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.
Yanbing Gu, Zhirui Ji, Fumei Chi, Zhuang Qiao, Chengnan Xu, Junxiang Zhang, Zongshan Zhou, Qinglong Dong
. Genome-wide identification and expression analysis of the WRKY gene family in peach[J]. Hereditas(Beijing), 2016
, 38(3)
: 254
-270
.
DOI: 10.16288/j.yczz.15-235
[1] Eulgem T, Rushton PJ, Robatzek S, Somssich IE. The WRKY superfamily of plant transcription factors. Trends Plant Sci , 2000, 5(5): 199-206.
[2] Rushton PJ, Somssich IE, Ringler P, Shen QJ. WRKY transcription factors. Trends Plant Sci , 2010, 15(5): 247-258.
[3] Sun CX, Palmqvist S, Olsson H, Borén M, Ahlandsberg S, Jansson C. A novel WRKY transcription factor, SUSIBA2, participates in sugar signaling in barley by binding to the sugar-responsive elements of the iso1 promoter. Plant Cell , 2003, 15(9): 2076-2092.
[4] Zhang Y, Wang L. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol , 2005, 5(1): 1.
[5] Chen LG, Song Y, Li SJ, Zhang LP, Zou CS, Yu DQ. The role of WRKY transcription factors in plant abiotic stresses. BBA-Gene Regul Mech , 2012, 1819(2): 120-128.
[6] Ishiguro S, Nakamura K. Characterization of a cDNA encoding a novel DNA-binding protein, SPF1, that recognizes SP8 sequences in the 5' upstream regions of genes coding for sporamin and β-amylase from sweet potato. Mol Gen Genet , 1994, 244(6): 563-571.
[7] Rushton PJ, Macdonald H, Huttly AK, Lazarus CM, Hooley R. Members of a new family of DNA-binding proteins bind to a conserved cis-element in the promoters of α-Amy2 genes. Plant Mol Biol , 1995, 29(4): 691-702.
[8] Rushton PJ, Torres JT, Parniske M, Wernert P, Hahlbrock K, Somssich IE. Interaction of elicitor-induced DNA-binding proteins with elicitor response elements in the promoters of parsley PR1 genes. EMBO J , 1996, 15(20): 5690-5700.
[9] de Pater S, Greco V, Pham K, Memelink J, Kijine J. Characterization of a zinc-dependent transcriptional activator from Arabidopsis . Nucleic Acids Res , 1996, 24(23): 4624-4631.
[10] Johnson SC, Kolevski B, Smyth DR. Transparent testa glabra2 , a trichome and seed coat development gene of Arabidopsis , encodes a WRKY transcription factor. Plant Cell , 2002, 14(6): 1359-1375.
[11] Lagacé M, Matton DP. Characterization of a WRKY transcription factor expressed in late torpedo-stage embryos of Solanum chacoense . Planta , 2004, 219(1): 185-189.
[12] Robatzek S, Somssich IE. Targets of At WRKY6 regulation during plant senescence and pathogen defense. Genes Dev , 2002, 16(9): 1139-1149.
[13] Xie Z, Zhang ZL, Zou XL, Yang GX, Komatsu S, Shen QJ. Interactions of two abscisic-acid induced WRKY genes in repressing gibberellin signaling in aleurone cells. Plant J , 2006, 46(2): 231-242.
[14] Dong JX, Chen CH, Chen ZX. Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response. Plant Mol Biol , 2003, 51(1): 21-37.
[15] Ülker B, Somssich IE. WRKY transcription factors: from DNA binding towards biological function. Curr Opin Plant Biol , 2004, 7(5): 491-498.
[16] Fu QT, Yu DQ. Expression profiles of AtWRKY25 , AtWRKY26 and AtWRKY33 under abiotic stresses . Hereditas (Beijing) , 2010, 32(8): 848-856. 付乾堂, 余迪求. 拟南芥 AtWRKY25 , AtWRKY26 和 AtWRKY33 在非生物胁迫条件下的表达分析. 遗传, 2010, 32(8): 848-856.
[17] Ross CA, Liu Y, Shen QJ. The WRKY gene family in rice ( Oryza sativa ). J Integr Plant Biol , 2007, 49(6): 827-842.
[18] Huang SX, Gao YF, Liu JK, Peng XL, Niu XL, Fei ZJ, Cao SQ, Liu YS. Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum . Mol Genet Genomics , 2012, 287(6): 495-513.
[19] Ling J, Jiang WJ, Zhang Y, Yu HJ, Mao ZC, Gu XF, Huang SW, Xie BY. Genome-wide analysis of WRKY gene family in Cucumis sativus . BMC Genomics , 2011, 12(1): 471.
[20] He HS, Dong Q, Shao YH, Jiang HY, Zhu SW, Cheng BJ, Xiang Y. Genome-wide survey and characterization of the WRKY gene family in Populus trichocarpa . Plant Cell Rep , 2012, 31(7): 1199-1217.
[21] Gu YB, Ji ZR, Chi FM, Qiao Z, Xu CN, Zhang JX, Dong QL, Zhou ZS. Bioinformatics and expression analysis of the WRKY gene family in apple. Sci Agric Sin , 2015, 48(16): 3221-3238. 谷彦冰, 冀志蕊, 迟福
