蔷薇科苹果、梨和桃RKD转录因子家族比较分析  

Comparative analysis of RKD transcription factor family of apple, pear and peach in Rosaceae

作　　者：王寻 张天恩 由春香[1] 韩月彭[2] 王小非[1] 郝玉金[1] WANG Xun;ZHANG Tian'en;YOU Chunxiang;HAN Yuepeng;WANG Xiaofei;HAO Yujin(Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency,State Key Laboratory of Crop Biology,College of Horticulture Science and Engineering,Shandong Agricultural University,Taian,Shandong 271018,China;Key Laboratory of Plant Germplasm Enhancement and Specialty Agricultu)

机构地区：[1]山东农业大学园艺科学与工程学院,作物生物学国家重点实验室,山东果蔬优质高效生产协同创新中心,山东泰安271018 [2]中国科学院武汉植物园,中国科学院植物种质创新与特色农业重点实验室,武汉430074

出　　处：《植物生理学报》2020年第10期2132-2148,共17页Plant Physiology Journal

基　　金：国家重点研发计划项目(2018YFD1000100);国家现代苹果产业技术体系资助项目(CARS-27);山东省农业良种工程(2019LZGC007);云南省科技计划项目(2019ZG002-1-03)。

摘　　要：RKD(RWP-RK domain protein)蛋白是植物中重要且保守的一类转录因子,模式植物拟南芥(Arabidopsis thaliana)中的研究表明其在配子发育与胚胎发生中具有至关重要的作用。基于全基因组公开数据,利用RWPRK保守氨基酸序列模型进行检索,在3种蔷薇科果树苹果(Malus pumila)、西洋梨(Pyrus communis)、桃(Prunus persica)中分别筛选到10个MpRKD、8个PcRKD、4个PpRKD成员。通过比较基因组学分析,对苹果、梨、桃RKD基因的系统进化关系、结构域组成与差异、核酸信号序列与蛋白结构比较进行初步探究。苹果、梨、桃RKD蛋白与拟南芥、蒺藜苜蓿(Medicago truncatula)RKD蛋白聚类提示存在两类RKD蛋白,即Ⅰ类蛋白与Ⅱ类蛋白,其中Ⅰ类蛋白分为Ⅰ-1~Ⅰ-3三个分支。多序列比对与保守位点分析发现4组RKD已出现分化;在结构域组成上,部分RKD成员(MpRKD5和PcRKD7等)还具有除RWP-RK结构域的其他结构域,同时利用蛋白三维建模比较它们之间的差异,暗示此类蛋白产生亚功能化或新功能化现象。在RKD基因结构组成上,分组内的外显子-内含子模式更为相似,相比于苹果、梨,桃RKD基因外显子数目较少。苹果、梨、桃RKD基因亚细胞定位预测结果显示大部分蛋白位于细胞核中,有些成员可能有细胞质定位;启动子顺式元件分析发现具有组织特异性调控元件,涉及分生组织、胚等;苹果RKD基因电子表达数据也证实此类基因的组织特异表达模式,并且不同基因存在差异。由此推测,蔷薇科3个物种苹果、梨、桃RKD基因功能具有保守性与独特性。RKD(RWP-RK domain protein) is an important and conserved transcription factor in plants. In model plant Arabidopsis thaliana, studies about RKD genes have shown that it plays a crucial role in gamete development and embryogenesis. Based on the open data about genome-wide, 10 MpRKDs, 8 PcRKDs and 4 PpRKDs members were selected from 3 species of Rosaceae(apple, pear and peach), by using the RWP-RK conserved amino acid sequence model. Through comparative genomics analysis, the phylogenetic relationship, composition and difference of domain, nucleic acid signal sequence and protein structure comparison of RKD genes in apple, pear and peach were preliminarily investigated. Clustering analysis of RKD proteins from Malus pumila, Pyrus communis, Prunus persica, Arabidopsis thaliana and Medicago truncatula suggests there are two types of RKD proteins, namely RKD(Ⅰ) proteins and RKD(Ⅱ) proteins, and class Ⅰ is consisted of three branches(Ⅰ-1, Ⅰ-2, Ⅰ-3). By multisequence alignment and conservative sites analysis of RKD amino acids, we found that four groups have already differentiated;In terms of the domain composition, some RKD members(MpRKD5 and PcRKD7, etc.) also carry other domains other than the RWP-RK domain, at the same time, 3D protein modelings are used to compare the differences between them, which suggests that such proteins produce subfunctionalization or neofunctionalization. In terms of RKD gene structure composition, the exon-intron pattern is more similar within the group, there are fewer exons in RKD genes in peach than in apple and pear. The subcellular localization of RKD genes in apple, pear and peach were predicted, the results show that most of the proteins were located in nucleus, and some members might have cytoplasmic localization;The cis-element analysis of the promoter revealed that them have tissue-specific regulatory elements, involving meristems and embryos;The electronic expression data of apple RKD genes also confirms the characteristic expression patterns of these genes, and ther

关 键 词：蔷薇科果树 RKD转录因子 系统进化 结构域 组织特异表达 

分 类 号：S661.1[农业科学—果树学] S661.2[农业科学—园艺学] S662.1