A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block
Identifieur interne : 007560 ( Main/Merge ); précédent : 007559; suivant : 007561A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block
Auteurs : James Breen [Australie] ; Thomas Wicker ; Xiuying Kong [République populaire de Chine] ; Juncheng Zhang [République populaire de Chine] ; Wujun Ma [Australie] ; Etienne Paux [France] ; Catherine Feuillet [France] ; Rudi Appels [Australie] ; Matthew Bellgard [Australie]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2010.
Abstract
The complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase) level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between species tends to imply an important functional or regional constraint that does not permit a change in genomic structure. The
BAC shotgun sequencing of the hexaploid wheat (
We propose that
Sequence data from this article have been deposited with the GenBank Data Libraries under accession no. GQ422824
Url:
DOI: 10.1186/1471-2229-10-98
PubMed: 20507561
PubMed Central: 3017796
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PMC:3017796Le document en format XML
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Street, Perth 6150, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150</wicri:regionArea><wicri:noRegion>Perth 6150</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Molecular Plant Breeding Co-operative Research Centre (MPBCRC) Murdoch University, South Street, Perth 6150, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Molecular Plant Breeding Co-operative Research Centre (MPBCRC) Murdoch University, South Street, Perth 6150</wicri:regionArea><wicri:noRegion>Perth 6150</wicri:noRegion></affiliation></author><author><name sortKey="Wicker, Thomas" sort="Wicker, Thomas" uniqKey="Wicker T" first="Thomas" last="Wicker">Thomas Wicker</name><affiliation><nlm:aff id="I3">Institute of Plant Biology, University Zurich, Zollikerstrasse 107, Zurich, CH-8008 Switzerland</nlm:aff><wicri:noCountry code="subfield">CH-8008 Switzerland</wicri:noCountry></affiliation></author><author><name sortKey="Kong, Xiuying" sort="Kong, Xiuying" uniqKey="Kong X" first="Xiuying" last="Kong">Xiuying Kong</name><affiliation wicri:level="1"><nlm:aff id="I4">Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhang, Juncheng" sort="Zhang, Juncheng" uniqKey="Zhang J" first="Juncheng" last="Zhang">Juncheng Zhang</name><affiliation wicri:level="1"><nlm:aff id="I4">Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Ma, Wujun" sort="Ma, Wujun" uniqKey="Ma W" first="Wujun" last="Ma">Wujun Ma</name><affiliation wicri:level="1"><nlm:aff id="I1">Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150</wicri:regionArea><wicri:noRegion>Perth 6150</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I5">State Agricultural Biotechnology Centre (SABC), Murdoch University, South Street, Perth 6150, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>State Agricultural Biotechnology Centre (SABC), Murdoch University, South Street, Perth 6150</wicri:regionArea><wicri:noRegion>Perth 6150</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I6">Department of Agriculture and Food, Western Australia (DAFWA), 3 Baron Hay Court, Perth, 6151 Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Agriculture and Food, Western Australia (DAFWA), 3 Baron Hay Court, Perth</wicri:regionArea><wicri:noRegion>Perth</wicri:noRegion></affiliation></author><author><name sortKey="Paux, Etienne" sort="Paux, Etienne" uniqKey="Paux E" first="Etienne" last="Paux">Etienne Paux</name><affiliation wicri:level="1"><nlm:aff id="I7">UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, INRA Site de Crouël, 63100 Clermont-ferrand, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, INRA Site de Crouël, 63100 Clermont-ferrand</wicri:regionArea><wicri:noRegion>63100 Clermont-ferrand</wicri:noRegion><wicri:noRegion>63100 Clermont-ferrand</wicri:noRegion></affiliation></author><author><name sortKey="Feuillet, Catherine" sort="Feuillet, Catherine" uniqKey="Feuillet C" first="Catherine" last="Feuillet">Catherine Feuillet</name><affiliation wicri:level="1"><nlm:aff id="I7">UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, INRA Site de Crouël, 63100 Clermont-ferrand, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, INRA Site de Crouël, 63100 Clermont-ferrand</wicri:regionArea><wicri:noRegion>63100 Clermont-ferrand</wicri:noRegion><wicri:noRegion>63100 Clermont-ferrand</wicri:noRegion></affiliation></author><author><name sortKey="Appels, Rudi" sort="Appels, Rudi" uniqKey="Appels R" first="Rudi" last="Appels">Rudi Appels</name><affiliation wicri:level="1"><nlm:aff id="I1">Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150</wicri:regionArea><wicri:noRegion>Perth 6150</wicri:noRegion></affiliation></author><author><name sortKey="Bellgard, Matthew" sort="Bellgard, Matthew" uniqKey="Bellgard M" first="Matthew" last="Bellgard">Matthew Bellgard</name><affiliation wicri:level="1"><nlm:aff id="I1">Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150</wicri:regionArea><wicri:noRegion>Perth 6150</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Plant Biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase) level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between species tends to imply an important functional or regional constraint that does not permit a change in genomic structure. The <italic>ctg1034 </italic>contig completed in this paper was initially studied because it was assigned to the <italic>Sr2 </italic>resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features.</p></sec><sec><title>Results</title><p>BAC shotgun sequencing of the hexaploid wheat (<italic>Triticum aestivum </italic>cv. Chinese Spring) genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig <italic>ctg1034 </italic>into a 783,553 bp genomic sequence. This <italic>ctg1034 </italic>sequence was annotated for biological features such as genes and transposable elements. A three-gene island was identified among >80% repetitive DNA sequence. Using bioinformatics analysis there were no observable similarity in their gene functions. The <italic>ctg1034 </italic>gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of <italic>Brachypodium distachyon</italic>, <italic>Oryza sativa</italic>, <italic>Sorghum bicolor </italic>and <italic>Zea mays</italic>, even though the intergenic space and introns were divergent.</p></sec><sec><title>Conclusion</title><p>We propose that <italic>ctg1034 </italic>is located within the heterochromatic C-band region of deletion bin 3BL7 based on the identification of heterochromatic tandem repeats and presence of significant matches to chromodomain-containing <italic>gypsy </italic>LTR retrotransposable elements. We also speculate that this location, among other highly repetitive sequences, may account for the relative stability in gene order and orientation within the gene island.</p><p>Sequence data from this article have been deposited with the GenBank Data Libraries under accession no. GQ422824</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Gupta, Pk" uniqKey="Gupta P">PK Gupta</name></author><author><name sortKey="Mir, Rr" uniqKey="Mir R">RR Mir</name></author><author><name sortKey="Mohan, A" uniqKey="Mohan A">A Mohan</name></author><author><name sortKey="Kumar, J" uniqKey="Kumar J">J Kumar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gill, Bs" uniqKey="Gill B">BS Gill</name></author><author><name sortKey="Appels, R" uniqKey="Appels R">R Appels</name></author><author><name sortKey="Botha Oberholster, Am" uniqKey="Botha Oberholster A">AM Botha-Oberholster</name></author><author><name sortKey="Buell, Cr" uniqKey="Buell C">CR Buell</name></author><author><name sortKey="Bennetzen, Jl" uniqKey="Bennetzen J">JL Bennetzen</name></author><author><name sortKey="Chalhoub, B" uniqKey="Chalhoub B">B Chalhoub</name></author><author><name sortKey="Chumley, F" uniqKey="Chumley 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Barrell</name></author><author><name sortKey="Parkhill, J" uniqKey="Parkhill J">J Parkhill</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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