Construction Of Barley Gene Family Database And Characterization Of MTERF Family

As the fourth largest cereal crop wordwide,barley is widely used in livestock feed,brewing materials and human consumption.Due to its short short residual period,barley adapt to complex agricultural environment,such as drought,salinity,and low temperature.Based on the updated barley Morex V2 assembly,we identified 77 barley gene families composed of 5,593 genes.Among them,a total of 2,093 genes were identified as transcription factors.The phylogenetic tree,expression pattern,and homologous genes of gene family were further analyzed and were integrated into the database.Our database has a user-friendly web interface with multiple search,browse,analysis,and download functions.Furthermore,we performed a comprehensive analysis of the identification,evolution,function,and genetic variation of the mitochondrial transcription factor(m TERF)family.The main research contents are as follows:(1)A total of 77 barley gene families were identified based on Pfam IDs.We idenfied37 transcription factor gene families,with an average of 74 genes of each family.The LRR-RLK gene family had 502 genes,which ranked the largest gene family.By contrast,the Whirly transcription factor family with the least members had only two genes.The length of protein sequences of each gene ranged from 68 to 2,388 aa.The Myosin gene family was the longest.The cis-acting regulatory elements associated with light response,hormone response,structural composition,plant growth and development/tissue specificity and stress response were further identified.The results showed that the light response cis-acting regulatory elements was the most abundant,which contained a total of 23 kinds consisting of 6,652 cis-acting elements.Eleven hormone response elements were also identified,including 10,792 elements related to hormones such as auxin,abscisic acid,and gibberellin.Based on the RNA-seq dataset,the expression profiles from different tissues/stages and abiotic stresses were analyzed.A total of 286 differentially expressed genes were identified under cold treatment,132 of which were up-regulated.Under salt treatment,the Phytocyanins family HORVU.MOREX.r2.Un G0630370 was the most upregulated with 15.5 times in the root meristem region,and there were 251 differentially expressed genes in the elongation region,of which 54.81% were upregulated genes.(2)To better share and utilizate the datasets,the Hypertext Markup Language(HTML),Cascading Style Sheets(CSS),and Hypertext Preprocessor(PHP)was employed to build a user-friendly database website framework(BGFD: www.barleygfdb.com),Our database contained seven main parts,including Home,Search,Introduction,Blast,JBrowse,Download,and About.The BGFD integrated transcriptome,resequencing,expression profile,and other information,which provides a friendly interface.(3)Finally,the mitochondrial transcription termination factor(m TERF)family was further identified and characterized,and a total of 60 m TERF genes were identified.Based on the phylogenetic analysis,the m TERF gene family was divided into 9 subfamilies,among which subfamily IX contained 39 members,while subfamily I,III,V and VII had only one member.The gene structure and the distribution pattern of conservative motifs in the same subfamily were relatively conservative.Analysis of gene duplication events showed that all tandem duplication occurred on chromosome 6,and 6 pairs of gene duplication were associated with chromosome 6.In expression profile analysis,Hvm TERF21 was induced by salt stress,and q RT-PCR showed that Hvm TERF21 was up-regulated after 6 and 24 h salt treatment,which preliminarily confirmed the function of this gene.A total of 481 SNPs associated with Hvm TERF gene were detected by resequencing analysis,and the genetic relationship between wild and landrace barley populations was studied using principal component analysis and population structure analysis.In this study,we constructed the barley gene family database by integrating multiple omics data for the first time and the m TERF gene family was selected for in-depth analysis based on the newly released barley reference assembly.This study forms the basis for further molecular cloning of functional genes in barley,and also provides an important platform for genetic improvement in barley.