Rice-wheat synteny: a gene-by-gene analysis of the long arm of rice chromosome 11.

摘要

The DNA sequence of the long arm of rice chromosome 11 has been deciphered by two centers under the Indian Initiative for Rice Genome Sequencing (IIRGS). The phase 2 and/or finished sequences of > 100 BAC/PAC clones in the minimum tiling path of thischromosome arm is now publicly available in the GenBank database of NCBI. A total of 3113 genes have been predicted using different gene prediction software. A gene-by-gene BLAST search of the NCBI wheat EST database of over 420,000 cDNA sequences revealed that 38.2 percent of the predicted rice genes show significant homology with some wheat ESTs. A BLAST search of such 1192 rice genes with the GrainGenes database of sequence contigs containing bin-mapped wheat ESTs allowed 135 genes to be placed in wheat bins located mostly on the wheat chromosomes of homoeologous groups 4 and 3. Although some of these bin-mapped wheat contigs cross locate to chromosomes of other homoeologous groups, this could be ascribed mainly to the existence of translocations within the hexaploid wheat genome. Local disruptions in the order of these genes suggest that there have been many rearrangements including insertions, deletions, duplications and translocations that will complicate the synteny comparison. However, the enhanced resolution of comparative sequence analysis, especially in the conserved regions, will facilitate selection of markers for saturation mapping and genome sequencing of the gene-rich regions of wheat chromosomes.