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
<p>Abstract</p> <p>Background</p> <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 colin...
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| Format: | Article |
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BMC
2010-05-01
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| Series: | BMC Plant Biology |
| Online Access: | http://www.biomedcentral.com/1471-2229/10/98 |
| _version_ | 1819178835602571264 |
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| author | Ma Wujun Zhang Juncheng Kong Xiuying Wicker Thomas Breen James Paux Etienne Feuillet Catherine Appels Rudi Bellgard Matthew |
| author_facet | Ma Wujun Zhang Juncheng Kong Xiuying Wicker Thomas Breen James Paux Etienne Feuillet Catherine Appels Rudi Bellgard Matthew |
| author_sort | Ma Wujun |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <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 <it>ctg1034 </it>contig completed in this paper was initially studied because it was assigned to the <it>Sr2 </it>resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features.</p> <p>Results</p> <p>BAC shotgun sequencing of the hexaploid wheat (<it>Triticum aestivum </it>cv. Chinese Spring) genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig <it>ctg1034 </it>into a 783,553 bp genomic sequence. This <it>ctg1034 </it>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 <it>ctg1034 </it>gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of <it>Brachypodium distachyon</it>, <it>Oryza sativa</it>, <it>Sorghum bicolor </it>and <it>Zea mays</it>, even though the intergenic space and introns were divergent.</p> <p>Conclusion</p> <p>We propose that <it>ctg1034 </it>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 <it>gypsy </it>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> |
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| spelling | doaj.art-196fb379aec049349bc374e130931fd22022-12-21T18:11:25ZengBMCBMC Plant Biology1471-22292010-05-011019810.1186/1471-2229-10-98A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked blockMa WujunZhang JunchengKong XiuyingWicker ThomasBreen JamesPaux EtienneFeuillet CatherineAppels RudiBellgard Matthew<p>Abstract</p> <p>Background</p> <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 <it>ctg1034 </it>contig completed in this paper was initially studied because it was assigned to the <it>Sr2 </it>resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features.</p> <p>Results</p> <p>BAC shotgun sequencing of the hexaploid wheat (<it>Triticum aestivum </it>cv. Chinese Spring) genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig <it>ctg1034 </it>into a 783,553 bp genomic sequence. This <it>ctg1034 </it>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 <it>ctg1034 </it>gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of <it>Brachypodium distachyon</it>, <it>Oryza sativa</it>, <it>Sorghum bicolor </it>and <it>Zea mays</it>, even though the intergenic space and introns were divergent.</p> <p>Conclusion</p> <p>We propose that <it>ctg1034 </it>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 <it>gypsy </it>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>http://www.biomedcentral.com/1471-2229/10/98 |
| spellingShingle | Ma Wujun Zhang Juncheng Kong Xiuying Wicker Thomas Breen James Paux Etienne Feuillet Catherine Appels Rudi Bellgard Matthew 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 BMC Plant Biology |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| url | http://www.biomedcentral.com/1471-2229/10/98 |
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