Computational identification and systematic analysis of the ACR gene family in Oryza sativa

Based on sequence similarity search and domain detection, nine ACT domain repeat protein-coding genes (the "ACR" genes) in rice were identified, which were mainly distributed on the chromosomes 2, 3, 4, and 8. An InterPro database search indicated that four copies of the ACT domain linearly occupied the entire polypeptide. The first three ACT domains were linked by two different sequences. However, the fourth ACT domain was extremely close to ACT3. Gene structure comparisons showed large differences in exon numbers, from three to eight, among members of the rice ACR gene family. In addition, it appeared that gene duplication might be operative when the compositions of exons and introns were analyzed. Phylogenetic analysis divided the ACR gene family into five distinct groups, and this division was generally according to the expression patterns of the ACR genes. The Arabidopsis and rice ACR proteins were clustered across together, suggesting that these ACR genes might originate from an ancient common ancestor. Notably, the identification of orthologues and paralogues would be useful for rice gene functional annotation.