title: [Genome-wide identification and expression analysis of the WRKY gene family in peach].
abstract: The WRKY transcription factors are one of the largest families of transcriptional regulators and play diverse regulatory roles in biotic and abiotic stresses, plant growth and development processes. In this study, the WRKY DNA-binding domain (Pfam Database number: PF03106) downloaded from Pfam protein families database was exploited to identify WRKY genes from the peach (Prunus persica 'Lovell') genome using HMMER 3.0. The obtained amino acid sequences were analyzed with DNAMAN 5.0, WebLogo 3, MEGA 5.1, MapInspect and MEME bioinformatics softwares. Totally 61 peach WRKY genes were found in the peach genome. Our phylogenetic analysis revealed that peach WRKY genes were classified into three Groups: Ⅰ, Ⅱ and Ⅲ. The WRKY N-terminal and C-terminal domains of Group Ⅰ (group I-N and group I-C) were monophyletic. The Group Ⅱ was sub-divided into five distinct clades (groupⅡ-a, Ⅱ-b, Ⅱ-c, Ⅱ-d and Ⅱ-e). Our domain analysis indicated that the WRKY regions contained a highly conserved heptapeptide stretch WRKYGQK at its N-terminus followed by a zinc-finger motif. The chromosome mapping analysis showed that peach WRKY genes were distributed with different densities over 8 chromosomes. The intron-exon structure analysis revealed that structures of the WRKY gene were highly conserved in the peach. The conserved motif analysis showed that the conserved motifs 1, 2 and 3, which specify the WRKY domain, were observed in all peach WRKY proteins, motif 5 as the unknown domain was observed in group Ⅱ-d, two WRKY domains were assigned to GroupⅠ. SqRT-PCR and qRT-PCR results indicated that 16 PpWRKY genes were expressed in roots, stems, leaves, flowers and fruits at various expression levels. Our analysis thus identified the PpWRKY gene families, and future functional studies are needed to reveal its specific roles.
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.
authors.forename: Yan-bing
authors.initials: YB
authors.lastname: Gu
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.
authors.forename: Zhi-rui
authors.initials: ZR
authors.lastname: Ji
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.
authors.forename: Fu-mei
authors.initials: FM
authors.lastname: Chi
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.
authors.forename: Zhuang
authors.initials: Z
authors.lastname: Qiao
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.
authors.forename: Cheng-nan
authors.initials: CN
authors.lastname: Xu
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.
authors.forename: Jun-xiang
authors.initials: JX
authors.lastname: Zhang
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.
authors.forename: Zong-shan
authors.initials: ZS
authors.lastname: Zhou
authors.affiliation: Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.
authors.forename: Qing-long
authors.initials: QL
authors.lastname: Dong
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D010944:Plants / Q000737:chemistry / Q000145:classification / Q000235:genetics; D017434:Protein Structure, Tertiary; D000068239:Prunus persica / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors