 560), with a mean of 535 loci detected per transcriptome accession across the four test cases (median = 584, standard deviation = 226, range = 0–909; results for individual data sets are reported in <xref ref-type="fig" rid="fig4">Fig. 4B</xref>). The distribution of shared SCN loci identified across all sampled accessions within each of the four test cases showed a negative trend (<xref ref-type="fig" rid="fig4">Fig. 4C</xref>); few loci were shared by all accessions, and most loci were detected in only one to three accessions. Nevertheless, at least 13% (<italic>Solanum</italic>) to 22% (Lamiales and <italic>Draba</italic>) of the SCN loci were shared by at least half of the sampled accessions in each test case (mean = 18%, median = 18%, and standard deviation = 0.05% across all four test cases), providing adequate data for downstream assessments of phylogenetic utility and primer or probe development.</p><fig id="fig4" position="float"><label>Fig. 4.</label><caption><p>MarkerMiner 1.0 results for four test cases involving SCN locus discovery at different phylogenetic scales: e.g., interfamilial (Lamiales: 77 transcriptomes), intrafamilial (Amaryllidaceae s.l.: 7 transcriptomes), and intergeneric (<italic>Solanum</italic> L. and <italic>Draba</italic> L.: 6 transcriptomes each). Three graphs illustrate the following for each of the test cases: (A) the total number of detected SCN loci, (B) the distribution of SCN loci detected per taxon, and (C) the distribution of shared SCN loci detected across sampled accessions.</p></caption><graphic xlink:href="apps.1400115fig4"></graphic></fig><p>The phylogenetic utility of putative single-copy genes amplified using primers developed via a preliminary version of MarkerMiner (developed by S. Chamala) was documented in <italic>Metrosideros</italic> Banks ex Gaertn. (<xref rid="bib18" ref-type="bibr">Pillon et al., 2014</xref>). Intron regions were amplified by designing primers on flanking exons using putative intron-exon boundary information determined by aligning cDNA sequences with those of <italic>Arabidopsis</italic> genes.</p><p>Researchers should be aware that loci detected by MarkerMiner might not be single-copy in their clade of study. Evaluation of the single-copy status of genes is needed within the clade of interest, for example using phylogenetic (e.g., <xref rid="bib17" ref-type="bibr">Pillon et al., 2013</xref>) or other (e.g., <xref rid="bib8" ref-type="bibr">Duarte et al., 2010</xref>) approaches.</p></sec></sec><sec sec-type="conclusions"><title>CONCLUSIONS</title><p>MarkerMiner, as demonstrated by our tests with oneKP data, represents an easy-to-use and effective tool for phylogenetic marker development. Researchers with limited bioinformatics training and limited access to high-performance computing resources can use MarkerMiner to identify hundreds of putative SCN genes for phylogenomic analyses of any angiosperm group of interest. While we acknowledge that transcriptomic approaches to marker development may result in large numbers of missing loci across the surveyed samples (as demonstrated by each of our four test cases with oneKP data), the cautionary emphasis placed on individual gene absences may be overstated. First, most of the putative single-copy genes detected by MarkerMiner have general “housekeeping” functions (<xref rid="bib8" ref-type="bibr">Duarte et al., 2010</xref>; <xref rid="bib7" ref-type="bibr">De Smet et al., 2013</xref>). Thus, individual gene absences across surveyed transcriptomes are more likely to represent differences in sequencing quality and coverage across samples than actual gene losses. These differences can be mitigated with careful sample preparation and planning of marker development projects involving NGS (e.g., standardized tissue collection practices and realistic limits to multiplexing). Second, our MarkerMiner results indicated that a large proportion of the putative SCN loci are generally shared by at least half of the surveyed transcriptomes. Despite missing data across our oneKP transcriptomes, MarkerMiner was able to recover ample data for assessments of phylogenetic utility and downstream marker development applications with as few as six transcriptomes.</p><p>The downstream processes for selecting and developing markers for targeted sequencing are more or less the same for approaches that use either transcriptomic or genome skimming data, with the caveat that the phylogenetic utility of noncoding loci cannot be assessed a priori from transcriptome data. 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Four test cases are shown: (1) Amaryllidaceae s.l., (2) Lamiales (including outgroups from Boraginales, Gentianales, and Solanales), (3) <italic>Draba</italic>, and (4) <italic>Solanum</italic>.</p></caption><table frame="hsides" rules="groups"><thead><tr><td rowspan="1" colspan="1">APG III clade</td><td rowspan="1" colspan="1">Order</td><td rowspan="1" colspan="1">Family</td><td rowspan="1" colspan="1">Taxon</td><td rowspan="1" colspan="1">oneKP sample ID</td></tr></thead><tbody><tr><td rowspan="1" colspan="1"><bold>Amaryllidaceae s.l.</bold></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1"> Monocots</td><td rowspan="1" colspan="1">Asparagales</td><td rowspan="1" colspan="1">Amaryllidaceae s.l.</td><td rowspan="1" colspan="1"><italic>Allium sativum</italic> L.</td><td rowspan="1" colspan="1">GJPF</td></tr><tr><td rowspan="1" colspan="1"> Monocots</td><td rowspan="1" colspan="1">Asparagales</td><td rowspan="1" colspan="1">Amaryllidaceae s.l.</td><td rowspan="1" colspan="1"><italic>Agapanthus africanus</italic> (L.) Hoffmanns.</td><td rowspan="1" colspan="1">PRFO</td></tr><tr><td rowspan="1" colspan="1"> Monocots</td><td rowspan="1" colspan="1">Asparagales</td><td rowspan="1" colspan="1">Amaryllidaceae s.l.</td><td rowspan="1" colspan="1"><italic>Narcissus viridiflorus</italic> Schousb.</td><td rowspan="1" colspan="1">IQYY</td></tr><tr><td rowspan="1" colspan="1"> Monocots</td><td rowspan="1" colspan="1">Asparagales</td><td rowspan="1" colspan="1">Amaryllidaceae s.l.</td><td rowspan="1" colspan="1"><italic>Phycella cyrtanthoides</italic> (Sims) Lindl.</td><td rowspan="1" colspan="1">DMIN</td></tr><tr><td rowspan="1" colspan="1"> Monocots</td><td rowspan="1" colspan="1">Asparagales</td><td rowspan="1" colspan="1">Amaryllidaceae s.l.</td><td rowspan="1" colspan="1"><italic>Rhodophiala</italic><italic>splendens</italic> (Renjifo) Traub</td><td rowspan="1" colspan="1">JDTY</td></tr><tr><td rowspan="1" colspan="1"> Monocots</td><td rowspan="1" colspan="1">Asparagales</td><td rowspan="1" colspan="1">Amaryllidaceae s.l.</td><td rowspan="1" colspan="1"><italic>Traubia modesta</italic> (Phil.) Ravenna</td><td rowspan="1" colspan="1">ZKPF</td></tr><tr><td rowspan="1" colspan="1"> Monocots</td><td rowspan="1" colspan="1">Asparagales</td><td rowspan="1" colspan="1">Amaryllidaceae s.l.</td><td rowspan="1" colspan="1"><italic>Zephyranthes treatiae</italic> S. Watson</td><td rowspan="1" colspan="1">DPFW</td></tr><tr><td rowspan="1" colspan="1"><bold>Lamiales</bold></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Boraginales</td><td rowspan="1" colspan="1">Boraginaceae</td><td rowspan="1" colspan="1"><italic>Ehretia acuminata</italic> R. Br.</td><td rowspan="1" colspan="1">EMAL</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Boraginales</td><td rowspan="1" colspan="1">Boraginaceae</td><td rowspan="1" colspan="1"><italic>Lennoa madreporoides</italic> La Llave & Lex.</td><td rowspan="1" colspan="1">SMUR</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Boraginales</td><td rowspan="1" colspan="1">Boraginaceae</td><td rowspan="1" colspan="1"><italic>Mertensia paniculata</italic> (Aiton) G. Don</td><td rowspan="1" colspan="1">DKFZ</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Boraginales</td><td rowspan="1" colspan="1">Boraginaceae</td><td rowspan="1" colspan="1"><italic>Phacelia campanularia</italic> A. Gray</td><td rowspan="1" colspan="1">YQIJ</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Boraginales</td><td rowspan="1" colspan="1">Boraginaceae</td><td rowspan="1" colspan="1"><italic>Pholisma arenarium</italic> Nutt.</td><td rowspan="1" colspan="1">HANM</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Gentianales</td><td rowspan="1" colspan="1">Gentianaceae</td><td rowspan="1" colspan="1"><italic>Exacum affine</italic> Balf. f.</td><td rowspan="1" colspan="1">KPUM</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Gentianales</td><td rowspan="1" colspan="1">Rubiaceae</td><td rowspan="1" colspan="1"><italic>Galium boreale</italic> L.</td><td rowspan="1" colspan="1">WQRD</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Acanthaceae</td><td rowspan="1" colspan="1"><italic>Anisacanthus quadrifidus</italic> (Vahl) Nees</td><td rowspan="1" colspan="1">PCGJ</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Acanthaceae</td><td rowspan="1" colspan="1"><italic>Ruellia brittoniana</italic> Leonard</td><td rowspan="1" colspan="1">AYIY</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Acanthaceae</td><td rowspan="1" colspan="1"><italic>Sanchezia</italic> Ruiz & Pav.</td><td rowspan="1" colspan="1">NBMW</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Acanthaceae</td><td rowspan="1" colspan="1"><italic>Strobilanthes dyeriana</italic> Mast.</td><td rowspan="1" colspan="1">WEAC</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Bignoniaceae</td><td rowspan="1" colspan="1"><italic>Kigelia africana</italic> (Lam.) Benth.</td><td rowspan="1" colspan="1">QKEI</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Bignoniaceae</td><td rowspan="1" colspan="1"><italic>Kigelia africana</italic> (Lam.) Benth.</td><td rowspan="1" colspan="1">SVQC</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Bignoniaceae</td><td rowspan="1" colspan="1"><italic>Mansoa alliacea</italic> (Lam.) A. H. Gentry</td><td rowspan="1" colspan="1">TKEK</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Bignoniaceae</td><td rowspan="1" colspan="1"><italic>Tabebuia umbellata</italic> (Sond.) Sandwith</td><td rowspan="1" colspan="1">UTQR</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Byblidaceae</td><td rowspan="1" colspan="1"><italic>Byblis gigantea</italic> Lindl.</td><td rowspan="1" colspan="1">GDZS</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Calceolariaceae</td><td rowspan="1" colspan="1"><italic>Calceolaria pinifolia</italic> Cav.</td><td rowspan="1" colspan="1">DCCI</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Gesneriaceae</td><td rowspan="1" colspan="1"><italic>Saintpaulia ionantha</italic> H. Wendl.</td><td rowspan="1" colspan="1">RWKR</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Gesneriaceae</td><td rowspan="1" colspan="1"><italic>Sinningia tuberosa</italic> (Mart.) H. E. Moore</td><td rowspan="1" colspan="1">DTNC</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Gratiolaceae</td><td rowspan="1" colspan="1"><italic>Bacopa caroliniana</italic> (Walter) B. L. Rob.</td><td rowspan="1" colspan="1">CLRW</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Agastache rugosa</italic> (Fisch. & C. A. Mey.) Kuntze</td><td rowspan="1" colspan="1">PUCW</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Ajuga reptans</italic> L.</td><td rowspan="1" colspan="1">UCNM</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Lavandula angustifolia</italic> Mill.</td><td rowspan="1" colspan="1">FYUH</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Leonurus japonicus</italic> Houtt.</td><td rowspan="1" colspan="1">SNNC</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Marrubium vulgare</italic> L.</td><td rowspan="1" colspan="1">EAAA</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Melissa officinalis</italic> L.</td><td rowspan="1" colspan="1">TAGM</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Clinopodium</italic><italic>serpyllifolium</italic> (M. Bieb.) Kuntze subsp. <italic>fruticosum</italic> (L.) Bräuchler</td><td rowspan="1" colspan="1">WHNV</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Nepeta cataria</italic> L.</td><td rowspan="1" colspan="1">FUMQ</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Oxera neriifolia</italic> (Montrouz.) Beauvis.</td><td rowspan="1" colspan="1">GNPX</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Oxera pulchella</italic> Labill.</td><td rowspan="1" colspan="1">RTNA</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Pogostemon cablin</italic> (Blanco) Benth.</td><td rowspan="1" colspan="1">GETL</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Poliomintha bustamanta</italic> B. L. Turner</td><td rowspan="1" colspan="1">XMBA</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Prunella vulgaris</italic> L.</td><td rowspan="1" colspan="1">PHCE</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Pycnanthemum tenuifolium</italic> Schrad.</td><td rowspan="1" colspan="1">DYFF</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Rosmarinus officinalis</italic> L.</td><td rowspan="1" colspan="1">FDMM</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Salvia</italic> L.</td><td rowspan="1" colspan="1">EQDA</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Scutellaria montana</italic> Chapm.</td><td rowspan="1" colspan="1">ATYL</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Plectranthus scutellarioides</italic> (L.) R. Br.</td><td rowspan="1" colspan="1">BAHE</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Teucrium chamaedrys</italic> L.</td><td rowspan="1" colspan="1">LRRR</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lamiaceae</td><td rowspan="1" colspan="1"><italic>Thymus vulgaris</italic> L.</td><td rowspan="1" colspan="1">IYDF</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lentibulariaceae</td><td rowspan="1" colspan="1"><italic>Pinguicula agnata</italic> Casper</td><td rowspan="1" colspan="1">MXFG</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lentibulariaceae</td><td rowspan="1" colspan="1"><italic>Pinguicula caudata</italic> Schltdl.</td><td rowspan="1" colspan="1">JCMU</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Lentibulariaceae</td><td rowspan="1" colspan="1"><italic>Utricularia</italic> L.</td><td rowspan="1" colspan="1">HRUR</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Oleaceae</td><td rowspan="1" colspan="1"><italic>Chionanthus retusus</italic> Paxton</td><td rowspan="1" colspan="1">KTAR</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Oleaceae</td><td rowspan="1" colspan="1"><italic>Forestiera segregata</italic> (Jacq.) Krug & Urb.</td><td rowspan="1" colspan="1">UEEN</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Oleaceae</td><td rowspan="1" colspan="1"><italic>Ligustrum sinense</italic> Lour.</td><td rowspan="1" colspan="1">MZLD</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Oleaceae</td><td rowspan="1" colspan="1"><italic>Olea europaea</italic> L.</td><td rowspan="1" colspan="1">TORX</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Orobanchaceae</td><td rowspan="1" colspan="1"><italic>Conopholis americana</italic> (L.) Wallr.</td><td rowspan="1" colspan="1">FAMO</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Orobanchaceae</td><td rowspan="1" colspan="1"><italic>Epifagus virginiana</italic> (L.) W. P. C. Barton</td><td rowspan="1" colspan="1">URZI</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Orobanchaceae</td><td rowspan="1" colspan="1"><italic>Epifagus virginiana</italic> (L.) W. P. C. Barton</td><td rowspan="1" colspan="1">XMOG</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Orobanchaceae</td><td rowspan="1" colspan="1"><italic>Lindenbergia philippinensis</italic> Benth.</td><td rowspan="1" colspan="1">WUZV</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Orobanchaceae</td><td rowspan="1" colspan="1"><italic>Lindenbergia philippinensis</italic> Benth.</td><td rowspan="1" colspan="1">ZVFS</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Orobanchaceae</td><td rowspan="1" colspan="1"><italic>Orobanche fasciculata</italic> Nutt.</td><td rowspan="1" colspan="1">PHOQ</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Orobanchaceae</td><td rowspan="1" colspan="1"><italic>Orobanche fasciculata</italic> Nutt.</td><td rowspan="1" colspan="1">VTOK</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Paulowniaceae</td><td rowspan="1" colspan="1"><italic>Paulownia fargesii</italic> Franch.</td><td rowspan="1" colspan="1">UMUL</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Pedaliaceae</td><td rowspan="1" colspan="1"><italic>Uncarina grandidieri</italic> (Baill.) Stapf</td><td rowspan="1" colspan="1">ZRIN</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Plantaginaceae</td><td rowspan="1" colspan="1"><italic>Antirrhinum majus</italic> L.</td><td rowspan="1" colspan="1">EBOL</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Plantaginaceae</td><td rowspan="1" colspan="1"><italic>Antirrhinum majus</italic> L.</td><td rowspan="1" colspan="1">TPUT</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Plantaginaceae</td><td rowspan="1" colspan="1"><italic>Antirrhinum braun-blanquetii</italic> Rothm.</td><td rowspan="1" colspan="1">YRHD</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Plantaginaceae</td><td rowspan="1" colspan="1"><italic>Digitalis purpurea</italic> L.</td><td rowspan="1" colspan="1">GNRI</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Plantaginaceae</td><td rowspan="1" colspan="1"><italic>Plantago maritima</italic> L.</td><td rowspan="1" colspan="1">YKZB</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Plantaginaceae</td><td rowspan="1" colspan="1"><italic>Plantago virginica</italic> L.</td><td rowspan="1" colspan="1">PTBJ</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Rhemanniaceae</td><td rowspan="1" colspan="1"><italic>Rehmannia glutinosa</italic> Steud.</td><td rowspan="1" colspan="1">OWAS</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Schlegeliaceae</td><td rowspan="1" colspan="1"><italic>Schlegelia</italic><italic>parasitica</italic> (Sw.) Miers ex Griseb.</td><td rowspan="1" colspan="1">GAKQ</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Schlegeliaceae</td><td rowspan="1" colspan="1"><italic>Schlegelia parasitica</italic> (Sw.) Miers ex Griseb.</td><td rowspan="1" colspan="1">CWLL</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Schlegeliaceae</td><td rowspan="1" colspan="1"><italic>Schlegelia violacea</italic> Griseb.</td><td rowspan="1" colspan="1">EDXZ</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Scrophulariaceae</td><td rowspan="1" colspan="1"><italic>Anticharis glandulosa</italic> Asch.</td><td rowspan="1" colspan="1">EJBY</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Scrophulariaceae</td><td rowspan="1" colspan="1"><italic>Buddleja</italic> L.</td><td rowspan="1" colspan="1">GRFT</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Scrophulariaceae</td><td rowspan="1" colspan="1"><italic>Buddleja lindleyana</italic> Lindl.</td><td rowspan="1" colspan="1">XRLM</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Scrophulariaceae</td><td rowspan="1" colspan="1"><italic>Celsia arcturus</italic> Jacq.</td><td rowspan="1" colspan="1">SIBR</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Scrophulariaceae</td><td rowspan="1" colspan="1"><italic>Verbascum</italic> L.</td><td rowspan="1" colspan="1">XXYA</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Tetrachondraceae</td><td rowspan="1" colspan="1"><italic>Polypremum procumbens</italic> L.</td><td rowspan="1" colspan="1">COBX</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Verbenaceae</td><td rowspan="1" colspan="1"><italic>Lantana camara</italic> L.</td><td rowspan="1" colspan="1">PSHB</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Verbenaceae</td><td rowspan="1" colspan="1"><italic>Phyla dulcis</italic> (Trevir.) Moldenke</td><td rowspan="1" colspan="1">MQIV</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Lamiales</td><td rowspan="1" colspan="1">Verbenaceae</td><td rowspan="1" colspan="1"><italic>Verbena hastata</italic> L.</td><td rowspan="1" colspan="1">GCFE</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Solanales</td><td rowspan="1" colspan="1">Convolvulaceae</td><td rowspan="1" colspan="1"><italic>Ipomoea pubescens</italic> Lam.</td><td rowspan="1" colspan="1">EMBR</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Solanales</td><td rowspan="1" colspan="1">Solanaceae</td><td rowspan="1" colspan="1"><italic>Solanum ptychanthum</italic> Dunal</td><td rowspan="1" colspan="1">DLJZ</td></tr><tr><td rowspan="1" colspan="1"><bold><italic>Draba</italic></bold></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/rosids/malvids</td><td rowspan="1" colspan="1">Brassicales</td><td rowspan="1" colspan="1">Brassicaceae</td><td rowspan="1" colspan="1"><italic>Draba aizoides</italic> L.</td><td rowspan="1" colspan="1">HABV</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/rosids/malvids</td><td rowspan="1" colspan="1">Brassicales</td><td rowspan="1" colspan="1">Brassicaceae</td><td rowspan="1" colspan="1"><italic>Draba hispida</italic> Willd.</td><td rowspan="1" colspan="1">GTSV</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/rosids/malvids</td><td rowspan="1" colspan="1">Brassicales</td><td rowspan="1" colspan="1">Brassicaceae</td><td rowspan="1" colspan="1"><italic>Draba magellanica</italic> Lam.</td><td rowspan="1" colspan="1">UVQL</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/rosids/malvids</td><td rowspan="1" colspan="1">Brassicales</td><td rowspan="1" colspan="1">Brassicaceae</td><td rowspan="1" colspan="1"><italic>Draba oligosperma</italic> Hook.</td><td rowspan="1" colspan="1">LAPO</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/rosids/malvids</td><td rowspan="1" colspan="1">Brassicales</td><td rowspan="1" colspan="1">Brassicaceae</td><td rowspan="1" colspan="1"><italic>Draba ossetica</italic> (Rupr.) Sommier & Levier</td><td rowspan="1" colspan="1">LJQF</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/rosids/malvids</td><td rowspan="1" colspan="1">Brassicales</td><td rowspan="1" colspan="1">Brassicaceae</td><td rowspan="1" colspan="1"><italic>Draba</italic><italic>sachalinensis</italic> Trautv.</td><td rowspan="1" colspan="1">BXBF</td></tr><tr><td rowspan="1" colspan="1"><bold><italic>Solanum</italic></bold></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Solanales</td><td rowspan="1" colspan="1">Solanaceae</td><td rowspan="1" colspan="1"><italic>Solanum cheesmaniae</italic> (L. Riley) Fosberg</td><td rowspan="1" colspan="1">UGJI</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Solanales</td><td rowspan="1" colspan="1">Solanaceae</td><td rowspan="1" colspan="1"><italic>Solanum dulcamara</italic> L.</td><td rowspan="1" colspan="1">GHLP</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Solanales</td><td rowspan="1" colspan="1">Solanaceae</td><td rowspan="1" colspan="1"><italic>Solanum lasiophyllum</italic> Humb. & Bonpl. ex Dunal</td><td rowspan="1" colspan="1">DLAI</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Solanales</td><td rowspan="1" colspan="1">Solanaceae</td><td rowspan="1" colspan="1"><italic>Solanum ptychanthum</italic> Dunal</td><td rowspan="1" colspan="1">DLJZ</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Solanales</td><td rowspan="1" colspan="1">Solanaceae</td><td rowspan="1" colspan="1"><italic>Solanum sisymbriifolium</italic> Lam.</td><td rowspan="1" colspan="1">NMDZ</td></tr><tr><td rowspan="1" colspan="1"> Core eudicots/asterids/lamiids</td><td rowspan="1" colspan="1">Solanales</td><td rowspan="1" colspan="1">Solanaceae</td><td rowspan="1" colspan="1"><italic>Solanum virginianum</italic> L.</td><td rowspan="1" colspan="1">LQJY</td></tr></tbody></table></table-wrap></app></app-group></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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