Identification and Characterization of MAPK Genes in Plants

Mitogen activated protein kinase (MAPK) gene families from the model plant Arabidopsis thaliana were downloaded from The Arabidopsis Information Resources (TAIR: http://www.arabidopsis.org/) database [88 (link)]. The MAPK gene families from rice were downloaded from the TIGR rice Genome Annotation Resources (http://rice.plantbiology.msu.edu/) database [89 (link)]. The protein sequences of MAPKs from Arabidopsis thaliana and rice were used as search queries in the publicly available phytozome database (http://www.phytozome.net/) to identify MAPK genes in other plant species [90 (link)]. Overall, 40 species were included in this study and reported in Table 1. To identify MAPK gene families of unknown species, BLASTP searches was conducted using orthologous protein sequences Arabidopsis thaliana and Oryza sativa MAPK genes as the query search [91 (link)]. The genes identified through BLAST searches were used for further analysis. First, the top 100 genes were kept for systemic evaluation and indexing. The genes with serine/threonine protein kinase domains and the activation loop T-E-Y or T-D-Y motifs were considered as probable MAPK genes, which were subsequently confirmed by scanning in scan prosite and smart software for the presence of MAPK domain [92 (link),93 (link)]. All datas were checked for redundancy and no any alternative splice variants were considered. Identified MAPK gene families from each species were again confirmed by running BLASTP searches against TAIR using the default parameters [92 (link),93 (link)]. The genes were considered MAPK genes when BLASTP search matches with Arabidopsis MAPKs.