Lu Youjun, Chen Wei, Zhao Lanjie, Yao Jinbo, Li Yan, Yang Weijun, Liu Ziyang, Zhang Yongshan, Sun Jie
College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832003, China.
Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China.
Genes Genomics. 2019 Apr;41(4):445-458. doi: 10.1007/s13258-018-0775-0. Epub 2019 Jan 4.
The phosphatidylethanolamine-binding protein (PEBP) gene family plays a crucial role in seed germination, reproductive transformation, and other important developmental processes in plants, but its distribution in Gossypium genomes or species, evolutionary properties, and the fates of multiple duplicated genes remain unclear.
The primary objectives of this study were to elucidate the distribution and characteristics of PEBP genes in Gossypium, as well as the evolutionary pattern of duplication and deletion, and functional differentiation of PEBPs in plants.
Using the PEBP protein sequences in Arabidopsis thaliana as queries, blast alignment was carried out for the identification of PEBP genes in four sequenced cotton species. Using the primers designed according to the PEBP genome sequences, PEBP genes were cloned from 15 representative genomes of Gossypium genus, and the gene structure, CDS sequence, protein sequence and properties were predicted and phylogenetic analysis was performed. Taking PEBP proteins of grape as reference, grouping of orthologous gene, analysis of phylogeny and divergence of PEBPs in nine species were conducted to reconstruct the evolutionary pattern of PEBP genes in plants.
We identified and cloned 160 PEBPs from 15 cotton species, and the phylogenetic analysis showed that the genes could be classified into the following three subfamilies: MFT-like, FT-like and TFL1-like. There were eight single orthologous group (OG) members in each diploid and 16 double OG members in each tetraploid. An analysis of the expression and selective pressure indicated that expression divergence and strong purification selection within the same OG presented in the PEBP gene family.
An evolutionary pattern of duplication and deletion of the PEBP family in the evolutionary history of Gossypium was suggested, and three pairs of genes resulted from different whole-genome duplication events.
磷脂酰乙醇胺结合蛋白（PEBP）基因家族在植物种子萌发、生殖转化及其他重要发育过程中发挥着关键作用，但其在棉属基因组或物种中的分布、进化特性以及多个重复基因的命运仍不清楚。
本研究的主要目的是阐明PEBP基因在棉属中的分布和特征，以及PEBP基因在植物中的重复和缺失进化模式和功能分化。
以拟南芥中的PEBP蛋白序列为查询序列，对四个已测序棉花物种进行blast比对以鉴定PEBP基因。根据PEBP基因组序列设计引物，从棉属15个代表性基因组中克隆PEBP基因，并预测基因结构、CDS序列、蛋白质序列和特性，进行系统发育分析。以葡萄的PEBP蛋白为参考，对九个物种中的直系同源基因进行分组、系统发育和PEBP分化分析，以重建植物中PEBP基因的进化模式。
我们从15个棉花物种中鉴定并克隆了160个PEBP基因，系统发育分析表明这些基因可分为以下三个亚家族：类MFT、类FT和类TFL1。每个二倍体中有八个单直系同源群（OG）成员，每个四倍体中有16个双OG成员。表达和选择压力分析表明，PEBP基因家族中同一OG内存在表达差异和强烈的纯化选择。
提出了棉属进化历史中PEBP家族的重复和缺失进化模式，且三对基因源于不同的全基因组重复事件。
