title: Genome-wide identification, classification and expression analysis of the PHD-finger protein family in Populus trichocarpa.
abstract: 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.
authors: 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.
authors: Shengnan
authors: S
authors: Wu
authors: Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China.
authors: Min
authors: M
authors: Wu
authors: Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.
authors: Qing
authors: Q
authors: Dong
authors: Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.
authors: Haiyang
authors: H
authors: Jiang
authors: Key Laboratory of Biomass Improvement and Conversion of Anhui Province, China.
authors: Ronghao
authors: R
authors: Cai
authors: 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.
authors: Yan
authors: Y
authors: Xiang
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D055106:Genome-Wide Association Study; D010940:Plant Proteins / Q000096:biosynthesis / Q000145:classification / Q000235:genetics; D063146:Polycomb-Group Proteins / Q000096:biosynthesis / Q000145:classification / Q000235:genetics; D032107:Populus / Q000235:genetics / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D063146:Polycomb-Group Proteins
keywords: Expression pattern; Phylogenetic analysis; Plant homeobox domain (PHD) proteins; Poplar