辣椒DUF966基因家族鉴定及表达模式分析

Identification and expression pattern analysis of pepper DUF966 gene family

【目的】鉴定辣椒DUF966基因家族成员,并分析其表达模式,为揭示该家族基因对辣椒生长发育和逆境响应的调控机制及辣椒抗逆育种提供理论参考。【方法】从Pfam数据库下载DUF966(PF06136)的隐马尔可夫模型种子序列,并以拟南芥和水稻DUF966家族蛋白序列作为参考序列,从辣椒基因组中鉴定出DUF966家族成员,利用生物信息学方法对其基因结构、保守基序、蛋白质特征、启动子顺式作用元件及miRNA和DUF966基因家族间的靶向关系进行系统分析,并利用转录组数据分析辣椒DUF966基因家族成员在不同组织生长发育及不同激素和胁迫处理下的表达模式。【结果】共鉴定到7个辣椒DUF966基因家族成员,将其命名为CaDUF966-1~CaDUF966-7。将辣椒DUF966基因家族成员分为3个亚群,其中,Ca DUF996-2和Ca DUF996-7属于I亚群,Ca DUF996-3和Ca DUF996-5属于II亚群,CaDUF996-1、CaDUF996-4和CaDUF996-6属于III亚群。7个CaDUF966s基因分布在1、2、6、11和12号染色体上。7个CaDUF966s基因含有2~5个内含子,外显子数为3~6个。所有CaDUF966s均为亲水的不稳定蛋白,亚细胞定位于细胞核内,共含有20个Motif(Motif 1~Motif 20),同一亚群CaDUF966s蛋白含有的Motif越相似。除CaDUF966-3蛋白外,其余6个CaDUF966s蛋白的二级结构和三维结构相似,均以无规则卷曲所占比例较大(36.31%~51.80%),以β-转角所占比例较小(8.56%~10.71%)。基于非同义替换率/同义替换率的比值(Ka/Ks)分析发现,DUF966基因家族成员在辣椒品种间和茄科物种间高度保守,同源基因对的Ka/Ks均小于1.000,表明其在进化过程中经历了强烈的纯化选择压力。7个CaDUF966s基因启动子区域共含有17个生物和非生物胁迫相关顺式作用元件、7个生长发育相关顺式作用元件及10个植物激素反应相关顺式作用元件。7个CaDUF966s基因具有明显的组织和时空特异性,说明CaDUF966s基因参与辣椒的生长发育和胁迫响应。9个miRNA通过切割作用靶向CaDUF966-3和CaDUF966-6基因,5个miRNA靶向CaDUF966-6基因,4个miRNA靶向CaDUF966-3基因。【结论】7个辣椒DUF966基因家族成员在不同组织生长发育过程及响应生物和非生物胁迫过程中具有调控作用。

【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 se-quences 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 pep-per DUF966 gene family in different tissues for growth and development as well as different hormone and stress treat-ments.【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 chro-mosomes 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 propor-tion ofβ-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 ele-ments,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 de-velopment 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.