PDF(Pubmed)
Abstract：
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.
摘要：
含有未知功能域（DUF）的蛋白质在真核基因组中普遍存在。DUF1216蛋白具有类似于拟南芥RNA聚合酶II转录亚单位样蛋白的介体蛋白的保守DUF1216结构域。DUF1216家族特别存在于十字花科中，然而,尚未对DUF1216基因进行全面的进化分析.我们对十字花科的DUF1216蛋白进行了首次全面的全基因组分析。在27种十字花科植物中鉴定出284个DUF1216基因，并根据系统发育分析分为四个亚科。对基因结构和保守基序的分析表明，同一亚家族中的DUF1216基因表现出相似的内含子/外显子模式和基序组成。DUF1216基因的大多数成员在N端含有一个信号肽，在大多数DUF1216中信号肽的第9位是半胱氨酸。合成分析表明，节段复制是甘蓝中DUF1216基因扩增的主要机制，芥菜型油菜，甘蓝型油菜,美尼菌，还有CarinataBrassica,而在拟南芥和风疹中，串联重复在DUF1216基因家族的扩展中起主要作用。DUF1216旁系同源物的Ka/Ks（非同义取代率/同义取代率）比率的分析表明，大多数基因对都经过了纯化选择。DUF1216基因在大多数十字花科物种的生殖组织中显示出特异性高表达，而其在芥菜中的表达在根中特别高。我们的研究为系统发育关系提供了新的见解，十字花科DUF1216成员的基因结构和表达模式，这为未来的功能分析提供了基础。
