Genome-Wide Analysis of PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) Genes in Plants Reveals the Eudicot-Wide PDAT Gene Expansion and Altered Selective Pressures Acting on the Core Eudicot PDAT Paralogs1[OPEN]
Identifieur interne : 001979 ( Ncbi/Merge ); précédent : 001978; suivant : 001980Genome-Wide Analysis of PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) Genes in Plants Reveals the Eudicot-Wide PDAT Gene Expansion and Altered Selective Pressures Acting on the Core Eudicot PDAT Paralogs1[OPEN]
Auteurs : Xue Pan ; Fred Y. Peng ; Randall J. WeselakeSource :
- Plant Physiology [ 0032-0889 ] ; 2015.
Abstract
Ancient gene duplication may have led to the diversification of a key acyltransferase of plant triacylglycerol synthesis in the core eudicots.
Url:
DOI: 10.1104/pp.114.253658
PubMed: 25585619
PubMed Central: 4348769
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PMC:4348769Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-Wide Analysis of <italic>PHOSPHOLIPID</italic>
:<italic>DIACYLGLYCEROL ACYLTRANSFERASE</italic>
(<italic>PDAT</italic>
) Genes in Plants Reveals the Eudicot-Wide <italic>PDAT</italic>
Gene Expansion and Altered Selective Pressures Acting on the Core Eudicot <italic>PDAT</italic>
Paralogs<xref ref-type="fn" rid="fn1"><sup>1</sup>
</xref>
<xref ref-type="fn" rid="fn2"><sup>[OPEN]</sup>
</xref>
</title>
<author><name sortKey="Pan, Xue" sort="Pan, Xue" uniqKey="Pan X" first="Xue" last="Pan">Xue Pan</name>
</author>
<author><name sortKey="Peng, Fred Y" sort="Peng, Fred Y" uniqKey="Peng F" first="Fred Y." last="Peng">Fred Y. Peng</name>
</author>
<author><name sortKey="Weselake, Randall J" sort="Weselake, Randall J" uniqKey="Weselake R" first="Randall J." last="Weselake">Randall J. Weselake</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-Wide Analysis of <italic>PHOSPHOLIPID</italic>
:<italic>DIACYLGLYCEROL ACYLTRANSFERASE</italic>
(<italic>PDAT</italic>
) Genes in Plants Reveals the Eudicot-Wide <italic>PDAT</italic>
Gene Expansion and Altered Selective Pressures Acting on the Core Eudicot <italic>PDAT</italic>
Paralogs<xref ref-type="fn" rid="fn1"><sup>1</sup>
</xref>
<xref ref-type="fn" rid="fn2"><sup>[OPEN]</sup>
</xref>
</title>
<author><name sortKey="Pan, Xue" sort="Pan, Xue" uniqKey="Pan X" first="Xue" last="Pan">Xue Pan</name>
</author>
<author><name sortKey="Peng, Fred Y" sort="Peng, Fred Y" uniqKey="Peng F" first="Fred Y." last="Peng">Fred Y. Peng</name>
</author>
<author><name sortKey="Weselake, Randall J" sort="Weselake, Randall J" uniqKey="Weselake R" first="Randall J." last="Weselake">Randall J. Weselake</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="2015">2015</date>
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<front><div type="abstract" xml:lang="en"><p>Ancient gene duplication may have led to the diversification of a key acyltransferase of plant triacylglycerol synthesis in the core eudicots.</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>
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<article-id pub-id-type="publisher-id">253658</article-id>
<article-id pub-id-type="doi">10.1104/pp.114.253658</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Articles</subject>
<subj-group subj-group-type="heading"><subject>Genes, Development, and Evolution</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Genome-Wide Analysis of <italic>PHOSPHOLIPID</italic>
:<italic>DIACYLGLYCEROL ACYLTRANSFERASE</italic>
(<italic>PDAT</italic>
) Genes in Plants Reveals the Eudicot-Wide <italic>PDAT</italic>
Gene Expansion and Altered Selective Pressures Acting on the Core Eudicot <italic>PDAT</italic>
Paralogs<xref ref-type="fn" rid="fn1"><sup>1</sup>
</xref>
<xref ref-type="fn" rid="fn2"><sup>[OPEN]</sup>
</xref>
</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Pan</surname>
<given-names>Xue</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Peng</surname>
<given-names>Fred Y.</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Weselake</surname>
<given-names>Randall J.</given-names>
</name>
<xref ref-type="corresp" rid="cor1">*</xref>
</contrib>
<aff id="aff1">Agricultural Lipid Biotechnology Program, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5</aff>
</contrib-group>
<author-notes><fn><p><ext-link ext-link-type="uri" xlink:href="http://www.plantphysiol.org/cgi/doi/10.1104/pp.114.253658">www.plantphysiol.org/cgi/doi/10.1104/pp.114.253658</ext-link>
</p>
</fn>
<corresp id="cor1"><label>*</label>
Address correspondence to <email>randall.weselake@ualberta.ca</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: Randall J. Weselake (<email>randall.weselake@ualberta.ca</email>
).</p>
</fn>
</author-notes>
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<volume>167</volume>
<issue>3</issue>
<fpage>887</fpage>
<lpage>904</lpage>
<history><date date-type="received"><day>13</day>
<month>11</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>10</day>
<month>1</month>
<year>2015</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_253658_ic1.gif"></self-uri>
<self-uri content-type="alt-lang-pdf zh" xlink:href="887.chinese.pdf"></self-uri>
<abstract abstract-type="precis"><p>Ancient gene duplication may have led to the diversification of a key acyltransferase of plant triacylglycerol synthesis in the core eudicots.</p>
</abstract>
<abstract><p>PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) is an enzyme that catalyzes the transfer of a fatty acyl moiety from the <italic>sn</italic>
-2 position of a phospholipid to the <italic>sn</italic>
-3-position of <italic>sn</italic>
-1,2-diacylglyerol, thus forming triacylglycerol and a lysophospholipid. Although the importance of PDAT in triacylglycerol biosynthesis has been illustrated in some previous studies, the evolutionary relationship of plant <italic>PDAT</italic>
s has not been studied in detail. In this study, we investigated the evolutionary relationship of the <italic>PDAT</italic>
gene family across the green plants using a comparative phylogenetic framework. We found that the <italic>PDAT</italic>
candidate genes are present in all examined green plants, including algae, lowland plants (a moss and a lycophyte), monocots, and eudicots. Phylogenetic analysis revealed the evolutionary division of the <italic>PDAT</italic>
gene family into seven major clades. The separation is supported by the conservation and variation in the gene structure, protein properties, motif patterns, and/or selection constraints. We further demonstrated that there is a eudicot-wide <italic>PDAT</italic>
gene expansion, which appears to have been mainly caused by the eudicot-shared ancient gene duplication and subsequent species-specific segmental duplications. In addition, selection pressure analyses showed that different selection constraints have acted on three core eudicot clades, which might enable paleoduplicated <italic>PDAT</italic>
paralogs to either become nonfunctionalized or develop divergent expression patterns during evolution. Overall, our study provides important insights into the evolution of the plant <italic>PDAT</italic>
gene family and explores the evolutionary mechanism underlying the functional diversification among the core eudicot <italic>PDAT</italic>
paralogs.</p>
</abstract>
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<notes><glossary><title>Glossary</title>
<def-list><def-item><term id="term1">TAG</term>
<def id="def1"><p>triacylglycerol</p>
</def>
</def-item>
<def-item><term id="term2">DAG</term>
<def id="def2"><p>diacylglycerol</p>
</def>
</def-item>
<def-item><term id="term3">ML</term>
<def id="def3"><p>maximum likelihood</p>
</def>
</def-item>
<def-item><term id="term4">PANTHER</term>
<def id="def4"><p>Protein Analysis Through Evolutionary Relationships</p>
</def>
</def-item>
<def-item><term id="term5">cDNA</term>
<def id="def5"><p>complementary DNA</p>
</def>
</def-item>
<def-item><term id="term6">TMD</term>
<def id="def6"><p>transmembrane domain</p>
</def>
</def-item>
<def-item><term id="term7">ER</term>
<def id="def7"><p>endoplasmic reticulum</p>
</def>
</def-item>
<def-item><term id="term8"><italic>K</italic>
<sub>s</sub>
</term>
<def id="def8"><p>synonymous substitution rate</p>
</def>
</def-item>
<def-item><term id="term9">CmC</term>
<def id="def9"><p>clade model C</p>
</def>
</def-item>
<def-item><term id="term10">LRT</term>
<def id="def10"><p>likelihood ratio test</p>
</def>
</def-item>
<def-item><term id="term11">MEME</term>
<def id="def11"><p>Multiple Expectation Maximization for Motif Elicitation</p>
</def>
</def-item>
<def-item><term id="term12">RAxML</term>
<def id="def12"><p>Randomized Axelerated Maximum Likelihood</p>
</def>
</def-item>
</def-list>
</glossary>
</notes>
</front>
</pmc>
<affiliations><list></list>
<tree><noCountry><name sortKey="Pan, Xue" sort="Pan, Xue" uniqKey="Pan X" first="Xue" last="Pan">Xue Pan</name>
<name sortKey="Peng, Fred Y" sort="Peng, Fred Y" uniqKey="Peng F" first="Fred Y." last="Peng">Fred Y. Peng</name>
<name sortKey="Weselake, Randall J" sort="Weselake, Randall J" uniqKey="Weselake R" first="Randall J." last="Weselake">Randall J. Weselake</name>
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