The coding products of WRKY gene family plays important roles in plant growth and development as well as in various stress responses. They have been identified in various plants, but only few in common tobacco (Nicotiana tabacum L.). In this study, 164 putative WRKY proteins in the common tobacco genome were identified by using the conserved WRKY sequence (PF03106) from the Pfam database. Phylogenetic trees, functional domain analysis, chromosomal localization, subcellular localization and tissue expression patterns were analyzed with the bioinformatics softwares, including DNAMAN 5.0, Weblogo 3, MEGA 5.1, MG2C and MEME. First of all, phylogenetic trees divided all the candidate genes into three subfamilies: Ⅰ, Ⅱ and Ⅲ, respectively, and subfamily Ⅱ could be further divided into five subgroups: group Ⅱ-a, -b, -c, -d and -e. Secondly, the WRKY regions contained a highly conserved heptapeptide stretch WRKYGQK followed by a zinc-finger motif. Most of the NtWRKY genes contained 2-5 exons and a highly conserved gene structure. Thirdly, 154 out of 164 NtWRKY genes were distributed with different densities on 24 chromosomes, and each subfamily with different patterns and frequency. The largest number of NtWRKY genes was found on chromosome VI, and only one on chromosome X. Fourthly, the majority of NtWRKY members located in the nucleus, with 74 percent of subfamily Ⅲ in the extracellular matrix. Lastly, the members in the same subfamily had different spatial and temporal expression profiles, with 11 NtWRKY genes in roots, stems and leaves expressed at various levels. The expression of genes NtWRKY26, NtWRKY30 and NtWRKY32 can be induced by Phytophthora nicotianae. Our research thus provides valuable information for NtWRKY gene cloning and functional characterization in common tobacco.
Xiaohua Xiang, Xinru Wu, Jiangtao Chao, Minglei Yang, Fan Yang, Guo Chen, Guanshan Liu, Yuanying Wang
. Genome-wide identification and expression analysis of the WRKY gene family in common tobacco (Nicotiana tabacum L.)[J]. Hereditas(Beijing), 2016
, 38(9)
: 840
-856
.
DOI: 10.16288/j.yczz.16-016
[1] Zhang YJ, Wang LJ. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol , 2005, 5(1): 1.
[2] Riechmann JL, Heard J, Martin G, Reuber L, Jiang CZ, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu GL. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science , 2000, 290(5499): 2105-2110.
[3] Martinez E. Multi-protein complexes in eukaryotic gene transcription. Plant Mol Biol , 2002, 50(6): 925-947.
[4] Eulgem T, Rushton PJ, Robatzek S, Somssich IE. The WRKY superfamily of plant transcription factors. Trends Plant Sci , 2000, 5(5): 199-206.
[5] 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.
[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, Somssich IE, Ringler P, Shen QJ. WRKY transcription factors. Trends Plant Sci , 2010, 15(5): 247-258.
[8] Cormack RS, Eulgem T, Rushton PJ, Köchner P, Hahlbrock K, Somssich IE. Leucine zipper-containing WRKY proteins widen the spectrum of immediate early elicitor-induced WRKY transcription factors in parsley. Biochim Biophys Acta , 2002, 1576(1-2): 92-100.
[9] Ishida T, Hattori S, Sano R, Inoue K, Shirano Y, Hayashi H, Shibata D, Sato S, Kato T, Tabata S, Okada K, Wadaa T. Arabidopsis TRANSPARENT TESTA GLABRA2 is directly regulated by R2R3 MYB transcription factors and is involved in regulation of GLABRA2 transcription in epidermal differentiation. Plant Cell , 2007, 19(8): 2531-2543.
[10] 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.
[11] 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.
[12] Cheong YH, Chang HS, Gupta R, Wang X, Zhu T, Luan S. Transcriptional profiling reveals novel interactions between wounding, pathogen, abiotic stress, and hormonal responses in Arabidopsis . Plant Physiol , 2002, 129(2): 661-677.
[13] Hara K, Yagi M, Kusano T, Sano H. Rapid systemic accumulation of transcripts encoding a tobacco WRKY transcription factor upon wounding. Mol Gen Genet , 2000, 263(1): 30-37.
[14] Yoda H, Ogawa M, Yamaguchi Y, Koizumi N, Kusano T, Sano H. Identification of early-responsive genes associated with the hypersensitive response to tobacco mosaic virus and characterization of a WRKY-type transcription factor in tobacco plants. Mol Gen Gent , 2002, 267(2): 154-161.
[15] de Pater S, Greco V, Pham K, Memelink J, Kijne J. Characterization of a zinc-dependent transcriptional activator from Arabidopsis . Nucl Acids Res , 1996, 24(23): 4624- 4631.
[16] Chen CH, Chen ZX. Isolation and characterization of two pathogen-and salicylic acid-induced genes encoding WRKY DNA-binding proteins from tobacco. Plant Mol Biol , 2000, 42(2): 387-396.
[17] 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, 迟福梅, 乔壮, 徐成楠, 张俊祥, 董庆龙, 周宗山. 苹果WRKY 基因家族生物信息学及表达分析. 中国农业科学, 2015, 48(16): 3221-3238.
[18] Su ZG, Yang AG, Sun YH, Luo CG, Liu GS, Zhou J, Li YY, Yang F, Zhao BY, Wang YY. Construction and analysis of tobacco SSH library induced by Phytophthora parasitica var. nicotianae . Acta Ag
