Genome-wide Identification, characterization and evolutionary analysis of C2H2-type zinc finger proteins (ZFPs) in Hordeum vulgare under salt stress

Abstract

Abstract Genome-wide identification of C2H2-type zinc finger proteins were identified 77 C2H2-type zinc finger proteins in H. vulgare. Due to the importance of the understanding stress response mechanisms, the current study were carried out to study the salinity stress response genes, qRT-PCR results were could identify the zinc finger protein 36 (HvZFP36) as salinity-responsive and also keeping in view that the HvZFP36 protein were down regulated with fold change 0.16 under salt stress. Domain analysis confirmed the presence of the Zinc finger C2H2-type domain on 77 Znf_C2H2 protein sequences. Motifs and introns/exons structure analysis indicates, that genes with closer phylogenetic relationships exhibited more similar genetic structures. The most HvZnf_C2H2 proteins were located in the nucleus and 20 putative nuclear localization signal (NLS) were predicted against 14 HvZnf_C2H2 proteins. Transmembrane helical were predicted the in HvZnf_C2H2_43 and HvZnf_C2H2_77 proteins and HvZnf_C2H2_9 protein were have been found to be more phosphorylated with serine, threonine and tyrosine. 3-D prediction of C2H2-type zinc finger proteins models have a C-score range from − 1.27 to − 3.39, which suggesting the structures proteins are constructed with high accuracy. 34 microRNAs were predicted against 30 HvZnf_C2H2 genes. HvZnf_C2H2 genes were physically located on the 7 chromosomes in H. vulgare genome. Ka/Ks ratio were indicated that the HvZnf_C2H2 genes were primarily influenced by purifying selection and we were suggested HvZnf_C2H2_7/HvZnf_C2H2_26 paralogous gene pairs were have a basic role of increase number of HvZnf_C2H2 genes family in H. vulgare. Phylogenetic analysis were classified HvZnf_C2H2 proteins into three clades. Synteny analysis resulting, 10 C2H2-type zinc finger proteins from clade I were have collinearity orthologous relationship in Zea mays, Solanum lycopersicum and Arabidopsis thaliana. Clade II were not have collinearity orthologous relationship in A. thaliana. HvZnf_C2H2_20 in clade III were have collinearity orthologous relationship in A. thaliana. The gene ontology enrichment analysis were confirmed the functional role of HvZnf_C2H2 as a stress responsive.