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[Genome-wide identification and expression analysis of the WRKY gene family in peach].
Yi Chuan. 2016 03; 38(3):254-70.YC

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+Show Affiliations

Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.

Pub Type(s)

English Abstract
Journal Article
Research Support, Non-U.S. Gov't

Language

chi

PubMed ID

27001479

Citation

Gu, Yan-bing, et al. "[Genome-wide Identification and Expression Analysis of the WRKY Gene Family in Peach]." Yi Chuan = Hereditas, vol. 38, no. 3, 2016, pp. 254-70.
Gu YB, Ji ZR, Chi FM, et al. [Genome-wide identification and expression analysis of the WRKY gene family in peach]. Yi Chuan. 2016;38(3):254-70.
Gu, Y. B., Ji, Z. R., Chi, F. M., Qiao, Z., Xu, C. N., Zhang, J. X., Zhou, Z. S., & Dong, Q. L. (2016). [Genome-wide identification and expression analysis of the WRKY gene family in peach]. Yi Chuan = Hereditas, 38(3), 254-70. https://doi.org/10.16288/j.yczz.15-235
Gu YB, et al. [Genome-wide Identification and Expression Analysis of the WRKY Gene Family in Peach]. Yi Chuan. 2016;38(3):254-70. PubMed PMID: 27001479.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - [Genome-wide identification and expression analysis of the WRKY gene family in peach]. AU - Gu,Yan-bing, AU - Ji,Zhi-rui, AU - Chi,Fu-mei, AU - Qiao,Zhuang, AU - Xu,Cheng-nan, AU - Zhang,Jun-xiang, AU - Zhou,Zong-shan, AU - Dong,Qing-long, PY - 2016/3/23/entrez PY - 2016/3/24/pubmed PY - 2016/7/1/medline SP - 254 EP - 70 JF - Yi chuan = Hereditas JO - Yi Chuan VL - 38 IS - 3 N2 - 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. SN - 0253-9772 UR - https://www.unboundmedicine.com/medline/citation/27001479/[Genome_wide_identification_and_expression_analysis_of_the_WRKY_gene_family_in_peach]_ DB - PRIME DP - Unbound Medicine ER -