Table_4_Genome-wide identification and expression analysis of the GRAS gene family in Dendrobium chrysotoxum.pdf

The GRAS gene family encodes transcription factors that participate in plant growth and development phases. They are crucial in regulating light signal transduction, plant hormone (e.g. gibberellin) signaling, meristem growth, root radial development, response to abiotic stress, etc. However, little is known about the features and functions of GRAS genes in Orchidaceae, the largest and most diverse angiosperm lineage. In this study, genome-wide analysis of the GRAS gene family was conducted in Dendrobium chrysotoxum (Epidendroideae, Orchidaceae) to investigate its physicochemical properties, phylogenetic relationships, gene structure, and expression patterns under abiotic stress in orchids. Forty-six DchGRAS genes were identified from the D. chrysotoxum genome and divided into ten subfamilies according to their phylogenetic relationships. Sequence analysis showed that most DchGRAS proteins contained conserved VHIID and SAW domains. Gene structure analysis showed that intronless genes accounted for approximately 70% of the DchGRAS genes, the gene structures of the same subfamily were the same, and the conserved motifs were also similar. The Ka/Ks ratios of 12 pairs of DchGRAS genes were all less than 1, indicating that DchGRAS genes underwent negative selection. The results of cis-acting element analysis showed that the 46 DchGRAS genes contained a large number of hormone-regulated and light-responsive elements as well as environmental stress-related elements. In addition, the real-time reverse transcription quantitative PCR (RT−qPCR) experimental results showed significant differences in the expression levels of 12 genes under high temperature, drought and salt treatment, among which two members of the LISCL subfamily (DchGRAS13 and DchGRAS15) were most sensitive to stress. Taken together, this paper provides insights into the regulatory roles of the GRAS gene family in orchids.

GRAS基因家族（GRAS gene family）编码参与植物生长与发育阶段的转录因子，其在调控光信号转导、植物激素（如赤霉素，gibberellin）信号、分生组织生长、根系径向发育以及非生物胁迫响应等过程中发挥关键作用。然而，作为被子植物中种类最多样、谱系最广的类群，兰科（Orchidaceae）植物GRAS基因的特征与功能却鲜为人知。本研究以兰科树兰亚科的鼓槌石斛（Dendrobium chrysotoxum）为材料，对其GRAS基因家族开展全基因组水平分析，以探究兰科植物GRAS基因的理化特性、系统发育关系、基因结构以及非生物胁迫下的表达模式。本研究从鼓槌石斛基因组中鉴定出46个DchGRAS基因，并根据系统发育关系将其划分为10个亚家族。序列分析结果显示，绝大多数DchGRAS蛋白包含保守的VHIID结构域与SAW结构域。基因结构分析表明，不含内含子的基因约占DchGRAS基因总数的70%；同一亚家族的基因结构高度一致，保守基序也极为相似。12对DchGRAS基因的Ka/Ks比值均小于1，表明DchGRAS基因经历了负选择。顺式作用元件（cis-acting element）分析结果显示，这46个DchGRAS基因中含有大量激素调控元件、光响应元件以及环境胁迫相关元件。此外，实时逆转录定量聚合酶链反应（real-time reverse transcription quantitative PCR, RT−qPCR）的实验结果显示，12个基因在高温、干旱和盐胁迫处理下的表达水平存在显著差异，其中LISCL亚家族的两个成员（DchGRAS13与DchGRAS15）对胁迫最为敏感。综上，本研究为解析兰科植物GRAS基因家族的调控功能提供了新的见解。