Comprehensive genomic survey, structural classification and expression analysis of C2H2 zinc finger protein gene family in Brassica rapa L.
Comprehensive genomic survey, structural classification and expression analysis of C2H2 zinc finger protein gene family in Brassica rapa L.
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DOI：
10.1371/journal.pone.0216071
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发表时间：
2019-05-06
期刊：
影响因子：
3.7
通讯作者：
Lu, Yun-Hai
中科院分区：
文献类型：
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作者：
Alam, Intikhab;Batool, Khadija;Lu, Yun-Hai
C2H2锌指蛋白（ZFP）基因已在许多生物体中得到广泛研究，可以作为转录因子发挥作用，参与包括植物生长发育和胁迫反应在内的许多生物过程。在当前的研究中，对白菜中的C2H2-ZFP基因进行了全面的基因组学分析。从现有的芸苔属基因组数据库中鉴定出总共 301 个白菜假定的 C2H2-ZFP (BrC2H2-ZFP) 基因，并通过分析 C2H2-ZF 结构域中的保守氨基酸残基及其组织、亚细胞定位、系统发育、附加结构域、染色体位置、同线性关系、Ka/Ks 比和表达模式进一步表征。我们还利用qRT-PCR技术分析了8个白菜C2H2-ZFP基因在盐和干旱胁迫条件下的表达模式。我们的结果表明，这些白菜C2H2-ZFP基因中约有三分之一起源于13至17 MYA左右的WGT引起的节段重复，其中三分之一在所有测试组织中高连续表达，并且通过预测支持其作为转录因子的功能作用，其中92%位于细胞核中，其中一些可能在植物生长发育中发挥重要作用。拟南芥和白菜的264个直系同源C2H2-ZFP基因对中，除2对外，Ka/Ks比值均小于1（范围为0.0116～1.4919，平均值为0.3082），表明这些基因在物种进化过程中主要经历了纯化选择。同一组基因对的估计分化时间范围为 6.23 至 38.60 MY，平均值为 18.29 MY，表明这些基因成员在物种进化过程中经历了不同的选择压力，导致了不同的进化速率。此外，这些白菜C2H2-ZFP 中的一些被证明以与其在拟南芥中的直向同源物相似的方式参与应激反应。拟南芥和白菜直系同源 C2H2-ZFP 基因的比较表明，这些 C2H2-ZFP 基因成员中的大多数编码的蛋白质在两个物种之间具有保守的亚细胞定位和功能域，但它们在五个组织或器官中的表达模式不同。因此，我们的研究为进一步确定芸苔属物种中每个C2H2-ZFP基因的功能提供了有价值的信息，并可能有助于选择合适的基因靶标以进行进一步的深入研究以及芸苔属作物的基因工程和改良。
C2H2 zinc finger protein (ZFP) genes have been extensively studied in many organisms and can function as transcription factors and be involved in many biological processes including plant growth and development and stress responses. In the current study, a comprehensive genomics analysis of the C2H2-ZFP genes in B. rapa was performed. A total of 301 B. rapa putative C2H2-ZFP (BrC2H2-ZFP) genes were identified from the available Brassica genome databases, and further characterized through analysis of conserved amino acid residues in C2H2-ZF domains and their organization, subcellular localization, phylogeny, additional domain, chromosomal location, synteny relationship, Ka/Ks ratio, and expression pattern. We also analyzed the expression patterns of eight B. rapa C2H2-ZFP genes under salt and drought stress conditions by using qRT-PCR technique. Our results showed that about one-third of these B. rapa C2H2-ZFP genes were originated from segmental duplication caused by the WGT around 13 to 17 MYA, one-third of them were highly and consecutively expressed in all tested tissues, and 92% of them were located in nucleus by prediction supporting then their functional roles as transcription factors, of which some may play important roles in plant growth and development. The Ka/Ks ratios of 264 orthologous C2H2-ZFP gene pairs between A. thaliana and B. rapa were all, except two, inferior to 1 (varied from 0.0116 to 1.4919, with an average value of 0.3082), implying that these genes had mainly experienced purifying selection during species evolution. The estimated divergence times of the same set of gene pairs ranged from 6.23 to 38.60 MY, with an average value of 18.29 MY, indicating that these gene members have undergone different selective pressures resulting in different evolutionary rates during species evolution. In addition, a few of these B. rapa C2H2-ZFPs were shown to be involved in stress responses in a similar way as their orthologs in A. thaliana. Comparison between A. thaliana and B. rapa orthologous C2H2-ZFP genes showed that the majority of these C2H2-ZFP gene members encodes proteins with conserved subcellular localization and functional domains between the two species but differed in their expression patterns in five tissues or organs. Thus, our study provides valuable information for further functional determination of each C2H2-ZFP gene across the Brassica species, and may help to select the appropriate gene targets for further in-depth studies, and genetic engineering and improvement of Brassica crops.