Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae)
Identifieur interne : 000A70 ( Pmc/Corpus ); précédent : 000A69; suivant : 000A71Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae)
Auteurs : Robert K. Jansen ; Martin F. Wojciechowski ; Elumalai Sanniyasi ; Seung-Bum Lee ; Henry DaniellSource :
- Molecular phylogenetics and evolution [ 1055-7903 ] ; 2008.
Abstract
Chickpea (
Url:
DOI: 10.1016/j.ympev.2008.06.013
PubMed: 18638561
PubMed Central: 2586962
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Complete plastid genome sequence of the chickpea (<italic>Cicer arietinum</italic>
) and the phylogenetic distribution of <italic>rps12</italic>
and <italic>clpP</italic>
intron losses among legumes (Leguminosae)</title>
<author><name sortKey="Jansen, Robert K" sort="Jansen, Robert K" uniqKey="Jansen R" first="Robert K." last="Jansen">Robert K. Jansen</name>
<affiliation><nlm:aff id="A1"> Section of Integrative Biology and Institute of Cellular and Molecular Biology, Biological Laboratories 404, University of Texas, Austin, TX 78712, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Wojciechowski, Martin F" sort="Wojciechowski, Martin F" uniqKey="Wojciechowski M" first="Martin F." last="Wojciechowski">Martin F. Wojciechowski</name>
<affiliation><nlm:aff id="A2"> School of Life Sciences, Genomics, Evolution and Bioinformatics Group, Arizona State University, Tempe, AZ 85287-4501, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Sanniyasi, Elumalai" sort="Sanniyasi, Elumalai" uniqKey="Sanniyasi E" first="Elumalai" last="Sanniyasi">Elumalai Sanniyasi</name>
<affiliation><nlm:aff id="A3"> University of Central Florida, College of Medicine, Department of Molecular Biology & Microbiology, Biomolecular Science, 4000 Central Florida Boulevard, Building #20, Room 336, Orlando, FL 32816-2364, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Lee, Seung Bum" sort="Lee, Seung Bum" uniqKey="Lee S" first="Seung-Bum" last="Lee">Seung-Bum Lee</name>
<affiliation><nlm:aff id="A3"> University of Central Florida, College of Medicine, Department of Molecular Biology & Microbiology, Biomolecular Science, 4000 Central Florida Boulevard, Building #20, Room 336, Orlando, FL 32816-2364, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Daniell, Henry" sort="Daniell, Henry" uniqKey="Daniell H" first="Henry" last="Daniell">Henry Daniell</name>
<affiliation><nlm:aff id="A3"> University of Central Florida, College of Medicine, Department of Molecular Biology & Microbiology, Biomolecular Science, 4000 Central Florida Boulevard, Building #20, Room 336, Orlando, FL 32816-2364, USA</nlm:aff>
</affiliation>
</author>
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<date when="2008">2008</date>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Complete plastid genome sequence of the chickpea (<italic>Cicer arietinum</italic>
) and the phylogenetic distribution of <italic>rps12</italic>
and <italic>clpP</italic>
intron losses among legumes (Leguminosae)</title>
<author><name sortKey="Jansen, Robert K" sort="Jansen, Robert K" uniqKey="Jansen R" first="Robert K." last="Jansen">Robert K. Jansen</name>
<affiliation><nlm:aff id="A1"> Section of Integrative Biology and Institute of Cellular and Molecular Biology, Biological Laboratories 404, University of Texas, Austin, TX 78712, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Wojciechowski, Martin F" sort="Wojciechowski, Martin F" uniqKey="Wojciechowski M" first="Martin F." last="Wojciechowski">Martin F. Wojciechowski</name>
<affiliation><nlm:aff id="A2"> School of Life Sciences, Genomics, Evolution and Bioinformatics Group, Arizona State University, Tempe, AZ 85287-4501, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Sanniyasi, Elumalai" sort="Sanniyasi, Elumalai" uniqKey="Sanniyasi E" first="Elumalai" last="Sanniyasi">Elumalai Sanniyasi</name>
<affiliation><nlm:aff id="A3"> University of Central Florida, College of Medicine, Department of Molecular Biology & Microbiology, Biomolecular Science, 4000 Central Florida Boulevard, Building #20, Room 336, Orlando, FL 32816-2364, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Lee, Seung Bum" sort="Lee, Seung Bum" uniqKey="Lee S" first="Seung-Bum" last="Lee">Seung-Bum Lee</name>
<affiliation><nlm:aff id="A3"> University of Central Florida, College of Medicine, Department of Molecular Biology & Microbiology, Biomolecular Science, 4000 Central Florida Boulevard, Building #20, Room 336, Orlando, FL 32816-2364, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Daniell, Henry" sort="Daniell, Henry" uniqKey="Daniell H" first="Henry" last="Daniell">Henry Daniell</name>
<affiliation><nlm:aff id="A3"> University of Central Florida, College of Medicine, Department of Molecular Biology & Microbiology, Biomolecular Science, 4000 Central Florida Boulevard, Building #20, Room 336, Orlando, FL 32816-2364, USA</nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">Molecular phylogenetics and evolution</title>
<idno type="ISSN">1055-7903</idno>
<idno type="eISSN">1095-9513</idno>
<imprint><date when="2008">2008</date>
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<front><div type="abstract" xml:lang="en"><p id="P1">Chickpea (<italic>Cicer arietinum</italic>
, Leguminosae), an important grain legume, is widely used for food and fodder throughout the world. We sequenced the complete plastid genome of chickpea, which is 125,319 bp in size, and contains only one copy of the inverted repeat (IR). The genome encodes 108 genes, including 4 rRNAs, 29 tRNAs, and 75 proteins. The genes <italic>rps16, infA</italic>
, and <italic>ycf4</italic>
are absent in the chickpea plastid genome, and <italic>ndhB</italic>
has an internal stop codon in the 5′exon, similar to other legumes. Two genes have lost their introns, one in the 3′exon of the transpliced gene <italic>rps12</italic>
, and the one between exons 1 and 2 of <italic>clpP</italic>
; this represents the first documented case of the loss of introns from both of these genes in the same plastid genome. An extensive phylogenetic survey of these intron losses was performed on 302 taxa across legumes and the related family Polygalaceae. The <italic>clpP</italic>
intron has been lost exclusively in taxa from the temperate “IR-lacking clade” (IRLC), whereas the <italic>rps12</italic>
intron has been lost in most members of the IRLC (with the exception of <italic>Wisteria</italic>
, <italic>Callerya, Afgekia</italic>
, and certain species of <italic>Millettia</italic>
, which represent the earliest diverging lineages of this clade), and in the tribe Desmodieae, which is closely related to the tribes Phaseoleae and Psoraleeae. Data provided here suggest that the loss of the <italic>rps12</italic>
intron occurred after the loss of the IR. The two new genomic changes identified in the present study provide additional support of the monophyly of the IR-loss clade, and resolution of the pattern of the earliest-branching lineages in this clade. The availability of the complete chickpea plastid genome sequence also provides valuable information on intergenic spacer regions among legumes and endogenous regulatory sequences for plastid genetic engineering.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article" xml:lang="EN"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">9304400</journal-id>
<journal-id journal-id-type="pubmed-jr-id">2616</journal-id>
<journal-id journal-id-type="nlm-ta">Mol Phylogenet Evol</journal-id>
<journal-title>Molecular phylogenetics and evolution</journal-title>
<issn pub-type="ppub">1055-7903</issn>
<issn pub-type="epub">1095-9513</issn>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">18638561</article-id>
<article-id pub-id-type="pmc">2586962</article-id>
<article-id pub-id-type="doi">10.1016/j.ympev.2008.06.013</article-id>
<article-id pub-id-type="manuscript">NIHMS73716</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Complete plastid genome sequence of the chickpea (<italic>Cicer arietinum</italic>
) and the phylogenetic distribution of <italic>rps12</italic>
and <italic>clpP</italic>
intron losses among legumes (Leguminosae)</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Jansen</surname>
<given-names>Robert K.</given-names>
</name>
<xref rid="A1" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wojciechowski</surname>
<given-names>Martin F.</given-names>
</name>
<xref rid="A2" ref-type="aff">b</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sanniyasi</surname>
<given-names>Elumalai</given-names>
</name>
<xref rid="A3" ref-type="aff">c</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lee</surname>
<given-names>Seung-Bum</given-names>
</name>
<xref rid="A3" ref-type="aff">c</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Daniell</surname>
<given-names>Henry</given-names>
</name>
<xref rid="A3" ref-type="aff">c</xref>
<xref rid="FN1" ref-type="author-notes">*</xref>
</contrib>
</contrib-group>
<aff id="A1"><label>a</label>
Section of Integrative Biology and Institute of Cellular and Molecular Biology, Biological Laboratories 404, University of Texas, Austin, TX 78712, USA</aff>
<aff id="A2"><label>b</label>
School of Life Sciences, Genomics, Evolution and Bioinformatics Group, Arizona State University, Tempe, AZ 85287-4501, USA</aff>
<aff id="A3"><label>c</label>
University of Central Florida, College of Medicine, Department of Molecular Biology & Microbiology, Biomolecular Science, 4000 Central Florida Boulevard, Building #20, Room 336, Orlando, FL 32816-2364, USA</aff>
<author-notes><corresp id="FN1"><label>*</label>
Corresponding author. Fax: +1 407 823 0956. E-mail address: <email>daniell@mail.ucf.edu</email>
(H. Daniell)</corresp>
</author-notes>
<pub-date pub-type="nihms-submitted"><day>16</day>
<month>10</month>
<year>2008</year>
</pub-date>
<pub-date pub-type="epub"><day>27</day>
<month>6</month>
<year>2008</year>
</pub-date>
<pub-date pub-type="ppub"><month>9</month>
<year>2008</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>1</day>
<month>3</month>
<year>2009</year>
</pub-date>
<volume>48</volume>
<issue>3</issue>
<fpage>1204</fpage>
<lpage>1217</lpage>
<abstract><p id="P1">Chickpea (<italic>Cicer arietinum</italic>
, Leguminosae), an important grain legume, is widely used for food and fodder throughout the world. We sequenced the complete plastid genome of chickpea, which is 125,319 bp in size, and contains only one copy of the inverted repeat (IR). The genome encodes 108 genes, including 4 rRNAs, 29 tRNAs, and 75 proteins. The genes <italic>rps16, infA</italic>
, and <italic>ycf4</italic>
are absent in the chickpea plastid genome, and <italic>ndhB</italic>
has an internal stop codon in the 5′exon, similar to other legumes. Two genes have lost their introns, one in the 3′exon of the transpliced gene <italic>rps12</italic>
, and the one between exons 1 and 2 of <italic>clpP</italic>
; this represents the first documented case of the loss of introns from both of these genes in the same plastid genome. An extensive phylogenetic survey of these intron losses was performed on 302 taxa across legumes and the related family Polygalaceae. The <italic>clpP</italic>
intron has been lost exclusively in taxa from the temperate “IR-lacking clade” (IRLC), whereas the <italic>rps12</italic>
intron has been lost in most members of the IRLC (with the exception of <italic>Wisteria</italic>
, <italic>Callerya, Afgekia</italic>
, and certain species of <italic>Millettia</italic>
, which represent the earliest diverging lineages of this clade), and in the tribe Desmodieae, which is closely related to the tribes Phaseoleae and Psoraleeae. Data provided here suggest that the loss of the <italic>rps12</italic>
intron occurred after the loss of the IR. The two new genomic changes identified in the present study provide additional support of the monophyly of the IR-loss clade, and resolution of the pattern of the earliest-branching lineages in this clade. The availability of the complete chickpea plastid genome sequence also provides valuable information on intergenic spacer regions among legumes and endogenous regulatory sequences for plastid genetic engineering.</p>
</abstract>
<kwd-group><kwd>Plastid genetic engineering</kwd>
<kwd>Genome evolution</kwd>
<kwd>Phylogeny of legumes</kwd>
<kwd>Leguminosae</kwd>
<kwd>Intron loss</kwd>
<kwd>Chickpea</kwd>
<kwd><italic>Cicer</italic>
</kwd>
</kwd-group>
<contract-num rid="GM1">R01 GM063879-05</contract-num>
<contract-sponsor id="GM1">National Institute of General Medical Sciences : NIGMS</contract-sponsor>
</article-meta>
</front>
</pmc>
</record>
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