Computational Identification and Systematic Classification of Novel Cytochrome P450 Genes in Salvia miltiorrhiza
Identifieur interne : 000227 ( Pmc/Curation ); précédent : 000226; suivant : 000228Computational Identification and Systematic Classification of Novel Cytochrome P450 Genes in Salvia miltiorrhiza
Auteurs : Haimei Chen [République populaire de Chine] ; Bin Wu [République populaire de Chine] ; David R. Nelson [États-Unis] ; Kai Wu [République populaire de Chine] ; Chang Liu [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
Url:
DOI: 10.1371/journal.pone.0115149
PubMed: 25493946
PubMed Central: 4262458
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Computational Identification and Systematic Classification of Novel Cytochrome P450 Genes in <italic>Salvia miltiorrhiza</italic></title><author><name sortKey="Chen, Haimei" sort="Chen, Haimei" uniqKey="Chen H" first="Haimei" last="Chen">Haimei Chen</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Wu, Bin" sort="Wu, Bin" uniqKey="Wu B" first="Bin" last="Wu">Bin Wu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Nelson, David R" sort="Nelson, David R" uniqKey="Nelson D" first="David R." last="Nelson">David R. Nelson</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee</wicri:regionArea></affiliation></author><author><name sortKey="Wu, Kai" sort="Wu, Kai" uniqKey="Wu K" first="Kai" last="Wu">Kai Wu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Chang" sort="Liu, Chang" uniqKey="Liu C" first="Chang" last="Liu">Chang Liu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25493946</idno><idno type="pmc">4262458</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262458</idno><idno type="RBID">PMC:4262458</idno><idno type="doi">10.1371/journal.pone.0115149</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000227</idno><idno type="wicri:Area/Pmc/Curation">000227</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Computational Identification and Systematic Classification of Novel Cytochrome P450 Genes in <italic>Salvia miltiorrhiza</italic></title><author><name sortKey="Chen, Haimei" sort="Chen, Haimei" uniqKey="Chen H" first="Haimei" last="Chen">Haimei Chen</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Wu, Bin" sort="Wu, Bin" uniqKey="Wu B" first="Bin" last="Wu">Bin Wu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Nelson, David R" sort="Nelson, David R" uniqKey="Nelson D" first="David R." last="Nelson">David R. Nelson</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee</wicri:regionArea></affiliation></author><author><name sortKey="Wu, Kai" sort="Wu, Kai" uniqKey="Wu K" first="Kai" last="Wu">Kai Wu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Chang" sort="Liu, Chang" uniqKey="Liu C" first="Chang" last="Liu">Chang Liu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</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>Salvia miltiorrhiza</italic> is one of the most economically important medicinal plants. Cytochrome P450 (CYP450) genes have been implicated in the biosynthesis of its active components. However, only a dozen full-length CYP450 genes have been described, and there is no systematic classification of CYP450 genes in <italic>S. miltiorrhiza</italic>. We obtained 77,549 unigenes from three tissue types of <italic>S. miltiorrhiza</italic> using RNA-Seq technology. Combining our data with previously identified CYP450 sequences and scanning with the CYP450 model from Pfam resulted in the identification of 116 full-length and 135 partial-length CYP450 genes. The 116 genes were classified into 9 clans and 38 families using standard criteria. The RNA-Seq results showed that 35 CYP450 genes were co-expressed with CYP76AH1, a marker gene for tanshinone biosynthesis, using r≥0.9 as a cutoff. The expression profiles for 16 of 19 randomly selected CYP450 obtained from RNA-Seq were validated by qRT-PCR. Comparing against the KEGG database, 10 CYP450 genes were found to be associated with diterpenoid biosynthesis. Considering all the evidence, 3 CYP450 genes were identified to be potentially involved in terpenoid biosynthesis. Moreover, we found that 15 CYP450 genes were possibly regulated by antisense transcripts (r≥0.9 or r≤–0.9). Lastly, a web resource (SMCYP450, <ext-link ext-link-type="uri" xlink:href="http://www.herbalgenomics.org/samicyp450">http://www.herbalgenomics.org/samicyp450</ext-link>) was set up, which allows users to browse, search, retrieve and compare CYP450 genes and can serve as a centralized resource.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Lijuan, M" uniqKey="Lijuan M">M Lijuan</name></author><author><name sortKey="Xuezhu, Z" uniqKey="Xuezhu Z">Z Xuezhu</name></author><author><name sortKey="Haiping, Z" uniqKey="Haiping Z">Z Haiping</name></author><author><name sortKey="Yiru, G" uniqKey="Yiru G">G Yiru</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ma, Y" uniqKey="Ma Y">Y Ma</name></author><author><name sortKey="Yuan, L" uniqKey="Yuan L">L Yuan</name></author><author><name sortKey="Wu, B" uniqKey="Wu B">B Wu</name></author><author><name sortKey="Li, X" uniqKey="Li X">X 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25493946</article-id><article-id pub-id-type="pmc">4262458</article-id><article-id pub-id-type="publisher-id">PONE-D-14-38370</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0115149</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology and Life Sciences</subject><subj-group><subject>Cell Biology</subject><subj-group><subject>Molecular Cell Biology</subject></subj-group></subj-group><subj-group><subject>Biochemistry</subject><subj-group><subject>Biosynthesis</subject></subj-group></subj-group><subj-group><subject>Computational Biology</subject><subj-group><subject>Biological Data Management</subject></subj-group></subj-group><subj-group><subject>Genetics</subject><subj-group><subject>Gene Expression</subject><subject>Gene Function</subject></subj-group></subj-group><subj-group><subject>Molecular Biology</subject></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Computer and Information Sciences</subject><subj-group><subject>Computing Systems</subject><subj-group><subject>Molecular Computing</subject></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Computational Identification and Systematic Classification of Novel Cytochrome P450 Genes in <italic>Salvia miltiorrhiza</italic></article-title><alt-title alt-title-type="running-head">Identification and Classification CYP450 Genes in <italic>Salvia miltiorrhiza</italic></alt-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Chen</surname><given-names>Haimei</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Wu</surname><given-names>Bin</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Nelson</surname><given-names>David R.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wu</surname><given-names>Kai</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Chang</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Jain</surname><given-names>Mukesh</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>National Institute of Plant Genome Research, India</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>cliu@implad.ac.cn</email></corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: CL. Performed the experiments: HC. Analyzed the data: HC KW DRN. Contributed reagents/materials/analysis tools: HC BW. Contributed to the writing of the manuscript: HC BW.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>10</day><month>12</month><year>2014</year></pub-date><volume>9</volume><issue>12</issue><elocation-id>e115149</elocation-id><history><date date-type="received"><day>26</day><month>8</month><year>2014</year></date><date date-type="accepted"><day>19</day><month>11</month><year>2014</year></date></history><permissions><copyright-year>2014</copyright-year><copyright-holder>Chen et al</copyright-holder><license><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><p><italic>Salvia miltiorrhiza</italic> is one of the most economically important medicinal plants. Cytochrome P450 (CYP450) genes have been implicated in the biosynthesis of its active components. However, only a dozen full-length CYP450 genes have been described, and there is no systematic classification of CYP450 genes in <italic>S. miltiorrhiza</italic>. We obtained 77,549 unigenes from three tissue types of <italic>S. miltiorrhiza</italic> using RNA-Seq technology. Combining our data with previously identified CYP450 sequences and scanning with the CYP450 model from Pfam resulted in the identification of 116 full-length and 135 partial-length CYP450 genes. The 116 genes were classified into 9 clans and 38 families using standard criteria. The RNA-Seq results showed that 35 CYP450 genes were co-expressed with CYP76AH1, a marker gene for tanshinone biosynthesis, using r≥0.9 as a cutoff. The expression profiles for 16 of 19 randomly selected CYP450 obtained from RNA-Seq were validated by qRT-PCR. Comparing against the KEGG database, 10 CYP450 genes were found to be associated with diterpenoid biosynthesis. Considering all the evidence, 3 CYP450 genes were identified to be potentially involved in terpenoid biosynthesis. Moreover, we found that 15 CYP450 genes were possibly regulated by antisense transcripts (r≥0.9 or r≤–0.9). Lastly, a web resource (SMCYP450, <ext-link ext-link-type="uri" xlink:href="http://www.herbalgenomics.org/samicyp450">http://www.herbalgenomics.org/samicyp450</ext-link>) was set up, which allows users to browse, search, retrieve and compare CYP450 genes and can serve as a centralized resource.</p></abstract><funding-group><funding-statement>This work was supported by grants from the National Science Foundation to CLIU (No. 81373912), HMC (No. 81202859) and BW (No. 81274015); the Program for Changjiang Scholars and Innovative Research Teams in the Universities from Ministry of Education of China (IRT1150). The funding agencies had no role in the study design, data collection and analysis, decision to publish, or manuscript preparation.</funding-statement></funding-group><counts><page-count count="28"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>The authors confirm that all data underlying the findings are fully available without restriction. RNA-Seq data has been deposited in the SRA database under accession numbers SRR1043988, SRR1045051 and SRR1020591 respectively.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>The authors confirm that all data underlying the findings are fully available without restriction. RNA-Seq data has been deposited in the SRA database under accession numbers SRR1043988, SRR1045051 and SRR1020591 respectively.</p></notes></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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