Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210000, China.
Genes (Basel). 2020 Feb 6;11(2):174. doi: 10.3390/genes11020174.
The rapid alkalinization factor (RALF) gene family is essential for the plant growth and development. However, there is little known about these genes among Rosaceae species. Here, we identify 124 RALF-like genes from seven Rosaceae species, and 39 genes from Arabidopsis, totally 163 genes, divided into four clades according to the phylogenetic analysis, which includes 45 mature RALF genes from Rosaceae species. The YISY motif and RRXL cleavage site are typical features of true RALF genes, but some variants were detected in our study, such as YISP, YIST, NISY, YINY, YIGY, YVGY, FIGY, YIAY, and RRVM. Motif1 is widely distributed among all the clades. According to screening of cis-regulatory elements, GO annotation, expression sequence tags (EST), RNA-seq, and RT-qPCR, we reported that 24 genes coding mature proteins related to tissue development, fungal infection, and hormone response. Purifying selection may play an important role in the evolutionary process of genes among Rosaceae species according to the result from ka/ks. The tandem duplication event just occurs in four gene pairs ( and , and , and , and and ) from four Rosaceae species. Our research provides a wide overview of RALF-like genes in seven Rosaceae species involved in identification, classification, structure, expression, and evolution analysis.
快速碱化因子 (RALF) 基因家族对于植物的生长和发育至关重要。然而，蔷薇科物种中的这些基因知之甚少。在这里，我们从七个蔷薇科物种中鉴定出 124 个 RALF 样基因，从拟南芥中鉴定出 39 个基因，总共 163 个基因，根据系统发育分析分为四个分支，其中包括 45 个来自蔷薇科物种的成熟 RALF 基因。YISY 基序和 RRXL 切割位点是真正 RALF 基因的典型特征，但在我们的研究中也检测到了一些变体，如 YISP、YIST、NISY、YINY、YIGY、YVGY、FIGY、YIAY 和 RRVM。Motif1 广泛分布于所有分支。根据顺式调控元件的筛选、GO 注释、表达序列标签 (EST)、RNA-seq 和 RT-qPCR，我们报告了 24 个编码与组织发育、真菌感染和激素反应相关的成熟蛋白的基因。根据 ka/ks 的结果，选择净化可能在蔷薇科物种中基因的进化过程中发挥重要作用。串联重复事件仅发生在四个基因对（和、和、和、和）中，来自四个蔷薇科物种。我们的研究提供了对七个蔷薇科物种中 RALF 样基因的广泛概述，包括鉴定、分类、结构、表达和进化分析。
