Identification and expression pattern analysis of pepper DUF966 gene family

【Objective】 The purpose of the study was to identify the DUF966 family members in pepper and analyze their expression patterns, in order toprovide theoretical references for revealing the regulatory roles of this family genes in the growth and development and the response to adversity of pepper, as well as for peppers anti-adversity breeding.【Method】 The Hidden Markov Model seed sequences of DUF966(PF06136) were downloaded from Pfam database, and the sequences of DUF966 family proteins in Arabidopsis and rice were used as reference sequences. The members of DUF966 family were identified from the pepper genome. The gene structure, conserved motif, protein characteristics, promoter cis acting elements, and targeting relationships between miRNAs and the DUF966 gene family were systematically analyzed by bioinformatics methods.And the transcriptome data were used to analyze the expression patterns of members of the pepper DUF966 gene family in different tissues for growth and development as well as different hormone and stress treatments.【Result】 A total of seven members of pepper DUF966 gene family were identified and named as CaDUF966-1 to CaDUF966-7. The members of the pepper DUF966 gene family were categorized into three subgroups, of which CaDUF996-2 and CaDUF996-7 belonged to subgroup I, CaDUF996-3 and CaDUF996-5 belonged to subgroup II, and CaDUF996-1, CaDUF996-4, and CaDUF996-6 belonged to subgroup III. The seven CaDUF966s genes were on chromosomes 1, 2, 6, 11, and 12. The seven CaDUF966s contained 2 to 5 introns, and the number of exons ranged from 3 to 6.All CaDUF966s were unstable and hydrophilic proteins. The subcellular localization was located in the nucleus and contained a total of 20 Motifs(Motif 1-Motif 20), the more similar the Motifs contained in the same subpopulation of CaDUF966s proteins.Except for CaDUF966-3 protein, the secondary and three-dimensional structures of the remaining six CaDUF966s proteins were similar, with a larger proportion of irregular curls(36.31%-51.8%) and a smaller proportion of β-turns(8.56%-10.71%). Based on the ratio of non-synonymous substitution rate/synonymous substitution rate(Ka/Ks) analysis, it was found that DUF966 members were highly conserved among pepper cultivars and Solanaceae species, and the Ka/Ks values of homologous gene pairs were all less than 1.000, indicating that DUF966 members underwent strong purification selection pressure during evolution. The promoter regions of the seven CaDUF966s genes contained a total of 17 biotic and abiotic stress associated cis acting elements, 7 growth and development associated cis acting elements, and 10 phytohormone response associated cis acting elements. Seven CaDUF966s genes had obvious tissue and spatio-temporal specificity, suggesting that the CaDUF966s genes were involved in the growth, development, and stress-response responses of peppers. Nine miRNAs targeted to CaDUF966-3 and CaDUF966-6 genes by cleavage, five miRNAs targeted to CaDUF966-6 genes, and four miRNAs targeted to CaDUF966-3 genes.Seven CaDUF966s genes had significant tissue and spatiotemporal specificity, suggesting that CaDUF966s genes were involved in growth and development and stress response response in pepper. Nine miRNAs targeted to CaDUF966-3 and CaDUF966-6 genes by cleavage, five miRNAs targeted to CaDUF966-6 genes and four miRNAs targeted to CaDUF966-3 genes.【Conclusion】 Seven pepper DUF966 gene family members have regulatory roles in the growth and development of different tissues and in response to biotic and abiotic stresses.