Comparative DNA sequence analysis involving wheat, brachypodium and rice genomes using mapped wheat ESTs

Abstract

Comparative genomics is a powerful approach to transfer genomic information from a sequenced genome to closely related species. We conducted a comparative genomics study between wheat and brachypodium genomes, using 8 210 mapped wESTs for BLASTn against the high-quality genome sequence of brachypodium. As many as 5 208 wESTs spread over all the 21 wheat chromosomes showed significant similarity with genomic regions in all the five brachypodium chromosomes (Bd1 to Bd5). Wheat ESTs belonging to seven homoeologous groups were also used to construct seven consensus maps (WC1 to WC7) for wheat chromosomes. Each consensus wheat chromosome matched only one or two brachypodium chromosomes. Following are the broad syntenic relationship that were observed between brachypodium and wheat chromosomes: WC1-Bd2/Bd3, WC2-Bd1/Bd5, WC3-Bd2, WC4-Bd1, WC5-Bd4/Bd1/Bd3, WC6-Bd3 and WC7-Bd1/Bd3. Eighty two (82) conserved syntenic blocks were also identified between wheat and brachypodium genomes. Ka/Ks analysis was performed on 153 sequence pairs, of which 98 had Ka/Ks ratio <1 suggesting their evolution under purifying selection involving no divergence in encoded amino acids. Results of this study suggested that after divergence from a common ancestral genome the common syntenic features maintained between genomes of wheat and brachypodium.