[Genome-wide identification, phylogenetic analysis and expression profiling of the MKK gene family in Arabidopsis pumila].

Abstract

Mitogen-activated protein kinase kinase (MAPKK or MKK) is an important component of the MAPK cascade, which plays important roles in plant growth and development as well as in various stress responses. At present, the MKK gene family has been identified in a variety of plants, but there has been no systematic study in Cruciferous plant Arabidopsis pumila. To explore the evolution and function of the MKK gene family in Arabidopsis pumila, 16 ApMKK genes were identified from the Arabidopsis pumila genome by genome-wide analysis, and they were distributed on 10 chromosomes of Arabidopsis pumila. According to phylogenetic analysis and multiple sequence alignment, these putative genes were divided into five known subfamilies, i.e, Groups A, B, C, D, and E, which includes 5, 2, 4, 3, 2 members, respectively. Evolutionary and syntenic analysis showed that there are seven pairs of duplication genes in Arabidopsis pumila: ApMKK1-1/1-2, ApMKK2-1/2-2, ApMKK3-1/3-2, ApMKK4-1/4-2, ApMKK5-1/5-2, ApMKK9-1/9-2, and ApMKK10-1/10-2. Ka/Ks and Tajima analysis indicated that evolution of ApMKK1-1/1-2 was accelerated after the duplication event. Combining the distribution of cis-element in the promoter region of ApMKKs and the expression profile of ApMKKs in mature leaves, stems, flowers and fruits as well as under salt stress, we found that the expressions of paralogous genes (duplication genes) were tissue-specific and their functions were diversified. The expression patterns of some duplicated genes in tissues were different, but the expression patterns under salt stress were basically the same. These results lay the foundation for analyzing the complex mechanisms of MKK-mediated growth and development and abiotic stress signal transduction pathways in Arabidopsis pumila.