张丹丹, 杨瑶君, 江纳, 等. 黄藤家族的全基因组鉴定及系统进化分析[J]. 西南林业大学学报(自然科学), 2021, 41(6): 126–138 . DOI: 10.11929/j.swfu.202003051
引用本文: 张丹丹, 杨瑶君, 江纳, 等. 黄藤家族的全基因组鉴定及系统进化分析[J]. 西南林业大学学报(自然科学), 2021, 41(6): 126–138 . DOI: 10.11929/j.swfu.202003051
Zhang Dandan, Yang Yaojun, Jiang Na, Fu Chun. Genome-Wide Identification and Phylogenetic Analysis of the Dof Gene Family in Daemonorops jenkinsiana[J]. Journal of Southwest Forestry University, 2021, 41(6): 126-138. DOI: 10.11929/j.swfu.202003051
Citation: Zhang Dandan, Yang Yaojun, Jiang Na, Fu Chun. Genome-Wide Identification and Phylogenetic Analysis of the Dof Gene Family in Daemonorops jenkinsiana[J]. Journal of Southwest Forestry University, 2021, 41(6): 126-138. DOI: 10.11929/j.swfu.202003051

黄藤Dof家族的全基因组鉴定及系统进化分析

Genome-Wide Identification and Phylogenetic Analysis of the Dof Gene Family in Daemonorops jenkinsiana

  • 摘要: 为了揭示黄藤全基因组中Dof基因家族的生物学功能,利用生物信息学手段,对黄藤Dof基因家族进行了全基因组鉴定,并系统分析了黄藤与其他9个物种Dof基因家族分子进化关系。结果表明:黄藤基因组中含有25个Dof基因,亚细胞定位预测发现它们均位于细胞核,跨膜结构预测到黄藤所有的Dof蛋白成员均不具有跨膜结构;黄藤的Dof蛋白家族均为不稳定亲水蛋白,其二级结构由α−螺旋、无规则卷曲为主导,其三级结构主要由α−螺旋和β−转角进行复杂的空间构象变化组成;黄藤Dof蛋白成员的氨基酸个数为184到586 AA,pI范围为4.71~9.57;根据系统进化分析,黄藤Dof基因家族分为ClassⅠ −ClassⅣ共4个亚组, 其中ClassⅡ成员最多(8个),约占总数的32%;其次是ClassⅣ(7个)、ClassⅠ(5个)和ClassⅢ(5个);从组别上来看,ClassⅡ成员分化速度是最快的,与原始祖先的亲缘关系最远。从组中来看,ClassⅡ中成员DjDof9和DjDof10分化最快,与原始祖先的亲缘关系最远,DjDof12和DjDof24分化较慢,与原始祖先的亲缘关系相对较近;黄藤与拟南芥的进化关系表明两者亲缘关系不是很近;黄藤与其他9个物种的Dof 基因的系统进化分析表明黄藤与甘蓝型油菜和小麦有较近的亲缘关系,序列同源性也较高,与可可亲缘关系最远。

     

    Abstract: In order to reveal the biological function of the Dof gene family in the whole genome of Daemonorops jenkinsiana, we used bioinformatics method to identify the whole genome of the Dof gene family of D. jenkinsiana, and systematically analyzed the molecular evolution relationship between the Dof gene family of D. jenkinsiana and other 9 species. The results showed that there were 25 Dof genes in the genome of D. jenkinsiana, subcellular localization predicted that they were all located in the nucleus, the transmembrane structure predicted that all of the Dof protein members of D. jenkinsiana did not have transmembrane structure; the Dof protein family of D. jenkinsiana was unstable hydrophilic protein, and the secondary structure was mainly composed of α−helix, random coil, the third-order structure is mainly composed of α−helix and β−turn with complex spatial conformational changes; the number of amino acids of Dof protein members in D. jenkinsiana is 184 to 586 AA, and the pI range is 4.71 to 9.57. According to the phylogenetic analysis, the Dof gene family of D. jenkinsiana is divided into 4 subgroups of classⅠ–classⅣ. Among them, class Ⅱ has the most members (8 members), accounting for 32% of the total; class Ⅳ (7 members), class Ⅰ (5 members) and class Ⅲ (5 members) are the second; in terms of group, class Ⅱ has the fastest differentiation speed and the farthest genetic relationship with the original ancestors. From the group, DjDof9 and DjDof10 in class Ⅱ differentiate the fastest, have the longest genetic relationship with the original ancestors, DjDof12 and DjDof24 differentiate slowly, and have relatively close genetic relationship with the original ancestors. The phylogenetic analysis of Dof genes between D. jenkinsiana and other 9 species showed that there was not close genetic relationship between D. jenkinsiana and Arabidopsis thaliana, and the phylogenetic analysis of Dof genes showed that D. jenkinsiana was closely related to Brassica napus and Triticum aestivum, and had high sequence homology, and the farthest relationship with cacao.

     

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