Identification And Expression Profile Analysis Of MAPK And MKK Gene Family In Arabidopsis Pumila

Mitogen-activated protein kinase(MAPK)cascade is a universal signal transduction module in eukaryotes,and plays an important role in plant growth and development,hormone response,and various biotic and abiotic stress responses.The study of the MAPK cascade and its preliminary functions can be helpful to clarify the signal transduction network of plant stress resistance,which will lay the foundation for analyzing the complex mechanisms of MAPK cascade-mediated growth and development and abiotic stress signal transduction pathways in plants.At present,three gene families: MAPK kinase kinase(MAPKKK)?MAPK kinase(MAPKK or MKK)and MAPK of MAPK cascade have been identified in a variety of plants,but there has been no systematic study in Cruciferous plant Arabidopsis pumila which grows in arid,desert,and saline-alkali soil environments in Xinjiang.There are a lot of stress resistance genes worth exploring in Arabidopsis pumila.To explore the evolution and function of the MAPK cascade gene family in Arabidopsis pumila,systematical identification,phylogenetic analysis,and expression profiling of the MAPK and MKK gene families in Arabidopsis pumila were carried out through genome-wide analysis in this study.Object: Genome-wide identification of MAPK and MKK gene families in Arabidopsis pumila;evolution analysis of MAPK and MKK gene family;preliminary function analysis of MAPK and MKK gene family members.Methods: Based on the whole genome data of Arabidopsis pumila(not yet published),the genome-wide search and identification of the Ap MAPK and Ap MKK family members were conducted,and the chromosomal location,multiple sequence alignment,motif distribution,exon-intron structure,and distribution of cis-acting elements in the promoter region of the MAPK and MKK family members were analyzed;In addition,we compared the phylogenetic relationships of the MAPK and MKK gene families of Arabidopsis pumila,rice and related species of Arabidopsis pumila.We also performed Ka/Ks,Tajima relative rate test and syntenic analysis for duplicated genes.RNA-seq data was used to study the expression patterns of Ap MAPK and Ap MKK genes in different tissues and different time points under salt stress.q RT-PCR was used to analyze expression profiling of the Ap MAPK family genes under drought,high temperature,SA,and ABA treatments.Results:(1)38 ApMAPK genes and 16 ApMKK genes were identified from the whole genome database of Arabidopsis pumila.The MAPK and MKK family members were distributed respectively on 12,10 chromosomes of Arabidopsis pumila.Ap MAPK proteins consisted of 249 to 620 amino acids.The calculated molecular weights of Ap MAPK proteins ranged from 28.94 to 70.85 k Da,and their isoelectric points had distinct degree of variability between 4.86 and 9.44.Ap MKK proteins were composed of 312 to 367 amino acids.The calculated molecular weights of Ap MKK proteins ranged from 34.53 to 62.75 k Da,and their isoelectric points had distinct degree of variability between 5.72 and 9.27.(2)According to phylogenetic analysis and multiple sequence alignment,the Ap MAPK family members were divided into two types: TEY type and TDY type,TEY type Ap MAPKs were divided into 3 subfamilies which are Group A,Group B,and Group C,respectively,and TDY type Ap MAPKs alone formed a distant subfamily Group D;All Ap MKK genes were divided into five known subfamilies,i.e.Groups A,B,C,D,and E,which included 5,2,4,3,2 members,respectively.(3)Members of the same subfamily had the same motif distribution and number of exons,and each subgroup had its own unique motif.(4)Molecular evolution and syntenic analysis showed that there were 18 pairs of duplicated genes(except Ap MAPK17-1/17-2)in the MAPK gene family of Arabidopsis pumila,in which the evolution of Ap MAPK11-1/11-2 was accelerated following the duplication event;there were 7 pairs of duplicated genes in the MKK gene family: Ap MKK1-1/1-2,Ap MKK2-1/2-2,Ap MKK3-1/3-2,Ap MKK4-1/4-2,Ap MKK5-1/5-2,Ap MKK9-1/9-2 and Ap MKK10-1/10-2,of which Ap MKK1-1/1-2 undergone accelerated evolution after the duplication event;Both Ap MAPK and Ap MKK duplicated genes undergone purification selection.(5)Both Ap MAPK and Ap MKK gene family members had tissue expression specificity and functional diversity.(6)There were differences in the motif distribution and gene structure between 3 pairs of duplicated genes: Ap MAPK11-1/11-2,Ap MAPK15-1/15-2,and Ap MKK3-1/3-2 which had different expression patterns in different tissues and various abiotic stresses including high salinity,drought,and high temperature,and their types of cis-elements in the promoter regions were also significantly different.(7)Ap MAPK6-1,Ap MAPK6-2,Ap MAPK7-1 and Ap MAPK7-2 were continuously up-regulated under various abiotic stresses.Conclusion: There are 38 MAPK genes and 16 MKK genes in Arabidopsis pumila;The Ap MAPK family members are divided into four subfamilies,namely Group A,Group B,Group C,and Group D;The Ap MKK family members are divided into five subfamilies,namely Group A,Group B,Group C,Group D,and Group E.There are 18 and 7 pairs of duplicated genes in Ap MAPK and Ap MKK gene families,respectively,and all of them undergone purification selection.The evolution rate of Ap MAPK11-1/11-2 and Ap MKK1-1/1-2 were accelerated following the occurrence of duplication events.Both Ap MAPK and Ap MKK gene family members have tissue expression specificity and functional diversity,and the same Ap MAPK or Ap MKK subfamily genes have similar motif distribution and gene structure.There are structural differences,regulatory element differences,and functional differences between some Ap MAPK duplicated genes or Ap MKK duplicated genes.Gene structure differences of duplicated genes directly cause functional differences.Most Ap MAPK family genes are significantly up-regulated under high temperature,drought stress,and SA treatment,and respond quickly under ABA treatment.Ap MAPK6-1,Ap MAPK6-2,Ap MAPK7-1,and Ap MAPK7-2 are involved in immune defense and a variety of abiotic stress signal transduction pathways.