Species-Specific Expansion and Molecular Evolution of the 3-hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Plants
Identifieur interne : 001197 ( Pmc/Curation ); précédent : 001196; suivant : 001198Species-Specific Expansion and Molecular Evolution of the 3-hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Plants
Auteurs : Wei Li [République populaire de Chine] ; Wei Liu [République populaire de Chine] ; Hengling Wei [République populaire de Chine] ; Qiuling He [République populaire de Chine] ; Jinhong Chen [République populaire de Chine] ; Baohong Zhang [États-Unis] ; Shuijin Zhu [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
The terpene compounds represent the largest and most diverse class of plant secondary metabolites which are important in plant growth and development. The 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR; EC 1.1.1.34) is one of the key enzymes contributed to terpene biosynthesis. To better understand the basic characteristics and evolutionary history of the HMGR gene family in plants, a genome-wide analysis of HMGR genes from 20 representative species was carried out. A total of 56 HMGR genes in the 14 land plant genomes were identified, but no genes were found in all 6 algal genomes. The gene structure and protein architecture of all plant HMGR genes were highly conserved. The phylogenetic analysis revealed that the plant HMGRs were derived from one ancestor gene and finally developed into four distinct groups, two in the monocot plants and two in dicot plants. Species-specific gene duplications, caused mainly by segmental duplication, led to the limited expansion of HMGR genes in
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DOI: 10.1371/journal.pone.0094172
PubMed: 24722776
PubMed Central: 3983158
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Zhejiang University, Hangzhou, Zhejiang</wicri:regionArea></affiliation></author><author><name sortKey="Wei, Hengling" sort="Wei, Hengling" uniqKey="Wei H" first="Hengling" last="Wei">Hengling Wei</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan</wicri:regionArea></affiliation></author><author><name sortKey="He, Qiuling" sort="He, Qiuling" uniqKey="He Q" first="Qiuling" last="He">Qiuling He</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang</wicri:regionArea></affiliation></author><author><name sortKey="Chen, Jinhong" sort="Chen, Jinhong" uniqKey="Chen J" first="Jinhong" last="Chen">Jinhong Chen</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Baohong" sort="Zhang, Baohong" uniqKey="Zhang B" first="Baohong" last="Zhang">Baohong Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Department of Biology, East Carolina University, Greenville, North Carolina, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, East Carolina University, Greenville, North Carolina</wicri:regionArea></affiliation></author><author><name sortKey="Zhu, Shuijin" sort="Zhu, Shuijin" uniqKey="Zhu S" first="Shuijin" last="Zhu">Shuijin Zhu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24722776</idno><idno type="pmc">3983158</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983158</idno><idno type="RBID">PMC:3983158</idno><idno type="doi">10.1371/journal.pone.0094172</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">001198</idno><idno type="wicri:Area/Pmc/Curation">001197</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Species-Specific Expansion and Molecular Evolution of the 3-hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Plants</title><author><name sortKey="Li, Wei" sort="Li, Wei" uniqKey="Li W" first="Wei" last="Li">Wei Li</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Wei" sort="Liu, Wei" uniqKey="Liu W" first="Wei" last="Liu">Wei Liu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang</wicri:regionArea></affiliation></author><author><name sortKey="Wei, Hengling" sort="Wei, Hengling" uniqKey="Wei H" first="Hengling" last="Wei">Hengling Wei</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan</wicri:regionArea></affiliation></author><author><name sortKey="He, Qiuling" sort="He, Qiuling" uniqKey="He Q" first="Qiuling" last="He">Qiuling He</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang</wicri:regionArea></affiliation></author><author><name sortKey="Chen, Jinhong" sort="Chen, Jinhong" uniqKey="Chen J" first="Jinhong" last="Chen">Jinhong Chen</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Baohong" sort="Zhang, Baohong" uniqKey="Zhang B" first="Baohong" last="Zhang">Baohong Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Department of Biology, East Carolina University, Greenville, North Carolina, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, East Carolina University, Greenville, North Carolina</wicri:regionArea></affiliation></author><author><name sortKey="Zhu, Shuijin" sort="Zhu, Shuijin" uniqKey="Zhu S" first="Shuijin" last="Zhu">Shuijin Zhu</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang</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>The terpene compounds represent the largest and most diverse class of plant secondary metabolites which are important in plant growth and development. The 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR; EC 1.1.1.34) is one of the key enzymes contributed to terpene biosynthesis. To better understand the basic characteristics and evolutionary history of the HMGR gene family in plants, a genome-wide analysis of HMGR genes from 20 representative species was carried out. A total of 56 HMGR genes in the 14 land plant genomes were identified, but no genes were found in all 6 algal genomes. The gene structure and protein architecture of all plant HMGR genes were highly conserved. The phylogenetic analysis revealed that the plant HMGRs were derived from one ancestor gene and finally developed into four distinct groups, two in the monocot plants and two in dicot plants. Species-specific gene duplications, caused mainly by segmental duplication, led to the limited expansion of HMGR genes in <italic>Zea mays</italic>, <italic>Gossypium raimondii</italic>, <italic>Populus trichocarpa</italic> and <italic>Glycine max</italic> after the species diverged. The analysis of Ka/Ks ratios and expression profiles indicated that functional divergence after the gene duplications was restricted. The results suggested that the function and evolution of HMGR gene family were dramatically conserved throughout the plant kingdom.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Degenhardt, J" uniqKey="Degenhardt J">J Degenhardt</name></author><author><name sortKey="Kollner, Tg" uniqKey="Kollner T">TG Kollner</name></author><author><name sortKey="Gershenzon, J" uniqKey="Gershenzon J">J Gershenzon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tholl, D" uniqKey="Tholl D">D Tholl</name></author><author><name sortKey="Lee, S" uniqKey="Lee S">S Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Keeling, Ci" uniqKey="Keeling C">CI Keeling</name></author><author><name sortKey="Bohlmann, J" uniqKey="Bohlmann J">J Bohlmann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Heiling, S" uniqKey="Heiling S">S 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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">24722776</article-id><article-id pub-id-type="pmc">3983158</article-id><article-id pub-id-type="publisher-id">PONE-D-14-00049</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0094172</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>Biotechnology</subject><subj-group><subject>Plant Biotechnology</subject><subj-group><subject>Plant Genomics</subject></subj-group></subj-group></subj-group><subj-group><subject>Computational Biology</subject><subj-group><subject>Comparative Genomics</subject><subject>Genome Evolution</subject></subj-group></subj-group><subj-group><subject>Evolutionary Biology</subject><subj-group><subject>Evolutionary Systematics</subject><subj-group><subject>Phylogenetics</subject><subj-group><subject>Plant Phylogenetics</subject></subj-group></subj-group></subj-group><subj-group><subject>Evolutionary Genetics</subject></subj-group></subj-group><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject></subj-group></subj-group><subj-group><subject>Plant Science</subject></subj-group></subj-group></article-categories><title-group><article-title>Species-Specific Expansion and Molecular Evolution of the 3-hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Plants</article-title><alt-title alt-title-type="running-head">Expansion and Molecular Evolution of HMGR Gene</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Li</surname><given-names>Wei</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Wei</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wei</surname><given-names>Hengling</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>He</surname><given-names>Qiuling</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Jinhong</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Baohong</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhu</surname><given-names>Shuijin</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>Department of Agronomy, Zhejiang University, Hangzhou, Zhejiang, China</addr-line></aff><aff id="aff2"><label>2</label><addr-line>State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Department of Biology, East Carolina University, Greenville, North Carolina, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Zhang</surname><given-names>Tianzhen</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Nanjing Agricultural University, China</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>shjzhu@zju.edu.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: SZ W. Li BZ. Performed the experiments: W. Li W. Liu HW JC QH. Analyzed the data: W. Li HW. Contributed reagents/materials/analysis tools: HW. Wrote the paper: W. Li SZ BZ.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>10</day><month>4</month><year>2014</year></pub-date><volume>9</volume><issue>4</issue><elocation-id>e94172</elocation-id><history><date date-type="received"><day>1</day><month>1</month><year>2014</year></date><date date-type="accepted"><day>11</day><month>3</month><year>2014</year></date></history><permissions><copyright-year>2014</copyright-year><copyright-holder>Li 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>The terpene compounds represent the largest and most diverse class of plant secondary metabolites which are important in plant growth and development. The 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR; EC 1.1.1.34) is one of the key enzymes contributed to terpene biosynthesis. To better understand the basic characteristics and evolutionary history of the HMGR gene family in plants, a genome-wide analysis of HMGR genes from 20 representative species was carried out. A total of 56 HMGR genes in the 14 land plant genomes were identified, but no genes were found in all 6 algal genomes. The gene structure and protein architecture of all plant HMGR genes were highly conserved. The phylogenetic analysis revealed that the plant HMGRs were derived from one ancestor gene and finally developed into four distinct groups, two in the monocot plants and two in dicot plants. Species-specific gene duplications, caused mainly by segmental duplication, led to the limited expansion of HMGR genes in <italic>Zea mays</italic>, <italic>Gossypium raimondii</italic>, <italic>Populus trichocarpa</italic> and <italic>Glycine max</italic> after the species diverged. The analysis of Ka/Ks ratios and expression profiles indicated that functional divergence after the gene duplications was restricted. The results suggested that the function and evolution of HMGR gene family were dramatically conserved throughout the plant kingdom.</p></abstract><funding-group><funding-statement>The works are support by the National Basic Research Program (973 program, No: 2010CB126006) and the National High Technology Research and Development Program of China (2011AA10A102, 2013AA102601). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="10"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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