The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
BMC Plant Biol. 2022 Jun 25;22(1):308. doi: 10.1186/s12870-022-03696-5.
GARP transcription factors perform critical roles in plant development and response to environmental stimulus, especially in the phosphorus (P) and nitrogen (N) sensing and uptake. Spirodela polyrhiza (giant duckweed) is widely used for phytoremediation and biomass production due to its rapid growth and efficient N and P removal capacities. However, there has not yet been a comprehensive analysis of the GRAP gene family in S. polyrhiza.
We conducted a comprehensive study of GRAP superfamily genes in S. polyrhiza. First, we investigated 35 SpGARP genes which have been classified into three groups based on their gene structures, conserved motifs, and phylogenetic relationship. Then, we identified the duplication events, performed the synteny analysis, and calculated the K/K ratio in these SpGARP genes. The regulatory and co-expression networks of SpGARPs were further constructed using cis-acting element analysis and weighted correlation network analysis (WGCNA). Finally, the expression pattern of SpGARP genes were analyzed using RNA-seq data and qRT-PCR, and several NIGT1 transcription factors were found to be involved in both N and P starvation responses.
The study provides insight into the evolution and function of GARP superfamily in S. polyrhiza, and lays the foundation for the further functional verification of SpGARP genes.
GARP 转录因子在植物发育和对环境刺激的反应中发挥着关键作用，特别是在磷（P）和氮（N）的感应和吸收中。浮萍（giant duckweed）由于其快速生长和高效的 N 和 P 去除能力，被广泛用于植物修复和生物质生产。然而，对于浮萍中的 GRAP 基因家族，尚未进行全面分析。
我们对浮萍中的 GRAP 超家族基因进行了全面研究。首先，我们研究了 35 个 SpGARP 基因，根据它们的基因结构、保守基序和系统发育关系将其分为三组。然后，我们鉴定了这些 SpGARP 基因中的复制事件，进行了同线性分析，并计算了 K/K 比值。使用顺式作用元件分析和加权相关网络分析（WGCNA）进一步构建了 SpGARPs 的调控和共表达网络。最后，使用 RNA-seq 数据和 qRT-PCR 分析了 SpGARP 基因的表达模式，并发现了几个 NIGT1 转录因子参与了 N 和 P 饥饿反应。
该研究深入了解了 GARP 超家族在浮萍中的进化和功能，为进一步验证 SpGARP 基因的功能奠定了基础。
