Genome-wide Identification, characterization and evolutionary analysis of SNF1-related kinase 1 (SnRK1) and late embryogenesis abundant (LEA) proteins gene family in Hordeum vulgare under drought stress

Abstract

Abstract The SNF1-related kinase 1 (SnRK1) and late embryogenesis abundant (LEA) proteins were identified, characterized and analyzed in H. vulgare. Results of qRT-PCR indicates the HvSnRK1 and HvLEA were up regulated with fold change 6.12 and 7.58, respectively under drought stress. Genome-wide analysis, were identified 13 SnRK1 and 7 LEA proteins in H. vulgare. Domain analysis confirmed the presence of the Protein kinase domain and LEA_4 on HvSnRK1 and HvLEA proteins, respectively. Motifs and genes structure analysis indicates, that genes with closer phylogenetic relationships exhibited more similar genetic structures. The most HvSnRK1 proteins were located in the cytoplasm whereas HvLEA proteins were located in the nucleus and mitochondria. 16 microRNAs were predicted against 7 HvSnRK1 genes whereas 1 microRNAs were predicted against 1 HvLEA gene. Predicted SnRK1 and LEA proteins models have a C-score range from − 0.75 and − 1.48 to -0.69 and − 0.20, respectively, which suggesting the structures of SnRK1 and LEA proteins are constructed with high accuracy. SnRK1 genes were found on chromosome 1, 2, 3, 4 and 5. LEA genes were found on chromosome 1, 3 and 4. Ka/Ks ratio were indicated that the SnRK1 and LEA genes were primarily influenced by purifying selection. Phylogenetic analysis were classified SnRK1 and LEA proteins into three clades for each one. Synteny analysis of SnRK1 and LEA proteins were have collinearity orthologous relationship in Z. mays. The gene ontology enrichment analysis were confirmed the functional role of SnRK1 and LEA as a stress responsive.