苹果WRKY基因家族生物信息学及表达分析

doi:10.3864/j.issn.0578-1752.2015.16.012

Abstract

Abstract: 【Objective】In this study, 132 putative WRKY proteins in the apple (Malus domestica Borkh.) genome were identified, so as to provide a basis for studying the theoretical roles of WRKY genes in the regulation of plant stress responses, growth and development, and to provide valuable information for WRKY genes cloning in apple.【Method】WRKY DNA-binding domain (PF03106) downloaded from Pfam protein families database was employed to identify WRKY genes from apple genome using HMMER 3.0. The obtained amino acid sequences were analyzed with the bioinformatics softwares, including DNAMAN 5.0, Weblogo 3, MEGA 5.1, MapInspect and MEME. RT-PCR was used to detect WRKY genes expression in different tissues of apple. 【Result】 Totally 132 apple WRKY genes were found in apple genome. The result of group identification and phylogenetic analysis revealed that apple WRKY genes were classified into Group I, Group II and Group III. Twenty-four MdWRKY proteins with two WRKY domains (group I-N and group I-C) containing CX₄CX_22-23HXH zinc-finger motif belonged to Group I. Seventy-nine Group II MdWRKY proteins had a single WRKY domain including CX_4–5CX₂₃HXH zinc-finger motif and could be further divided into five subgroups (Group II-a: 8 members, Group II-b: 12 members, Group II-c: 31 members, Group II-d: 14 members, and Group II-e: 14 members, respectively), whereas 29 Group III MdWRKY proteins contained a single WRKY domain with CX₇CX_23–24HXC zinc-finger motif. The results of domain analysis indicated that the WRKY regions contained a highly conserved heptapeptide stretch WRKYGQK at its N-terminus followed by a zinc-finger motif. Chromosome mapping analysis showed that apple WRKY genes were distributed with different densities on 17 chromosomes. The largest number of apple WRKY genes were found on chromosomes 1 and 9 (thirteen genes), followed by chromosome 12 (twelve genes). Only 4 genes located on chromosomes 2, 5 and 14. The results of gene structure analysis revealed that most of the WRKY gene contained 2-5 exons and WRKY gene structure were highly conserved in apple. Conserved motif analysis showed that the conserved motifs 1-6, which specify the WRKY domain, were observed in all apple WRKY proteins, motif 8 and motifs 7 and 9 as the unknown domain were observed in Group II-a and II-b and Group III, respectively. Two WRKY domains were assigned to Group I. RT-PCR results indicated that 12 MdWRKY genes were expressed in roots, stems, leaves, flowers and fruits at various expression levels.【Conclusion】These results suggested that MdWRKY gene family was highly and structurally conserved, and may be involved into the regulation of growth and development processes in apple.

Key words: apple, WRKY, transcription factor, bioinformatics, gene family

GU Yan-bing, JI Zhi-rui, CHI Fu-mei, QIAO Zhuang, XU Cheng-nan, ZHANG Jun-xiang, DONG Qing-long, ZHOU Zong-shan. Bioinformatics and Expression Analysis of the WRKY Gene Family in Apple[J].Scientia Agricultura Sinica, 2015, 48(16): 3221-3238.

0
/ / Recommend

Add to citation manager EndNote|Reference Manager|ProCite|BibTeX|RefWorks

URL: https://www.chinaagrisci.com/EN/10.3864/j.issn.0578-1752.2015.16.012

https://www.chinaagrisci.com/EN/Y2015/V48/I16/3221

References

[1] Eulgem T, Rushton P J, Robatzek S, Somssich I E. The WRKY superfamily of plant transcription factors. Trends in Plant Science, 2000, 5(5): 199-206.

[2] Rushton P J, Somssich I E, Ringler P, Shen Q J. WRKY transcription factors. Trends in Plant Science, 2010, 15(5): 247-258.

[3] Sun C, Palmqvist S, Olsson H, Boren 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. The 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 Evolution Biology, 2005, 5(1): 1.

[5] Chen L, Song Y, Li S, Zhang L, Zou C, Yu D. The role of WRKY transcription factors in plant abiotic stresses. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 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 beta-amylase from sweet potato. Molecular and General Genetics, 1994, 244(6): 563-571.

[7] Rushton PJ, Macdonald H, Huttly A K, Lazarus C M, Hooley R. Members of a new family of DNA-binding proteins bind to a conserved cis-element in the promoters of a-Amy2 genes. Plant Molecular Biology, 1995, 29(4): 691-702.

[8] Rushton P J, Torres J T, Parniske M, Wernert P, Hahlbrock K Somssich I E. Interaction of elicitor-induced DNA-binding proteins with elicitor response elements in the promoters of parsley PR1 genes. EMBO Journal, 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 Research, 1996, 24(23): 4624-4631.

[10] Johnson S C, Kolevski B, Smyth D R. Transparent testa glabra 2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor. The Plant Cell, 2002, 14(6): 1359-1375.

[11] Lagace M, Matton D P. 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 I E. Targets of AtWRKY6 regulation during plant senescence and pathogen defense. Genes & Development, 2002, 16(9): 1139-1149.

[13] Xie Z, Zhang Z L, Zou X, Yang G, Komatsu S, Shen Q J. Interactions of two abscisic-acid induced WRKY genes in repressing gibberellin signaling in aleurone cells. The Plant Journal, 2006, 46(2): 231-242.

[14] Dong J, Chen C, Chen Z. Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response. Plant Molecular Biology, 2003, 51(1): 21-37.

[15] Ulker B, Somssich I E. WRKY transcription factors: from DNA binding towards biological function. Current Opinion in Plant Biology, 2004, 7(5): 491-498.

[16] Ross C A, Liu Y, Shen Q J. The WRKY gene family in rice (Oryza sativa). Journal of Integrative Plant Biology, 2007, 49(6): 827-842.

[17] Huang S, Gao Y, Liu J, Peng X, Niu X, Fei Z, Cao S, Liu Y. Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Molecular Genetics and Genomics, 2012, 287(6): 495-513.

[18] Ling J, Jiang W, Zhang Y, Yu H, Mao Z, Gu X, Huang S, Xie B. Genome-wide analysis of WRKY gene family in Cucumis sativus. BMC Genomics, 2011, 12(1): 471.

[19] He H, Dong Q, Shao Y, Jiang H, Zhu S, Cheng B, Xiang Y. Genome-wide survey and characterization of the WRKY gene family in Populus trichocarpa. Plant Cell Reports, 2012, 31(7): 1199-1217.

[20] 许瑞瑞, 张世忠, 曹慧, 束怀瑞. 苹果WRKY转录因子家族基因生物信息学分析. 园艺学报, 2012, 39(10): 2049-2060.

Xu R R, Zhang S Z, Cao H, Shu H R. Bioinformatics analysis of WRKY transcription factor genes family in apple. Acta Horticulturae Sinica, 2012, 39(10): 2049-2060. (in Chinese)

[21] Dou L, Zhang X, Pang C, Song M, Wei H, Fan S, Yu S. Genome-wide analysis of the WRKY gene family in cotton. Molecular Genetics and Genomics, 2014, DOI 10.1007/s00438-01.

[22] Li H, Guo D, Yang Z, Tang X, Peng S. Genome-wide identification andcharacterization of WRKY gene family in Hevea brasiliensis. Genomics, 2014, 104(1): 14-23.

[23] Tian Y, Dong Q, Ji Z, Chi F, Cong P, Zhou Z. Genome-wide identification and analysis of the MADS-box gene family in apple. Gene, 2015, 555(2): 277-290.

[24] 董庆龙, 王海荣, 安淼, 余贤美, 王长君. 苹果NADP依赖的苹果酸酶基因克隆、序列和表达分析. 中国农业科学, 2013, 46(9): 1857-1866.

Dong Q L, Wang H R, An M, Yu X M, Wang C J. Cloning, sequence and expression analysis of NADP-malic enzyme genes in apple. Scientia Agricultura Sinica, 2013, 46(9): 1857-1866. (in Chinese)

[25] Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular evolutionary genetics analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 2011, 28(10): 2731-2739.

[26] 董庆龙, 冀志蕊, 迟福梅, 田义, 安秀红, 徐成楠, 周宗山. 苹果MADS-box转录因子的生物信息学及其在不同组织中的表达. 中国农业科学, 2014, 47(6): 1151-1161.

Dong Q L, Ji Z R, Chi F M, Tian Y, An X H, Xu C N, Zhou Z S. Bioinformatics of the MADS-box transcription factor and their expression in different apple tissues. Scientia Agricultura Sinica, 2014, 47(6): 1151-1161. (in Chinese)

[27] Hu L, Liu S. Genome-wide analysis of the MADS-box gene family in cucumber. Genome, 2012, 55: 245-256.

[28] Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar S K, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald L M, Gutin N, Lanchbury J, Macalma T, Mitchell J T, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu V T, King S T, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater M M, Masiero S, Lasserre P, Lespinasse Y, Allan A C, Bus V, Chagne D, Crowhurst R N, Gleave A P, Lavezzo E, Fawcett J A, Proost S, Rouze P, Sterck L, Toppo S, Lazzari B, Hellens R P, Durel C E, Gutin A, Bumgarner R E, Gardiner S E, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R. The genome of the domesticated apple (Malus×domestica Borkh.). Nature Genetics, 2010, 42(10): 833-839.

[29] Duan M R, Nan J, LiangY H, Mao P, Lu L, Li L, Wei C, Lai L, Li Y, Su X D. DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein. Nucleic Acids Research, 2007, 35(4): 1145-1154.

[30] Cannon S B, Mitra A, Baumgarten A, Young N D, May G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biology, 2004, 4(1): 10.

[31] Zhang S, Xu R, Luo X, Jiang Z, Shu H. Genome-wide identification and expression analysis of MAPK and MAPKK gene family in Malus domestica. Gene, 2013, 531(2): 377-387.

[32] Li X, Guo R, Li J, Singer S D, Zhang Y, Yin X, Wang X. Genome- wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily in apple (Malus×domestica Borkh.). Plant Physiology and Biochemistry, 2013, 71: 268-282.

[33] Su H, Zhang S, Yuan X, Chen C, Wang X F, Hao Y J. Genome-wide analysis and identification of stress-responsive genes of the NAM-ATAF1, 2-CUC2 transcription factor family in apple. Plant Physiology and Biochemistry, 2013, 71: 11-21.

[34] Wang X, Zhang S, Su L, Liu X, Hao Y. A genome-wide analysis of the LBD (LATERAL ORGAN BOUNDARIES Domain) gene family in Malus domestica with a functional characterization of MdLBD11. Plos One, 2013, 8(2): e57044.

[35] Cao Z H, Zhang S Z, Wang R K, Zhang R F, Hao Y J. Genome wide analysis of the apple MYB transcription factor family allows the identification of MdoMYB121 gene confering abiotic stress tolerance in plants. Plos One, 2013, 8(7): e69955.

[36] Yuan H Z, Zhao K, Lei H J, Shen X J, Liu Y, Liao X, Li T H. Genome-wide analysis of the GH3 family in apple (Malus×domestica). BMC Genomics, 2013, 14(1): 297.

Related Articles 15

[1]	LIU RUI, ZHAO YuHan, FU ZhongJu, GU XinYi, WANG YanXia, JIN XueHui, YANG Ying, WU WeiHuai, ZHANG YaLing. Distribution and Variation of PWL Gene Family in Rice Magnaporthe oryzae from Heilongjiang Province and Hainan Province [J]. Scientia Agricultura Sinica, 2023, 56(2): 264-274.
[2]	DONG YongXin,WEI QiWei,HONG Hao,HUANG Ying,ZHAO YanXiao,FENG MingFeng,DOU DaoLong,XU Yi,TAO XiaoRong. Establishment of ALSV-Induced Gene Silencing in Chinese Soybean Cultivars [J]. Scientia Agricultura Sinica, 2022, 55(9): 1710-1722.
[3]	LI ShiJia,LÜ ZiJing,ZHAO Jin. Identification of R2R3-MYB Subfamily in Chinese Jujube and Their Expression Pattern During the Fruit Development [J]. Scientia Agricultura Sinica, 2022, 55(6): 1199-1212.
[4]	CHEN XueSen, YIN HuaLin, WANG Nan, ZHANG Min, JIANG ShengHui, XU Juan, MAO ZhiQuan, ZHANG ZongYing, WANG ZhiGang, JIANG ZhaoTao, XU YueHua, LI JianMing. Interpretation of the Case of Bud Sports Selection to Promote the High-Quality and Efficient Development of the World’s Apple and Citrus Industry [J]. Scientia Agricultura Sinica, 2022, 55(4): 755-768.
[5]	LU Xiang, GAO Yuan, WANG Kun, SUN SiMiao, LI LianWen, LI HaiFei, LI QingShan, FENG JianRong, WANG DaJiang. Analysis of Aroma Characteristics in Different Cultivated Apple Strains [J]. Scientia Agricultura Sinica, 2022, 55(3): 543-557.
[6]	LAI ChunWang, ZHOU XiaoJuan, CHEN Yan, LIU MengYu, XUE XiaoDong, XIAO XueChen, LIN WenZhong, LAI ZhongXiong, LIN YuLing. Identification of Ethylene Synthesis Pathway Genes in Longan and Its Response to ACC Treatment [J]. Scientia Agricultura Sinica, 2022, 55(3): 558-574.
[7]	YOU YuWan,ZHANG Yu,SUN JiaYi,ZHANG Wei. Genome-Wide Identification of NAC Family and Screening of Its Members Related to Prickle Development in Rosa chinensis Old Blush [J]. Scientia Agricultura Sinica, 2022, 55(24): 4895-4911.
[8]	ZHANG Jie,JIANG ChangYue,WANG YueJin. Functional Analysis of the Interaction Between Transcription Factors VqWRKY6 and VqbZIP1 in Regulating the Resistance to Powdery Mildew in Chinese Wild Vitis quinquangularis [J]. Scientia Agricultura Sinica, 2022, 55(23): 4626-4639.
[9]	GUO ShaoLei,XU JianLan,WANG XiaoJun,SU ZiWen,ZHANG BinBin,MA RuiJuan,YU MingLiang. Genome-Wide Identification and Expression Analysis of XTH Gene Family in Peach Fruit During Storage [J]. Scientia Agricultura Sinica, 2022, 55(23): 4702-4716.
[10]	GAO XiaoQin,NIE JiYun,CHEN QiuSheng,HAN LingXi,LIU Lu,CHENG Yang,LIU MingYu. Geographical Origin Tracing of Fuji Apple Based on Mineral Element Fingerprinting Technology [J]. Scientia Agricultura Sinica, 2022, 55(21): 4252-4264.
[11]	PANG HaoWan,FU QianKun,YANG QingQing,ZHANG YuanYuan,FU FengLing,YU HaoQiang. Maize Transcription Factor ZmEREB93 Negatively Regulates Kernel Development [J]. Scientia Agricultura Sinica, 2022, 55(19): 3685-3696.
[12]	CHEN FengQiong, CHEN QiuSen, LIN JiaXin, WANG YaTing, LIU HanLin, LIANG BingRuoShi, DENG YiRu, REN ChunYuan, ZHANG YuXian, YANG FengJun, YU GaoBo, WEI JinPeng, WANG MengXue. Genome-Wide Identification of DIR Family Genes in Tomato and Response to Abiotic Stress [J]. Scientia Agricultura Sinica, 2022, 55(19): 3807-3821.
[13]	BaoHua CHU,FuGuo CAO,NingNing BIAN,Qian QIAN,ZhongXing LI,XueWei LI,ZeYuan LIU,FengWang MA,QingMei GUAN. Resistant Evaluation of 84 Apple Cultivars to Alternaria alternata f. sp. mali and Genome-Wide Association Analysis [J]. Scientia Agricultura Sinica, 2022, 55(18): 3613-3628.
[14]	XIE Bin,AN XiuHong,CHEN YanHui,CHENG CunGang,KANG GuoDong,ZHOU JiangTao,ZHAO DeYing,LI Zhuang,ZHANG YanZhen,YANG An. Response and Adaptability Evaluation of Different Apple Rootstocks to Continuous Phosphorus Deficiency [J]. Scientia Agricultura Sinica, 2022, 55(13): 2598-2612.
[15]	YANG ShengDi,MENG XiangXuan,GUO DaLong,PEI MaoSong,LIU HaiNan,WEI TongLu,YU YiHe. Co-Expression Network and Transcriptional Regulation Analysis of Sulfur Dioxide-Induced Postharvest Abscission of Kyoho Grape [J]. Scientia Agricultura Sinica, 2022, 55(11): 2214-2226.

Metrics

Viewed

Full text

Abstract

Cited

Shared

Discussed

Comments

Recommended 0

No Suggested Reading articles found!

Bioinformatics and Expression Analysis of the WRKY Gene Family in Apple

RichHTML

PDF

Cited

Abstract

Cite this article

share this article

References

Related Articles 15

Metrics

Comments

Recommended 0