Molecular evolution of the MLO gene family in Oryza sativa and their functional divergence

The present study identified 12 MLO genes in rice that were located on chromosomes 1, 2, 3, 4, 5, 6, 10, and 11 respectively without any obvious clustering. On a genome scale we showed that the expansion of rice MLO gene family was primarily attributed to segmental duplication produced by polyploidy, rather than through tandem amplification. Gene conversion events should also play important roles in the evolution of MLO genes. The results of relative rate ratio test and maximum likelihood analysis suggested that positive selection should have occurred after gene duplication and/or speciation, prompting the formation of distinct MLO subfamilies. Functional divergence analysis provided statistical evidence for shifted evolutionary rate after gene duplication. Compared to extracellular loop 3 and Ca(2+)-binding domain, much stronger functional constraints should impose on intracellular loop 2, although all of the three regions might be under purifying selection. The sliding window analysis of d(N)/d(S) ratio values identified one sequence region where strong functional constraints must impose on, and consequently should be crucial for functionality of MLO genes.