The Chloroplast Genome Sequence of Mungbean (Vigna radiata) Determined by High-throughput Pyrosequencing: Structural Organization and Phylogenetic Relationships
Identifieur interne : 000F93 ( Pmc/Checkpoint ); précédent : 000F92; suivant : 000F94The Chloroplast Genome Sequence of Mungbean (Vigna radiata) Determined by High-throughput Pyrosequencing: Structural Organization and Phylogenetic Relationships
Auteurs : S. Tangphatsornruang ; D. Sangsrakru ; J. Chanprasert ; P. Uthaipaisanwong ; T. Yoocha ; N. Jomchai ; S. TragoonrungSource :
- DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes [ 1340-2838 ] ; 2009.
Abstract
Mungbean is an economically important crop which is grown principally for its protein-rich dry seeds. However, genomic research of mungbean has lagged behind other species in the Fabaceae family. Here, we reported the complete chloroplast (cp) genome sequence of mungbean obtained by the 454 pyrosequencing technology. The mungbean cp genome is 151 271 bp in length which includes a pair of inverted repeats (IRs) of 26 474 bp separated by a small single-copy region of 17 427 bp and a large single-copy region of 80 896 bp. The genome contains 108 unique genes and 19 of these genes are duplicated in the IR. Of these, 75 are predicted protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. Relative to other plant cp genomes, we observed two distinct rearrangements: a 50-kb inversion between
Url:
DOI: 10.1093/dnares/dsp025
PubMed: 20007682
PubMed Central: 2818187
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The Chloroplast Genome Sequence of Mungbean (<italic>Vigna radiata</italic>) Determined by High-throughput Pyrosequencing: Structural Organization and Phylogenetic Relationships</title><author><name sortKey="Tangphatsornruang, S" sort="Tangphatsornruang, S" uniqKey="Tangphatsornruang S" first="S." last="Tangphatsornruang">S. Tangphatsornruang</name></author><author><name sortKey="Sangsrakru, D" sort="Sangsrakru, D" uniqKey="Sangsrakru D" first="D." last="Sangsrakru">D. Sangsrakru</name></author><author><name sortKey="Chanprasert, J" sort="Chanprasert, J" uniqKey="Chanprasert J" first="J." last="Chanprasert">J. Chanprasert</name></author><author><name sortKey="Uthaipaisanwong, P" sort="Uthaipaisanwong, P" uniqKey="Uthaipaisanwong P" first="P." last="Uthaipaisanwong">P. Uthaipaisanwong</name></author><author><name sortKey="Yoocha, T" sort="Yoocha, T" uniqKey="Yoocha T" first="T." last="Yoocha">T. Yoocha</name></author><author><name sortKey="Jomchai, N" sort="Jomchai, N" uniqKey="Jomchai N" first="N." last="Jomchai">N. Jomchai</name></author><author><name sortKey="Tragoonrung, S" sort="Tragoonrung, S" uniqKey="Tragoonrung S" first="S." last="Tragoonrung">S. Tragoonrung</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">20007682</idno><idno type="pmc">2818187</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818187</idno><idno type="RBID">PMC:2818187</idno><idno type="doi">10.1093/dnares/dsp025</idno><date when="2009">2009</date><idno type="wicri:Area/Pmc/Corpus">000E76</idno><idno type="wicri:Area/Pmc/Curation">000E75</idno><idno type="wicri:Area/Pmc/Checkpoint">000F93</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The Chloroplast Genome Sequence of Mungbean (<italic>Vigna radiata</italic>) Determined by High-throughput Pyrosequencing: Structural Organization and Phylogenetic Relationships</title><author><name sortKey="Tangphatsornruang, S" sort="Tangphatsornruang, S" uniqKey="Tangphatsornruang S" first="S." last="Tangphatsornruang">S. Tangphatsornruang</name></author><author><name sortKey="Sangsrakru, D" sort="Sangsrakru, D" uniqKey="Sangsrakru D" first="D." last="Sangsrakru">D. Sangsrakru</name></author><author><name sortKey="Chanprasert, J" sort="Chanprasert, J" uniqKey="Chanprasert J" first="J." last="Chanprasert">J. Chanprasert</name></author><author><name sortKey="Uthaipaisanwong, P" sort="Uthaipaisanwong, P" uniqKey="Uthaipaisanwong P" first="P." last="Uthaipaisanwong">P. Uthaipaisanwong</name></author><author><name sortKey="Yoocha, T" sort="Yoocha, T" uniqKey="Yoocha T" first="T." last="Yoocha">T. Yoocha</name></author><author><name sortKey="Jomchai, N" sort="Jomchai, N" uniqKey="Jomchai N" first="N." last="Jomchai">N. Jomchai</name></author><author><name sortKey="Tragoonrung, S" sort="Tragoonrung, S" uniqKey="Tragoonrung S" first="S." last="Tragoonrung">S. Tragoonrung</name></author></analytic><series><title level="j">DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</title><idno type="ISSN">1340-2838</idno><idno type="eISSN">1756-1663</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Mungbean is an economically important crop which is grown principally for its protein-rich dry seeds. However, genomic research of mungbean has lagged behind other species in the Fabaceae family. Here, we reported the complete chloroplast (cp) genome sequence of mungbean obtained by the 454 pyrosequencing technology. The mungbean cp genome is 151 271 bp in length which includes a pair of inverted repeats (IRs) of 26 474 bp separated by a small single-copy region of 17 427 bp and a large single-copy region of 80 896 bp. The genome contains 108 unique genes and 19 of these genes are duplicated in the IR. Of these, 75 are predicted protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. Relative to other plant cp genomes, we observed two distinct rearrangements: a 50-kb inversion between <italic>accD</italic>/<italic>rps16</italic> and <italic>rbcL/trnK-UUU</italic>, and a 78-kb rearrangement between <italic>trnH</italic>/<italic>rpl14</italic> and <italic>rps19</italic>/<italic>rps8</italic>. We detected sequence length polymorphism in the cp homopolymeric regions at the intra- and inter-specific levels in the <italic>Vigna</italic> species. Phylogenetic analysis demonstrated a close relationship between <italic>Vigna</italic> and <italic>Phaseolus</italic> in the phaseolinae subtribe and provided a strong support for a monophyletic group of the eurosid I.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Sugiura, M" uniqKey="Sugiura M">M. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">DNA Res</journal-id><journal-id journal-id-type="publisher-id">dnares</journal-id><journal-id journal-id-type="hwp">dnares</journal-id><journal-title-group><journal-title>DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</journal-title></journal-title-group><issn pub-type="ppub">1340-2838</issn><issn pub-type="epub">1756-1663</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">20007682</article-id><article-id pub-id-type="pmc">2818187</article-id><article-id pub-id-type="doi">10.1093/dnares/dsp025</article-id><article-id pub-id-type="publisher-id">dsp025</article-id><article-categories><subj-group subj-group-type="heading"><subject>Full Papers</subject></subj-group></article-categories><title-group><article-title>The Chloroplast Genome Sequence of Mungbean (<italic>Vigna radiata</italic>) Determined by High-throughput Pyrosequencing: Structural Organization and Phylogenetic Relationships</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Tangphatsornruang</surname><given-names>S.</given-names></name><xref ref-type="corresp" rid="cor1">*</xref></contrib><contrib contrib-type="author"><name><surname>Sangsrakru</surname><given-names>D.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Chanprasert</surname><given-names>J.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Uthaipaisanwong</surname><given-names>P.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Yoocha</surname><given-names>T.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Jomchai</surname><given-names>N.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Tragoonrung</surname><given-names>S.</given-names></name></contrib></contrib-group><aff><addr-line>Genome Institute, National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd, Klong 1, Klong Luang, Pathumthani 12120</addr-line>,<country>Thailand</country></aff><author-notes><corresp id="cor1"><label>*</label>To whom correspondence should be addressed. Tel. <phone>+66 2-564-6700</phone>. Fax. <fax>+66 2-564-6584</fax>. Email: <email>sithichoke.tan@biotec.or.th</email></corresp></author-notes><pub-date pub-type="ppub"><month>2</month><year>2010</year></pub-date><pub-date pub-type="epub"><day>10</day><month>12</month><year>2009</year></pub-date><pub-date pub-type="pmc-release"><day>10</day><month>12</month><year>2009</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>17</volume><issue>1</issue><fpage>11</fpage><lpage>22</lpage><history><date date-type="received"><day>11</day><month>9</month><year>2009</year></date><date date-type="accepted"><day>18</day><month>11</month><year>2009</year></date></history><permissions><copyright-statement>© The Author 2009. Published by Oxford University Press on behalf of Kazusa DNA Research Institute</copyright-statement><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.5">http://creativecommons.org/licenses/by-nc/2.5</ext-link>), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>Mungbean is an economically important crop which is grown principally for its protein-rich dry seeds. However, genomic research of mungbean has lagged behind other species in the Fabaceae family. Here, we reported the complete chloroplast (cp) genome sequence of mungbean obtained by the 454 pyrosequencing technology. The mungbean cp genome is 151 271 bp in length which includes a pair of inverted repeats (IRs) of 26 474 bp separated by a small single-copy region of 17 427 bp and a large single-copy region of 80 896 bp. The genome contains 108 unique genes and 19 of these genes are duplicated in the IR. Of these, 75 are predicted protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. Relative to other plant cp genomes, we observed two distinct rearrangements: a 50-kb inversion between <italic>accD</italic>/<italic>rps16</italic> and <italic>rbcL/trnK-UUU</italic>, and a 78-kb rearrangement between <italic>trnH</italic>/<italic>rpl14</italic> and <italic>rps19</italic>/<italic>rps8</italic>. We detected sequence length polymorphism in the cp homopolymeric regions at the intra- and inter-specific levels in the <italic>Vigna</italic> species. Phylogenetic analysis demonstrated a close relationship between <italic>Vigna</italic> and <italic>Phaseolus</italic> in the phaseolinae subtribe and provided a strong support for a monophyletic group of the eurosid I.</p></abstract><kwd-group><kwd>mungbean</kwd><kwd>chloroplast genome</kwd><kwd>454 pyrosequencing</kwd></kwd-group></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Chanprasert, J" sort="Chanprasert, J" uniqKey="Chanprasert J" first="J." last="Chanprasert">J. Chanprasert</name><name sortKey="Jomchai, N" sort="Jomchai, N" uniqKey="Jomchai N" first="N." last="Jomchai">N. Jomchai</name><name sortKey="Sangsrakru, D" sort="Sangsrakru, D" uniqKey="Sangsrakru D" first="D." last="Sangsrakru">D. Sangsrakru</name><name sortKey="Tangphatsornruang, S" sort="Tangphatsornruang, S" uniqKey="Tangphatsornruang S" first="S." last="Tangphatsornruang">S. Tangphatsornruang</name><name sortKey="Tragoonrung, S" sort="Tragoonrung, S" uniqKey="Tragoonrung S" first="S." last="Tragoonrung">S. Tragoonrung</name><name sortKey="Uthaipaisanwong, P" sort="Uthaipaisanwong, P" uniqKey="Uthaipaisanwong P" first="P." last="Uthaipaisanwong">P. Uthaipaisanwong</name><name sortKey="Yoocha, T" sort="Yoocha, T" uniqKey="Yoocha T" first="T." last="Yoocha">T. Yoocha</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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