Genome-wide Identification Of The Basic Leucine Zipper(bZIP) Gene Family In Cotton

Cotton is a global economic crop and an important economic crop in China.It is mainly used for the production of natural fibers and cottonseed oil.It is an important raw material for the textile industry.It is also a pioneer crop in saline-alkali land.Gossypium hirsutum L.is the most extensively planted-cotton species.Due to the intensification of land and cotton contention,cotton cultivation areas have been seriously affected,and gradually moved to remote inland plateaus and saline-alkali lands,which put forward higher requirements for cotton's salt tolerance.Therefore,the bioinformatics identification and genomics analysis of salt-tolerant genes in G.hirsutum has important reference value for analyzing the salt-tolerance mechanism of cotton and breeding salt-tolerant varieties.Based on the whole genome sequencing data of Gossypium hirsutum,Gossypium arboretum and Gossypium raimondii,this study used bioinformatics to analyze the basic region-leucine zipper(bZIP)transcription factors of three cotton species.The gene family has been identified and analyzed for genomics,providing a reference for the functional research and utilization of the bZIP genes in G.hirsutum.The main findings are as follows:1.151,85 and 86 bZIP genes were identified in the G.hirsutum,G.arboreum and G.raimondii genome respectively.Using BioEdit software,querying the full-length protein sequence of bZIP gene of Arabidopsis thaliana and rice(Oryza sativa L.),a total of 884 candidate genes were retrieved from the G.hirsutum genome.The full-length protein sequence was submitted to the HMMER and CDD databases,and 151 bZIP genes in G.hirsutum,85 in G.arboreum,and 86 in G.raimondii were identified respectively.These bZIP genes were named as GhbZIP1-GhbZIP151,GabZIP1-GabZIP85,and GrbZIP1-GrbZIP86 respectively,according to their positions on the chromosomes.2.Genomics analysis of the bZIP gene familiesThe prediction results of the physicochemical properties of the proteins showed that the length of the protein encoded by the bZIP gene in G.hirsutum was between 106 and 689 amino acids,the relative molecular weight(Mw)was 12.147 to 75.07 kDa,and the isoelectric point(pI)was 4.358 to 11.251.The GabZIP genes have a length between 90 and 689 amino acids,a relative molecular weight(Mw)of 10.397 to 75.169 kDa,and an isoelectric point(pI)of 4.358 to 10984.The G.raimondii bZIP gene encodes a protein with a length of 67 to 688 amino acids,a relative molecular weight(Mw)of 8.095 to 75.084 kDa,and an isoelectric point(pI)of 4.326 to 11.239.Subcellular localization prediction results showed that nearly all bZIP genes in these three species were located in nucleus,excetp for two bZIP genes(GhbZIP10 and GhbZIP83)of G.hirsutum and one bZIP gene(GrbZIP26)of G.raimondii located in chloroplasts.The results of gene structure analysis showed that the number of exons of bZIP gene in G.hirsutum was 1-13,and the length range was 113-1890 bp.Among them,53.6% of the genes contained 4-6 exons.The chromosomal physical map showed that 148 GhbZIP genes were unevenly distributed on 26 chromosomes,of which 73 and 75 were on A and D subgenome,respectively,and the rest 3 GhbZIP genes were located on 3 scaffolds.The number of GabZIP gene exons in Asiatic cotton is 1-8,and the length ranges from 89.3 to 1035 bp.Among them,35.3% of the genes contain 4 exons.The chromosomal physical map showed that 82 GabZIP genes were unevenly distributed on 13 chromosomes,and the other 3 GabZIP genes were localized on 3 Scaffolds.The number of exons of the GrbZIP gene in G.raimondii was 1 to 6,and the length ranged from 102 to 1354.5 bp.Among them,44.2% of the genes contained 2 or 4 exons.85 GrbZIP genes were unevenly distributed on 13 chromosomes,and one GrbZIP gene was located on Scaffold.Through the analysis of protein conserved motifs,a total of 30 protein conserved motifs were retrieved.The number of protein conserved motifs in each cotton species was 1-10.Some motifs are distributed in most subfamilies,while some motifs exist only in individual subfamilies.This difference provides a reference for studying the functional differences between different subfamilies of the bZIP gene family in cotton.Phylogenetic trees of bZIPs genes were built in these three cotton species.The bZIP genes were grouped into 12,10,11 subfamilies in G.hirsutum,G.arboreum and G.raimondii genome respectively.G subfamily only exists in GhbZIPs,and there is no D subfamily in GabZIPs.Other subfamilies all exist in three cotton species,Compared with Arabidopsis,these three cotton species have a novel N subfamily.Although the number of genes in each subfamily varies widely,the results of gene structure and protein conserved motif analysis support this classification.Gene replication analysis showed that a total of 86 pairs of replication genes were found in the GhbZIP genes.Combined with their positions on the chromosome,all of them were fragment replication.The results of environmental selection pressure analysis showed that 82 pairs of replicating genes Ka/Ks<1,indicating that these genes have undergone strong purification selection after replication and their functions have not undergone serious differentiation;4 pairs of replicating genes Ka/Ks>1,suggesting that a positive selection effect was experienced after fragment duplication.3.Expression analysis of bZIP Genes in G.hirsutum under salt stressIn order to investigate the expression pattern of bZIP gene in G.hirsutum under salt stress,this study used the transcriptome sequencing data of bZIP gene expression level in G.hirsutum after salt treatment to draw the heat map of expression.After analysis,it was found that the expression of bZIP gene in G.hirsutum under salt stress was up-regulated or down-regulated to varying degrees.The heat map shows that there are four modes of positive and negative regulation of the gene: continuous positive regulation,continuous negative regulation,and gradually returning to normal expression levels after positive and negative regulation.Based on its expression,it is speculated that 24 genes have significant regulatory functions in response to salt stress.These results indicate that bZIP gene can respond to salt stress in G.hirsutum and participate in expression regulation,which is closely related to G.hirsutum salt tolerance.