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Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

Identifieur interne : 002323 ( Main/Curation ); précédent : 002322; suivant : 002324

Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

Auteurs : Christopher Saski ; Seung-Bum Lee ; Siri Fjellheim ; Chittibabu Guda ; Robert K. Jansen ; Hong Luo ; Jeffrey Tomkins ; Odd Arne Rognli ; Henry Daniell ; Jihong Liu Clarke

Source :

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik [ 0040-5752 ] ; 2007.

RBID : PMC:2674615

Abstract

Comparisons of complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5′ end of ndhH is restricted to the three genera of the subfamily Pooideae (Agrostis, Hordeum and Triticum). Second, a 6 bp deletion in ndhK is shared by Agrostis, Hordeum, Oryza and Triticum, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identified 19–37 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identified 16–21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum officinarum and Sorghum bicolor, whereas no spacer regions were identical among Oryza sativa, Triticum aestivum, H. vulgare and A. stolonifera despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identified six C–U conversions in both Sorghum bicolor and H. vulgare but only one in A. stolonifera. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674615

DOI: 10.1007/s00122-007-0567-4
PubMed: 17534593
PubMed Central: 2674615

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PMC:2674615

Le document en format XML

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, <italic>Sorghum bicolor</italic>
 and <italic>Agrostis stolonifera</italic>
, and comparative analyses with other grass genomes</title>
<author><name sortKey="Saski, Christopher" sort="Saski, Christopher" uniqKey="Saski C" first="Christopher" last="Saski">Christopher Saski</name>
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<author><name sortKey="Lee, Seung Bum" sort="Lee, Seung Bum" uniqKey="Lee S" first="Seung-Bum" last="Lee">Seung-Bum Lee</name>
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<author><name sortKey="Fjellheim, Siri" sort="Fjellheim, Siri" uniqKey="Fjellheim S" first="Siri" last="Fjellheim">Siri Fjellheim</name>
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<author><name sortKey="Guda, Chittibabu" sort="Guda, Chittibabu" uniqKey="Guda C" first="Chittibabu" last="Guda">Chittibabu Guda</name>
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<author><name sortKey="Jansen, Robert K" sort="Jansen, Robert K" uniqKey="Jansen R" first="Robert K." last="Jansen">Robert K. Jansen</name>
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<author><name sortKey="Luo, Hong" sort="Luo, Hong" uniqKey="Luo H" first="Hong" last="Luo">Hong Luo</name>
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<author><name sortKey="Tomkins, Jeffrey" sort="Tomkins, Jeffrey" uniqKey="Tomkins J" first="Jeffrey" last="Tomkins">Jeffrey Tomkins</name>
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<author><name sortKey="Rognli, Odd Arne" sort="Rognli, Odd Arne" uniqKey="Rognli O" first="Odd Arne" last="Rognli">Odd Arne Rognli</name>
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<author><name sortKey="Daniell, Henry" sort="Daniell, Henry" uniqKey="Daniell H" first="Henry" last="Daniell">Henry Daniell</name>
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<author><name sortKey="Clarke, Jihong Liu" sort="Clarke, Jihong Liu" uniqKey="Clarke J" first="Jihong Liu" last="Clarke">Jihong Liu Clarke</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Complete chloroplast genome sequences of <italic>Hordeum vulgare</italic>
, <italic>Sorghum bicolor</italic>
 and <italic>Agrostis stolonifera</italic>
, and comparative analyses with other grass genomes</title>
<author><name sortKey="Saski, Christopher" sort="Saski, Christopher" uniqKey="Saski C" first="Christopher" last="Saski">Christopher Saski</name>
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<author><name sortKey="Fjellheim, Siri" sort="Fjellheim, Siri" uniqKey="Fjellheim S" first="Siri" last="Fjellheim">Siri Fjellheim</name>
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<author><name sortKey="Guda, Chittibabu" sort="Guda, Chittibabu" uniqKey="Guda C" first="Chittibabu" last="Guda">Chittibabu Guda</name>
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<author><name sortKey="Jansen, Robert K" sort="Jansen, Robert K" uniqKey="Jansen R" first="Robert K." last="Jansen">Robert K. Jansen</name>
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<author><name sortKey="Luo, Hong" sort="Luo, Hong" uniqKey="Luo H" first="Hong" last="Luo">Hong Luo</name>
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<author><name sortKey="Tomkins, Jeffrey" sort="Tomkins, Jeffrey" uniqKey="Tomkins J" first="Jeffrey" last="Tomkins">Jeffrey Tomkins</name>
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<author><name sortKey="Rognli, Odd Arne" sort="Rognli, Odd Arne" uniqKey="Rognli O" first="Odd Arne" last="Rognli">Odd Arne Rognli</name>
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<author><name sortKey="Daniell, Henry" sort="Daniell, Henry" uniqKey="Daniell H" first="Henry" last="Daniell">Henry Daniell</name>
</author>
<author><name sortKey="Clarke, Jihong Liu" sort="Clarke, Jihong Liu" uniqKey="Clarke J" first="Jihong Liu" last="Clarke">Jihong Liu Clarke</name>
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<series><title level="j">TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik</title>
<idno type="ISSN">0040-5752</idno>
<idno type="eISSN">1432-2242</idno>
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<front><div type="abstract" xml:lang="en"><p id="P1">Comparisons of complete chloroplast genome sequences of <italic>Hordeum vulgare</italic>
, <italic>Sorghum bicolor</italic>
 and <italic>Agrostis stolonifera</italic>
 to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5′ end of ndhH is restricted to the three genera of the subfamily Pooideae (<italic>Agrostis</italic>
, <italic>Hordeum</italic>
 and <italic>Triticum</italic>
). Second, a 6 bp deletion in <italic>ndhK</italic>
 is shared by <italic>Agrostis</italic>
, <italic>Hordeum</italic>
, <italic>Oryza</italic>
 and <italic>Triticum</italic>
, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identified 19–37 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identified 16–21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among <italic>Zea mays</italic>
, <italic>Saccharum officinarum</italic>
 and <italic>Sorghum bicolor</italic>
, whereas no spacer regions were identical among <italic>Oryza sativa</italic>
, <italic>Triticum aestivum</italic>
, <italic>H. vulgare</italic>
 and <italic>A. stolonifera</italic>
 despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identified six C–U conversions in both <italic>Sorghum bicolor</italic>
 and <italic>H. vulgare</italic>
 but only one in <italic>A. stolonifera</italic>
. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae.</p>
</div>
</front>
</TEI>
</record>

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Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

Source :

Abstract

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Le document en format XML

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Pour générer des pages wiki