TY - JOUR
T1 - A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat
T2 - Diverse gene function and genomic structure maintained in a tightly linked block
AU - Breen, James
AU - Wicker, Thomas
AU - Kong, Xiuying
AU - Zhang, Juncheng
AU - Ma, Wujun
AU - Paux, Etienne
AU - Feuillet, Catherine
AU - Appels, Rudi
AU - Bellgard, Matthew
N1 - Funding Information:
The BAC clones used in this study derived from the Minimal Tiling Path of ctg1034 in the chromosome 3B physical map of hexaploid wheat project within the International Wheat Genome Sequencing Consortium (IWGSC). The authors thank Fred Choulet provided the Perl scripts for identifying ISBP markers. Thanks to Yasunari Ogihara(Kihara Institute for Biological Research and Graduate School of Integrated Science, Yokohama City University, Japan) for advanced access to full-length cDNAs for wheat and Junhong Ma (SABC, Murdoch University, Australia) for laboratory work. The authors appreciated the help provided by Prof M Bevan to fill-in a gap in the Brachypodium genome sequence. Finally, thanks to David Dunn, Paula Moolhuijzen and all technical staff at the CCG for Bioinformatics support. Molecular Plant Breeding Co-operative Research Centre (MPBCRC) and Murdoch University generously supported funding for this work.
PY - 2010/5/27
Y1 - 2010/5/27
N2 - Background: 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 ctg1034 contig completed in this paper was initially studied because it was assigned to the Sr2 resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features.Results: BAC shotgun sequencing of the hexaploid wheat (Triticum aestivum cv. Chinese Spring) genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig ctg1034 into a 783,553 bp genomic sequence. This ctg1034 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 ctg1034 gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays, even though the intergenic space and introns were divergent.Conclusion: We propose that ctg1034 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 gypsy 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.Sequence data from this article have been deposited with the GenBank Data Libraries under accession no. GQ422824.
AB - Background: 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 ctg1034 contig completed in this paper was initially studied because it was assigned to the Sr2 resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features.Results: BAC shotgun sequencing of the hexaploid wheat (Triticum aestivum cv. Chinese Spring) genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig ctg1034 into a 783,553 bp genomic sequence. This ctg1034 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 ctg1034 gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays, even though the intergenic space and introns were divergent.Conclusion: We propose that ctg1034 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 gypsy 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.Sequence data from this article have been deposited with the GenBank Data Libraries under accession no. GQ422824.
UR - http://www.scopus.com/inward/record.url?scp=77952701365&partnerID=8YFLogxK
U2 - 10.1186/1471-2229-10-98
DO - 10.1186/1471-2229-10-98
M3 - Article
C2 - 20507561
AN - SCOPUS:77952701365
SN - 1471-2229
VL - 10
JO - BMC Plant Biology
JF - BMC Plant Biology
M1 - 98
ER -