Computational identification and phylogenetic analysis of the MAPK gene family in Oryza sativa

The MAPK cascade plays greatly important roles in signal transduction pathways. The present study computationally identified 16 rice MAPKs (OsMPKs). The results of EST and cDNA hitting supported the reliability of OsMPKs in rice. Gene structure comparison showed large differences in exon numbers, from 2 to 12, among members of the rice MAPK family. Rice MAPKs were located on chromosomes 1, 2, 3, 5, 6, 10, and 11, particularly being distributed on the 1, 5 and 6 chromosomes. On a genome scale we revealed that the rice MAPK family should have evolved through segmental duplication produced by polyploidy, rather than through tandem amplification. Phylogenetic analysis divided the plant MAPK family members into four distinct groups (A–D), supported by highly significant bootstrap values. 11 out of the 16 OsMPKs belonged to group D, suggesting dramatic evolutionary expansion of this group and rapid gene losses in other groups. The divergence between and within plant MAPK groups should predate the monocot-dicot split. Notably, the divergences between plant, animal, fungi and parasite MAPKs were apparent, although MAP kinases might be conserved during long space of evolutionary time. Moreover, some orthologs and paralogs could be identified from the phylogenetic tree. It is suggested that members within each group might serve similar functions in different species. Thus, the annotation of published MAPKs would greatly facilitate the functional investigation of uncharacterized MAP kinases. However, group D genes were more complicated, and required extensive additional studies. Overall, the first description of the whole MAPK family will be expected to result in significant progress in investigating the regulation mechanism of MAPKs in response to extracellular stimuli.