Genome-wide Analysis Of Abiotic Stresses And Hormone Signalling Related Gene Families In Brassica Rapa

A common goal of current plant genomics research is to create an expandable platform for global classification and analysis of plant gene family.A large fraction of genes in plant genomes are the product of gene duplication and novel gene creation processes.Hence,it’s necessary to provide a foundation for future research.In the meantime,the response of the plant to abiotic and hormone signalling under various stimulation,are primarily focused on for many researchers in the past decade.While,the completion of various crop genome analysis including B.rapa,provided useful information and helps in understanding their underlying genetic molecular mechanisms.Thus,we explored the B.rapa genome for multifunctional related gene families,such as GSTs,E2s,Homeobox,and PP2C that are largely known to participate in various stress signalling.GSTs is one of the most important multifunctional protein family,which has been playing a crucial role in the different aspects of plant growth.This extensive study about GSTs may establish a solid foundation for the brief functional analysis of BraGSTs in future.In this study,75 genes were identified in B.rapa.Phylogenetic analysis characterized them into eight different sub-classes,while Tau and Phi sub-class being the most numerous.The exon-intron structure and the motif composition of BraGSTs were exhibited accordingly to its sub-classes.Notably,we also investigated 15 tandem paralogous pairs of genes,which highlighted that all the pairs were purifying in nature as their synonymous values were lower than 1.00.Duplication analysis indicated that about 45.33%of genes mainly occurred through tandem duplication in B.rapa.Predominately,the tandem cluster of genes in sub-class Tau was greater than other sub-classes.Furthermore,among eight various hormonal treatments(ABA,GA,BR,ETH,IAA,IBA,NAA,and JA),most numbers of BraGSTs were activated by NAA,BR,and ABA treatments.This analysis has provided comprehensive information about GSTs family,which may assist in elucidating their exact functions in B.rapa.To understand ubiquitination mechanism,E2 ubiquitin-conjugating enzymes are the crucial part by playing a major role in regulating many biological processes in plants.Meanwhile,B.rapa is an important leafy vegetable crop and therefore its characterization along with its expression pattern of E2s under various stresses is imperative.In this study,83 genes were identified in B.rapa and were classified into four different classes based on domain information.Here,we analysed phylogenetic relationships,collinear correlation,gene duplication,interacting network and expression patterns of E2 genes in B.rapa.Furthermore,RT-PCR analysis for 8 various abiotic and hormone treatments namely(ABA,GA,JA,BR,PEG,NaCl,heat and cold stress)illustrated striking expression pattern under one or more treatment,speculating that these might be stress-responsive genes.The cis-elements and interaction network analyses implicating valuable clues of the important function of E2 genes in development and various stress responses in B.rapa.This study will further facilitate the functional analysis of E2s for improving stress resistance mechanism in B.rapa.Homeobox(HB)genes are crucial for plant growth and development processes.They encode transcription factors and responses to various stresses,as reported by recent emerging evidence.In this study,113 BraHB genes were identified in B.rapa.Based on domain organization and phylogenetic analysis,the BraHBs were grouped into nine subclasses,in which Homeobox leucine-zipper(HB LZP-Ⅲ)showed the highest number of genes(28)compared to other subclasses.The BraHBs exhibited similarities in exon-intron organization and motif composition among the members of the same subclasses.The analysis revealed that HB-Knotted was more preferentially retained than any other subclass of BraHB.Furthermore,we evaluated the impact of whole-genome triplication on the evolution of BraHBs.In order to analyse the subgenomes of B.rapa,we identified 39 paralogous pairs for which synonymous substitution values were lower than 1.00 for further purifying selection.Finally,the expression patterns of BraHBs across six tissues expressed dynamic variations combined with their responses against various stresses.The current study provides brief information on the Homeobox gene family in B.rapa.Our findings can serve as a reference for further functional analysis of BraHBs.The type 2C protein belongs to the major group of protein phosphatases(PP2Cs)known to participate in various responses,such as ABA signalling.In the present study,131 PP2C genes were identified in B.rapa and categorized into thirteen subgroups based on their phylogenetic relationships.These B.rapa PP2C are structurally conserved,based on amino acid sequence alignment,phylogenetic analysis,and conserved domains.We employed previously reported RNA-sequence data for various tissues(root,stem,leaf,flower,and silique)along with 29 paralogous gene pairs,indicating an overlapping expression pattern.The qRT-PCR analysis of 15 paralogous gene pairs under various stresses revealed distinct expression patterns such as to heat,cold,ABA,and drought.Consequently,some essential stress responsive BraPP2C genes were identified by demonstrating their importance in plant stress improvement in B.rapa.The evolutionary analysis for 15 paralogous gene pairs suggested that only three pairs were showing positive selection and the rest of others were purifying in nature.Furthermore,heat and PEG treatments significantly affected the photosynthetic efficiency and antioxidant enzyme,including superoxide dismutase(SOD),peroxidase(POD),catalase(CAT),and glutathione S-transferase(GST)accumulation in B.rapa.The presented results of this study hasten our understanding of the molecular evolution of the PP2C gene family in B.rapa.Thus,it will be ultimately helping in future research for facilitating the functional characterization of BraPP2C genes in developing the abiotic stress tolerant plants.In brief,we systematically carried out a whole genome-wide identification of B.rapa by various bioinformatic tools,such as the physicochemical properties,phylogenetic characterization,collinearity,gene structure and motif composition,evolutionary rates,and gene duplications.The cis-elements prediction analysis extended our repositories on the putative functions of GSTs,E2s,Homeobox,and PP2C in plant developments and various stress-related activities in B.rapa.Additionally,the expression profiling of various organs,abiotic and hormone stresses along their correlation analysis provided a stand-point of the critical role of GSTs,E2s,Homeobox,and PP2C for plant improvements.Thus,these findings will work as valuable resources for further investigation of various stress-responsive genes and will greatly aid in the functional validation of the GSTs,E2s,Homeobox,and PP2C genes in this important vegetable crop.