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Genome-wide identification and characterization of a plant-specific Dof transcription factor gene family in olive (Olea europaea) and its comparison with Arabidopsis
Horticulture, Environment, and Biotechnology ( IF 2.4 ) Pub Date : 2021-06-14 , DOI: 10.1007/s13580-021-00366-7
Mariyam , Muhammad Shafiq , Muhammad Haseeb , Rana Muhammad Atif , Syed Agha Armaghan Asad Abbas Naqvi , Numan Ali , Muhammad Arshad Javed , Fizza Gillani , Muhammad Saleem Haider

DNA binding with one finger (Dof) proteins are encoded by a ubiquitous plant-specific transcription factor gene family that plays a critical role in various biological processes including fruit ripening and organogenesis. The wild olive (Olea europaea var. sylvestris v1.0) genome was used to identify Dof gene family members using a set of bioinformatics tools. Gene structure, chromosome locations, phylogeny, protein motifs, miRNA targets and tissue-specific expression patterns were analyzed. Here, we identified 51 potential Dof genes unevenly distributed on all chromosomes and a few scaffolds. Dof proteins in olive clustered into eight subgroups (D1, B2, C3, C2.2, C1, C2.1, B1, and A) based on the established Arabidopsis classification. The prevalence of segmental duplication was observed as compared to tandem duplication, and this was the main factor underlying the expansion of the Dof gene family in olive. Tissue-specific expression profiling of OeuDof genes revealed that the majority of OeuDof genes were highly expressed in flowers, stem and meristem tissues. In seed and meristem tissues, cis-regulatory element (CRE) analysis revealed the presence of elements that are specifically responsive to light, circadian, auxin, and ABA. In addition, a comparative analysis between Dof genes in olive and Arabidopsis revealed eight groups or sub-families, although the C3 group of Arabidopsis was not represented in olive. This extensive genome evaluation of the Dof gene family in olive presents a reference for cloning and functional analysis of the members of this gene family.



中文翻译:

橄榄(Olea europaea)植物特异性Dof转录因子基因家族的全基因组鉴定和表征及其与拟南芥的比较

与单指 (Dof) 蛋白结合的 DNA 由无处不在的植物特异性转录因子基因家族编码,该家族在包括果实成熟和器官发生在内的各种生物过程中起关键作用。野生橄榄 ( Olea europaea var. sylvestris v1.0 ) 基因组用于使用一组生物信息学工具识别 Dof 基因家族成员。分析了基因结构、染色体位置、系统发育、蛋白质基序、miRNA 靶标和组织特异性表达模式。在这里,我们确定了 51 个潜在的Dof基因,它们不均匀分布在所有染色体和一些支架上。基于已建立的拟南芥,橄榄中的Dof蛋白分为八个亚组(D1、B2、C3、C2.2、C1、C2.1、B1 和 A)分类。与串联重复相比,观察到节段重复的流行,这是橄榄中Dof基因家族扩展的主要因素。Oeu Dof基因的组织特异性表达谱显示,大多数 Oeu Dof基因在花、茎和分生组织中高度表达。在种子和分生组织中,顺式调节元件 (CRE) 分析显示存在对光、昼夜节律、生长素和 ABA 有特异性反应的元素。此外,橄榄和拟南芥中Dof基因之间的比较分析揭示了 8 个组或亚科,尽管拟南芥的 C3 组没有代表橄榄。橄榄中Dof基因家族的广泛基因组评估为该基因家族成员的克隆和功能分析提供了参考。

更新日期:2021-06-14
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