Prediction of RNA editing sites and genome-wide characterization of PERK gene family in maize (Zea mays L.) in response to drought stress

Abstract

ObjectivesInadvertent climate changes continuously threating the crops production and thus affecting the livelihood of peoples across the world. The maize production at world level has severely been hampered by the drought stress. Proline-rich extensin-like receptor kinases (PERKs) are considered among the sub-class of plants larger protein family, receptor kinases. Member of PERK gene family play significant role in both abiotic and biotic stress and in various plant metabolic activities and pathways. MethodsAs of now, no comprehensive research is reported for PERK genes in maize. We have performed a genome wide in-silico analysis and identify twenty-three PERK genes in maize. We performed phylogenetic analysis, sequence logos, motif analysis, promoter analysis, chromosomal and subcellular localization, synteny and expression analysis using RNA seq data under drought stress. We also predict RNA editing sites in mitochondrial and chloroplast genome. ResultsPhylogenetic study of PERK genes from eight different plant species divided into four distinct clades. Four subclasses group of ZmPERKs were observed based on domain organization, motif pattern, and phylogenetic analysis. The exon–intron arrangement of the ZmPERK were conserved among members of the same subclasses. In the promoter region different cis-elements were found those were involved in the growth and development, as well as light and stress response. Through gene duplication analysis it was observed that segmental duplications in ZmPERKs played major role in maize evolution. The Ka/Ks ratios indicated that most ZmPERK genes during the evolution have experienced strong purifying selection. The conversion of cytosine (C) to uracil (U) was observed in all predicted editing sites (U). These transitions were mostly based on changes in the first andsecond codon bases. The in-silico expression analysis of transcriptome data revealed the differential expression of ZmPERK genes in response to drought stress and oil content accumulation. ConclusionThe current study provides base information on the PERK gene family in maize. Our findings can serve as a reference for further functional analysis of ZmPERKs. These genes can be further explored and used in breeding program to develop cultivars resilient to drought stress.