Wu Shengnan, Wu Min, Dong Qing, Jiang Haiyang, Cai Ronghao, Xiang Yan
Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China; Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.
Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China.
Gene. 2016 Jan 1;575(1):75-89. doi: 10.1016/j.gene.2015.08.042. Epub 2015 Aug 24.
The plant homeobox domain (PHD) proteins are widespread in eukaryotes, and play important roles in regulating chromatin and transcription. Comprehensive analyses of PHD-finger proteins have been performed in animals, but few plant PHD-finger proteins involved in growth and development have been characterized functionally. In this study, we conducted a genome-wide survey of PHD-finger proteins in Populus trichocarpa by describing the phylogenetic relationship, gene structure, and chromosomal location and microarray analyses of each predicted PHD-finger family member. We identified 73 PHD-finger genes (PtPHD1-73) and classified them into eleven subfamilies (A-K) by phylogenetic analysis. Seventy-two of the 73 genes were unevenly distributed on all 19 chromosomes, with seven segmental duplication events. Analysis of the Ka (non-synonymous substitution rate)/Ks (synonymous substitution rate) ratios suggested that the duplicated genes of the PHD-finger family mainly underwent purifying selection with restrictive functional divergence after the duplication events. Expression profiles analysis indicated that 67 PHD-finger genes were differentially expressed in various tissues. Quantitative real-time RT-PCR (qRT-PCR) analyses of nine selected PtPHD genes under high salinity, drought and cold stresses were also performed to explore their stress-related expression patterns. The results of this study provide a thorough overview of poplar PHD-finger proteins and will be valuable for further functional research of poplar PHD-finger genes to unravel their biological roles.
植物同源异型框结构域（PHD）蛋白广泛存在于真核生物中，在调节染色质和转录过程中发挥重要作用。在动物中已对PHD指蛋白进行了全面分析，但在植物中，很少有参与生长发育的PHD指蛋白得到功能鉴定。在本研究中，我们通过描述毛果杨中每个预测的PHD指家族成员的系统发育关系、基因结构、染色体定位和微阵列分析，对PHD指蛋白进行了全基因组调查。我们鉴定出73个PHD指基因（PtPHD1 - 73），并通过系统发育分析将它们分为11个亚家族（A - K）。73个基因中的72个不均匀地分布在所有19条染色体上，存在7个片段重复事件。对Ka（非同义替换率）/Ks（同义替换率）比值的分析表明，PHD指家族的重复基因在重复事件后主要经历了纯化选择，功能分歧受到限制。表达谱分析表明，67个PHD指基因在不同组织中差异表达。还对9个选定的PtPHD基因在高盐、干旱和寒冷胁迫下进行了定量实时RT-PCR（qRT-PCR）分析，以探索它们与胁迫相关的表达模式。本研究结果全面概述了杨树PHD指蛋白，对于进一步开展杨树PHD指基因的功能研究以揭示其生物学作用具有重要价值。
