DUF1216 promoter cis-acting element data.

Proteins containing domain of unknown function (DUF) are prevalent in eukaryotic genome. The DUF1216 proteins possess a conserved DUF1216 domain resembling to the mediator protein of Arabidopsis RNA polymerase II transcriptional subunit-like protein. The DUF1216 family are specifically existed in Brassicaceae, however, no comprehensive evolutionary analysis of DUF1216 genes have been performed. We performed a first comprehensive genome-wide analysis of DUF1216 proteins in Brassicaceae. Totally 284 DUF1216 genes were identified in 27 Brassicaceae species and classified into four subfamilies on the basis of phylogenetic analysis. The analysis of gene structure and conserved motifs revealed that DUF1216 genes within the same subfamily exhibited similar intron/exon patterns and motif composition. The majority members of DUF1216 genes contain a signal peptide in the N-terminal, and the ninth position of the signal peptide in most DUF1216 is cysteine. Synteny analysis revealed that segmental duplication is a major mechanism for expanding of DUF1216 genes in Brassica oleracea, Brassica juncea, Brassica napus, Lepidium meyneii, and Brassica carinata, while in Arabidopsis thaliana and Capsella rubella, tandem duplication plays a major role in the expansion of the DUF1216 gene family. The analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios for DUF1216 paralogous indicated that most of gene pairs underwent purifying selection. DUF1216 genes displayed a specifically high expression in reproductive tissues in most Brassicaceae species, while its expression in Brassica juncea was specifically high in root. Our studies offered new insights into the phylogenetic relationships, gene structures and expressional patterns of DUF1216 members in Brassicaceae, which provides a foundation for future functional analysis.包含未知功能结构域（domain of unknown function，DUF）的蛋白质在真核基因组中广泛分布。DUF1216类蛋白质拥有保守的DUF1216结构域，其结构与拟南芥RNA聚合酶II（RNA polymerase II）转录亚基样蛋白的中介蛋白相似。DUF1216基因家族仅存在于十字花科（Brassicaceae）植物中，但目前尚未有针对DUF1216基因的全面进化分析研究。本研究首次对十字花科植物中的DUF1216蛋白质进行了全基因组范围的综合分析。本研究在27个十字花科物种中共鉴定出284个DUF1216基因，并通过系统发育分析将其划分为4个亚家族。基因结构与保守基序分析显示，同一亚家族内的DUF1216基因具有相似的内含子/外显子排布模式与基序组成。绝大多数DUF1216基因的N端都含有信号肽，且大多数DUF1216蛋白的信号肽第9位氨基酸为半胱氨酸。共线性分析显示，片段重复是甘蓝（Brassica oleracea）、芥菜型油菜（Brassica juncea）、甘蓝型油菜（Brassica napus）、玛咖（Lepidium meyneii）以及埃塞俄比亚芥（Brassica carinata）中DUF1216基因扩张的主要驱动机制；而在拟南芥（Arabidopsis thaliana）和红碎米荠（Capsella rubella）中，串联重复则是该基因家族扩张的主要方式。针对DUF1216旁系同源基因的Ka/Ks（非同义替换率/同义替换率）比值分析表明，大多数基因对经历了纯化选择。在大多数十字花科物种中，DUF1216基因在生殖组织中呈现特异性高表达；而芥菜型油菜中的DUF1216基因则在根组织中特异性高表达。本研究为十字花科植物DUF1216家族成员的系统发育关系、基因结构及表达模式提供了新的见解，为后续的功能研究奠定了基础。