Table7_Genome-wide identification and expression analysis of the C2H2-zinc finger transcription factor gene family and screening of candidate genes involved in floral development in Coptis teeta Wall. (Ranunculaceae).xls

Background: C2H2-zinc finger transcription factors comprise one of the largest and most diverse gene superfamilies and are involved in the transcriptional regulation of flowering. Although a large number of C2H2 zinc-finger proteins (C2H2-ZFPs) have been well characterized in a number of model plant species, little is known about their expression and function in Coptis teeta. C. teeta displays two floral phenotypes (herkogamy phenotypes). It has been proposed that the C2H2-zinc finger transcription factor family may play a crucial role in the formation of floral development and herkogamy observed in C. teeta. As such, we performed a genome-wide analysis of the C2H2-ZFP gene family in C. teeta.
Results: The complexity and diversity of C. teeta C2H2 zinc finger proteins were established by evaluation of their physicochemical properties, phylogenetic relationships, exon-intron structure, and conserved motifs. Chromosome localization showed that 95 members of the C2H2 zinc-finger genes were unevenly distributed across the nine chromosomes of C. teeta, and that these genes were replicated in tandem and segmentally and had undergone purifying selection. Analysis of cis-acting regulatory elements revealed a possible involvement of C2H2 zinc-finger proteins in the regulation of phytohormones. Transcriptome data was then used to compare the expression levels of these genes during the growth and development of the two floral phenotypes (F-type and M-type). These data demonstrate that in groups A and B, the expression levels of 23 genes were higher in F-type flowers, while 15 genes showed higher expressions in M-type flowers. qRT-PCR analysis further revealed that the relative expression was highly consistent with the transcriptome data.
Conclusion: These data provide a solid basis for further in-depth studies of the C2H2 zinc finger transcription factor gene family in this species and provide preliminary information on which to base further research into the role of the C2H2 ZFPs gene family in floral development in C. teeta.

背景：C2H2型锌指转录因子（C2H2-zinc finger transcription factors）是当前已知规模最大、多样性最丰富的基因超家族之一，参与开花过程的转录调控。尽管已有大量C2H2型锌指蛋白（C2H2-zinc finger proteins, C2H2-ZFPs）在多种模式植物中得到充分功能鉴定，但目前对其在云南黄连（Coptis teeta）中的表达模式与生物学功能仍知之甚少。云南黄连存在两种花表型，即雌雄异位（herkogamy）表型。有研究推测，C2H2型锌指转录因子家族可能在云南黄连的花发育及雌雄异位性状形成过程中发挥关键调控作用。基于此，本研究对云南黄连的C2H2型锌指蛋白基因家族开展了全基因组水平的分析鉴定。
结果：本研究通过理化性质分析、系统发育关系解析、外显子-内含子结构预测以及保守基序分析，系统阐明了云南黄连C2H2型锌指蛋白的复杂性与多样性。染色体定位分析显示，95个C2H2型锌指基因不均匀分布于云南黄连的9条染色体上，且这些基因存在串联复制和片段复制事件，并经历了纯化选择作用。顺式作用调控元件（cis-acting regulatory elements）分析结果表明，C2H2型锌指蛋白可能参与植物激素的信号调控过程。随后，本研究利用转录组数据，对比分析了两类花表型（F型与M型）在生长发育过程中各C2H2-ZFP基因的表达水平。数据分析结果显示，在A、B两组基因中，共有23个基因在F型花中表达量显著上调，另有15个基因在M型花中表达量更高。实时荧光定量PCR（quantitative real-time PCR, qRT-PCR）验证结果进一步表明，基因的相对表达量与转录组测序数据高度吻合。
结论：本研究结果为后续深入解析该物种中C2H2型锌指转录因子基因家族的功能奠定了坚实基础，同时也为进一步探究C2H2型锌指蛋白家族在云南黄连花发育过程中的调控作用提供了初步的理论依据。