title: Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response.
abstract: Plant homeodomain (PHD)-finger proteins were found universally in eukaryotes and known as key players in regulating transcription and chromatin structure. Many PHD-finger proteins have been well studied on structure and function in animals. Whereas, only a few of plant PHD-finger factors had been characterized, and majority of PHD-finger proteins were functionally unclear. In this study, a complete comprehensive analysis of maize PHD family is presented. Sixty-seven PHD-finger genes in maize were identified and further divided into ten groups according to phylogenetic analysis that was supported by motif and intron/exon analysis. These genes were unevenly distributed on ten chromosomes and contained 12 segmental duplication events, suggesting that segmental duplications were the major contributors in expansion of the maize PHD family. The paralogous genes mainly experienced purifying selection with restrictive functional divergence after the duplication events on the basis of the Ka/Ks ratio. Gene digital expression analysis showed that the PHD family had a wide expression profile in maize development. In addition, 15 potential stress response genes were detected by promoter cis-element and expression analysis. Two proteins ZmPHD14 and ZmPHD19 were located in the nucleus. These results provided a solid base for future functional genome study of the PHD-finger family in maize and afforded important clues for characterizing and cloning potentially important candidates in response to abiotic stresses.
authors.affiliation: Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China. qqwangahau@163.com.
authors.forename: Qianqian
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China. liujinyang315@163.com.
authors.forename: Jinyang
authors.initials: J
authors.lastname: Liu
authors.affiliation: Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China. yuwangahau@163.com.
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China. zhaoyang2013@ahau.edu.cn.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China. hyjiang@ahau.edu.cn.
authors.forename: Haiyang
authors.initials: H
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China. beijiucheng@ahau.edu.cn.
authors.forename: Beijiu
authors.initials: B
authors.lastname: Cheng
mesh_terms: D000040:Abscisic Acid / Q000494:pharmacology; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D058674:Chromosome Duplication / Q000187:drug effects; D032461:Chromosomes, Plant / Q000235:genetics; D017124:Conserved Sequence; D055864:Droughts; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D005801:Genes, Homeobox; D017343:Genes, Plant; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D011092:Polyethylene Glycols / Q000494:pharmacology; D011401:Promoter Regions, Genetic; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012965:Sodium Chloride / Q000494:pharmacology; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics*; D013347:Subcellular Fractions / Q000187:drug effects / Q000378:metabolism; D026801:Synteny / Q000235:genetics; D003313:Zea mays / Q000187:drug effects / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D011092:Polyethylene Glycols; D012965:Sodium Chloride; D000040:Abscisic Acid
keywords: PHD family; abiotic stress; duplication; genome-wide analysis; maize