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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes<xref ref-type="fn" rid="fn1"><sup>1</sup></xref><xref ref-type="fn" rid="fn3"><sup>[OPEN]</sup></xref></title><author><name sortKey="Law, Meiyee" sort="Law, Meiyee" uniqKey="Law M" first="Meiyee" last="Law">Meiyee Law</name></author><author><name sortKey="Childs, Kevin L" sort="Childs, Kevin L" uniqKey="Childs K" first="Kevin L." last="Childs">Kevin L. Childs</name></author><author><name sortKey="Campbell, Michael S" sort="Campbell, Michael S" uniqKey="Campbell M" first="Michael S." last="Campbell">Michael S. Campbell</name></author><author><name sortKey="Stein, Joshua C" sort="Stein, Joshua C" uniqKey="Stein J" first="Joshua C." last="Stein">Joshua C. Stein</name></author><author><name sortKey="Olson, Andrew J" sort="Olson, Andrew J" uniqKey="Olson A" first="Andrew J." last="Olson">Andrew J. Olson</name></author><author><name sortKey="Holt, Carson" sort="Holt, Carson" uniqKey="Holt C" first="Carson" last="Holt">Carson Holt</name></author><author><name sortKey="Panchy, Nicholas" sort="Panchy, Nicholas" uniqKey="Panchy N" first="Nicholas" last="Panchy">Nicholas Panchy</name></author><author><name sortKey="Lei, Jikai" sort="Lei, Jikai" uniqKey="Lei J" first="Jikai" last="Lei">Jikai Lei</name></author><author><name sortKey="Jiao, Dian" sort="Jiao, Dian" uniqKey="Jiao D" first="Dian" last="Jiao">Dian Jiao</name></author><author><name sortKey="Andorf, Carson M" sort="Andorf, Carson M" uniqKey="Andorf C" first="Carson M." last="Andorf">Carson M. Andorf</name></author><author><name sortKey="Lawrence, Carolyn J" sort="Lawrence, Carolyn J" uniqKey="Lawrence C" first="Carolyn J." last="Lawrence">Carolyn J. Lawrence</name></author><author><name sortKey="Ware, Doreen" sort="Ware, Doreen" uniqKey="Ware D" first="Doreen" last="Ware">Doreen Ware</name></author><author><name sortKey="Shiu, Shin Han" sort="Shiu, Shin Han" uniqKey="Shiu S" first="Shin-Han" last="Shiu">Shin-Han Shiu</name></author><author><name sortKey="Sun, Yanni" sort="Sun, Yanni" uniqKey="Sun Y" first="Yanni" last="Sun">Yanni Sun</name></author><author><name sortKey="Jiang, Ning" sort="Jiang, Ning" uniqKey="Jiang N" first="Ning" last="Jiang">Ning Jiang</name></author><author><name sortKey="Yandell, Mark" sort="Yandell, Mark" uniqKey="Yandell M" first="Mark" last="Yandell">Mark Yandell</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25384563</idno><idno type="pmc">4280997</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4280997</idno><idno type="RBID">PMC:4280997</idno><idno type="doi">10.1104/pp.114.245027</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000386</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes<xref ref-type="fn" rid="fn1"><sup>1</sup></xref><xref ref-type="fn" rid="fn3"><sup>[OPEN]</sup></xref></title><author><name sortKey="Law, Meiyee" sort="Law, Meiyee" uniqKey="Law M" first="Meiyee" last="Law">Meiyee Law</name></author><author><name sortKey="Childs, Kevin L" sort="Childs, Kevin L" uniqKey="Childs K" first="Kevin L." last="Childs">Kevin L. Childs</name></author><author><name sortKey="Campbell, Michael S" sort="Campbell, Michael S" uniqKey="Campbell M" first="Michael S." last="Campbell">Michael S. Campbell</name></author><author><name sortKey="Stein, Joshua C" sort="Stein, Joshua C" uniqKey="Stein J" first="Joshua C." last="Stein">Joshua C. Stein</name></author><author><name sortKey="Olson, Andrew J" sort="Olson, Andrew J" uniqKey="Olson A" first="Andrew J." last="Olson">Andrew J. Olson</name></author><author><name sortKey="Holt, Carson" sort="Holt, Carson" uniqKey="Holt C" first="Carson" last="Holt">Carson Holt</name></author><author><name sortKey="Panchy, Nicholas" sort="Panchy, Nicholas" uniqKey="Panchy N" first="Nicholas" last="Panchy">Nicholas Panchy</name></author><author><name sortKey="Lei, Jikai" sort="Lei, Jikai" uniqKey="Lei J" first="Jikai" last="Lei">Jikai Lei</name></author><author><name sortKey="Jiao, Dian" sort="Jiao, Dian" uniqKey="Jiao D" first="Dian" last="Jiao">Dian Jiao</name></author><author><name sortKey="Andorf, Carson M" sort="Andorf, Carson M" uniqKey="Andorf C" first="Carson M." last="Andorf">Carson M. Andorf</name></author><author><name sortKey="Lawrence, Carolyn J" sort="Lawrence, Carolyn J" uniqKey="Lawrence C" first="Carolyn J." last="Lawrence">Carolyn J. Lawrence</name></author><author><name sortKey="Ware, Doreen" sort="Ware, Doreen" uniqKey="Ware D" first="Doreen" last="Ware">Doreen Ware</name></author><author><name sortKey="Shiu, Shin Han" sort="Shiu, Shin Han" uniqKey="Shiu S" first="Shin-Han" last="Shiu">Shin-Han Shiu</name></author><author><name sortKey="Sun, Yanni" sort="Sun, Yanni" uniqKey="Sun Y" first="Yanni" last="Sun">Yanni Sun</name></author><author><name sortKey="Jiang, Ning" sort="Jiang, Ning" uniqKey="Jiang N" first="Ning" last="Jiang">Ning Jiang</name></author><author><name sortKey="Yandell, Mark" sort="Yandell, Mark" uniqKey="Yandell M" first="Mark" last="Yandell">Mark Yandell</name></author></analytic><series><title level="j">Plant Physiology</title><idno type="ISSN">0032-0889</idno><idno type="eISSN">1532-2548</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>Reannotation of the maize genome using MAKER-P results in many revised and new gene models</italic>.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Plant Physiol</journal-id><journal-id journal-id-type="iso-abbrev">Plant Physiol</journal-id><journal-id journal-id-type="hwp">plantphysiol</journal-id><journal-id journal-id-type="publisher-id">aspb</journal-id><journal-title-group><journal-title>Plant Physiology</journal-title></journal-title-group><issn pub-type="ppub">0032-0889</issn><issn pub-type="epub">1532-2548</issn><publisher><publisher-name>American Society of Plant Biologists</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25384563</article-id><article-id pub-id-type="pmc">4280997</article-id><article-id pub-id-type="publisher-id">245027</article-id><article-id pub-id-type="doi">10.1104/pp.114.245027</article-id><article-categories><subj-group subj-group-type="heading"><subject>Breakthrough Technologies</subject></subj-group></article-categories><title-group><article-title>Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes<xref ref-type="fn" rid="fn1"><sup>1</sup></xref><xref ref-type="fn" rid="fn3"><sup>[OPEN]</sup></xref></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Law</surname><given-names>MeiYee</given-names></name></contrib><contrib contrib-type="author"><name><surname>Childs</surname><given-names>Kevin L.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Campbell</surname><given-names>Michael S.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Stein</surname><given-names>Joshua C.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Olson</surname><given-names>Andrew J.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Holt</surname><given-names>Carson</given-names></name></contrib><contrib contrib-type="author"><name><surname>Panchy</surname><given-names>Nicholas</given-names></name></contrib><contrib contrib-type="author"><name><surname>Lei</surname><given-names>Jikai</given-names></name></contrib><contrib contrib-type="author"><name><surname>Jiao</surname><given-names>Dian</given-names></name></contrib><contrib contrib-type="author"><name><surname>Andorf</surname><given-names>Carson M.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Lawrence</surname><given-names>Carolyn J.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Ware</surname><given-names>Doreen</given-names></name></contrib><contrib contrib-type="author"><name><surname>Shiu</surname><given-names>Shin-Han</given-names></name></contrib><contrib contrib-type="author"><name><surname>Sun</surname><given-names>Yanni</given-names></name></contrib><contrib contrib-type="author"><name><surname>Jiang</surname><given-names>Ning</given-names></name></contrib><contrib contrib-type="author"><name><surname>Yandell</surname><given-names>Mark</given-names></name><xref ref-type="corresp" rid="cor1">*</xref></contrib><aff id="aff1">The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);</aff><aff id="aff2">Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;</aff><aff id="aff3">Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;</aff><aff id="aff4">iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);</aff><aff id="aff5">Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);</aff><aff id="aff6">Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);</aff><aff id="aff7">Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; and</aff><aff id="aff9">United States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)</aff></contrib-group><author-notes><fn><p><ext-link ext-link-type="uri" xlink:href="http://www.plantphysiol.org/cgi/doi/10.1104/pp.114.245027">www.plantphysiol.org/cgi/doi/10.1104/pp.114.245027</ext-link></p></fn><corresp id="cor1"><label>*</label>Address correspondence to <email>myandell@genetics.utah.edu</email>.</corresp><fn id="afn1"><p>The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (<ext-link ext-link-type="uri" xlink:href="http://www.plantphysiol.org">www.plantphysiol.org</ext-link>) is: Mark Yandell (<email>myandell@genetics.utah.edu</email>).</p></fn></author-notes><pmc-comment>Fake ppub date generated by PMC from publisher pub-date/@pub-type='epub-ppub' </pmc-comment>
<pub-date pub-type="ppub"><month>1</month><year>2015</year></pub-date><pub-date pub-type="epub"><day>10</day><month>11</month><year>2014</year></pub-date><pub-date pub-type="pmc-release"><day>10</day><month>11</month><year>2014</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>167</volume><issue>1</issue><fpage>25</fpage><lpage>39</lpage><history><date date-type="received"><day>19</day><month>6</month><year>2014</year></date><date date-type="accepted"><day>02</day><month>11</month><year>2014</year></date></history><permissions><copyright-statement>© 2015 American Society of Plant Biologists. All Rights Reserved.</copyright-statement><copyright-year>2015</copyright-year></permissions><self-uri xlink:role="icon" xlink:href="PP_245027_ic1.gif"></self-uri><self-uri content-type="alt-lang-pdf zh" xlink:href="25.chinese.pdf"></self-uri><abstract abstract-type="precis"><p><italic>Reannotation of the maize genome using MAKER-P results in many revised and new gene models</italic>.</p></abstract><abstract><p>The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-P to update and revise the maize (<italic>Zea mays</italic>) B73 RefGen_v3 annotation build (5b+) in less than 3 h using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, well-supported protein-coding genes not present in the 5b+ annotation build, added additional untranslated regions to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of large and diverse evidence data sets), identified 104,215 pseudogene fragments, and created an additional 2,522 noncoding gene annotations. We also describe a method for de novo training of MAKER-P for the annotation of newly sequenced grass genomes. Collectively, these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes.</p></abstract><counts><page-count count="15"></page-count></counts><custom-meta-group><custom-meta><meta-name> DJS Export </meta-name><meta-value>v1</meta-value></custom-meta></custom-meta-group></article-meta><notes><glossary><title>Glossary</title><def-list><def-item><term id="term1">BAC</term><def id="def1"><p>bacterial artificial chromosome</p></def></def-item><def-item><term id="term2">TE</term><def id="def2"><p>transposable element</p></def></def-item><def-item><term id="term3">WGS</term><def id="def3"><p>whole-genome shotgun</p></def></def-item><def-item><term id="term4">cDNA</term><def id="def4"><p>complementary DNA</p></def></def-item><def-item><term id="term5">RNA-seq</term><def id="def5"><p>RNA sequencing</p></def></def-item><def-item><term id="term6">ncRNA</term><def id="def6"><p>noncoding RNA</p></def></def-item><def-item><term id="term7">TAIR</term><def id="def7"><p>The Arabidopsis Information Resource</p></def></def-item><def-item><term id="term8">UTR</term><def id="def8"><p>untranslated region</p></def></def-item><def-item><term id="term9">NCBI</term><def id="def9"><p>National Center for Biotechnology Information</p></def></def-item><def-item><term id="term10">AED</term><def id="def10"><p>annotation edit distance</p></def></def-item><def-item><term id="term11">CDF</term><def id="def11"><p>cumulative distribution function</p></def></def-item><def-item><term id="term12">miRNA</term><def id="def12"><p>microRNA</p></def></def-item><def-item><term id="term13">snoRNA</term><def id="def13"><p>small nucleolar RNA</p></def></def-item><def-item><term id="term14">MULE</term><def id="def14"><p>Mutator-like transposable element</p></def></def-item><def-item><term id="term15">rRNA</term><def id="def15"><p>ribosomal RNA</p></def></def-item></def-list></glossary></notes></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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