毛竹锌指同源结构域基因家族全基因组鉴定及表达分析

doi:10.3969/j.issn.1674-7968.2020.04.007

Abstract
Figure/Table
References
Related Citation (15)

Download: PDF (4875 KB) HTML (1 KB)
Export: BibTeX | EndNote (RIS)

Abstract The zinc finger-homeodomain (ZF-HD) is a family of homologous heterologous box proteins, a plant-specific transcription factor that plays an important role in plant growth and development. In order to explore the function of ZF-HD gene family in the growth and development of Phyllostachys edulis, the family's physicochemical properties, phylogenetic relationship, gene structures and expression patterns were analyzed in detail by bioinformatics based on Phyllostachys edulis genome and related transcriptome data in this study. The results showed that 23 ZF-HD members in the genome with fewer introns (1~2) of P. edulis, and their gene structures and motifs were relatively conservative. The amino acid sequences of ZF-HD gene family had different domains, including zinc-finger (ZF) and homeodomain (HD), which could bind to DNA. Phylogenetic tree showed that ZF-HD gene family could be divided into 6 subfamilies. Combined with the results of multiple sequence alignment and homologous modeling analysis, ZF-HD belonged to the C2H2-type Zn-finger domain super-gene family. The upstream promoter sequences contained multiple cis-acting elements related to hormone response. The collinearity relationship with rice (Oryza sativa) was higher than that with Arabidopsis thaliana, and there was a doubling event of gene duplication. In combination with Gene Ontology (GO) enrichment analysis, RNA-seq data of ZF-HD genes were analyzed under different hormone treatment conditions and in different stages of P. bud development. It was found that ZF-HD could respond to the regulation of exogenous gibberellin (GA) and naphthalene acetic acid (NAA). The high expression of some gene family members in P. edulis shoots indicated that they might be involved in the rapid growth and development of P. edulis shoots. The results of this study will help to reveal the biological functions of the ZF-HD gene family in the rapid growth and development of P. edulis.

Key words： Phyllostachys edulis Zinc finger-homeodomain (ZF-HD) Transcription factor Gene analysis Functional identification

Received: 28 August 2019

ZTFLH:

S795.7

Corresponding Authors: * zjzhang@zafu.edu.cn

	Service

	E-mail this article
	Add to my bookshelf
	Add to citation manager
	E-mail Alert
	RSS
	Articles by authors
	MA Rui-Fang
	CHEN Jia-Lu
	LIU Xiao-Yu
	ZHU Feng-Xiao
	RUAN Shi-Yu
	YU Pei-Yao
	ZHANG Zhi-Jun

Cite this article:

MA Rui-Fang,CHEN Jia-Lu,LIU Xiao-Yu, et al. Genome-wide Identification and Expression Analysis of Zinc Finger Homologous Domain Gene Family in Phyllostachys edulis[J]. 农业生物技术学报, 2020, 28(4): 645-657.

URL:

http://journal05.magtech.org.cn/Jwk_ny/EN/10.3969/j.issn.1674-7968.2020.04.007 OR http://journal05.magtech.org.cn/Jwk_ny/EN/Y2020/V28/I4/645

[1] 高斌, 陈娟娟, 崔顺立, 等. 2020. 花生bZIP基因家族全基因组鉴定及抗旱表达分析[J/OL]. 植物遗传资源学报, 21(01): 174-191.
(Gao B, Chen J J, Cui S L, et al.2020. Genome-wide identification and expression analysis of bZIP gene family under drought stress in peanut[J/OL]. Journal of Plant Genetic Resources, 21(01): 174-191.)
[2] 胡靖康. 2018. 番茄ZF-HD转录因子的全基因组挖掘及抗逆相关基因筛选[D]. 硕士学位论文, 东北农业大学, 导师: 许向阳, pp. 2-26.
(Hu J K.2018. Bioinformatic analysis and identification of some resistance-associated genes of ZF-HD gene family in tomato[D]. Thesis for M.S., Northeast Agricultural University, Supervisor: Xu X Y, pp. 2-26.)
[3] 李春艳. 2018. 玉米ZF-HD转录因子家族耐盐, 抗旱相关基因的鉴定及特性分析[D]. 硕士学位论文, 西南大学, 导师: 蔡一林, pp. 11-40.
(Li C Y.2018. Identification and characterization of drought and salt resistance-related genes of ZF-HD transcription factors family in maize[D]. Thesis for M.S., Southwest University, Supervisor: Cai Y L, pp. 11-40.)
[4] 吕天琦. 2019. 白菜C2H2型锌指蛋白基因家族的进化及DAZ3在转录水平调控花粉发育的研究[D]. 博士学位论文. 浙江大学, 导师: 曹家树, pp. 27-45.
(Lv T Q.2019. Studies on evolution of C2H2 zinc-finger protein gene family in Brassica campestris subsp.chinesis and transcriptional regulation of DAZ3 in pollen development[D]. Thesis for Ph.D., Zhejiang University, Supervisor: Cao J S, pp. 27-45.)
[5] 卢多. 2013. C2H2型锌指对生物大分子的识别[J]. 药学学报, 48(6): 834-841.
(Lu D.2013. C2H2 zinc-finger recognition of biomolecules[J]. Acta Pharmaceutica Sinica, 48(6): 834-841.)
[6] 任德全, 刘玉芬, 许丽敏, 等. 2011. 同源异型盒基因研究[J]. 安徽农业科学, 39(4): 1949-1950.
(Ren D Q, Liu Y F, Xu L M, et al.2011. Study on homeobox gene[J]. Journal of Anhui Agriculture Science, 39(4): 1949-1950.)
[7] 孙熹微, 窦雅静, 唐雯琪, 等. 2019. 椰子ZF-HD基因家族的鉴定及生物信息学分析[J/OL]. 热带作物学报, 1-14.
(Sun X W, Dou Y J, Tang W Q, et al.2019. Identification and bioinformatics analysis of coconut ZF-HD gene family[J/OL]. Chinese Journal of Tropical Crops, 1-14.)
[8] 陶贵耘, 傅鹰, 周明兵. 2018. 竹类植物快速生长的机理研究进展[J]. 农业生物技术学报, 26(05): 871-887.
(Tao G Y, Fu Y, Zhou M B.2018. Advances in studies on molecular mechanisms of rapid growth of bamboo species[J]. Journal of Agricultural Biotechnology, 26(05): 871-887.)
[9] 王静毅, 刘菊华, 贾彩红, 等. 2019. 香蕉C2H2类锌指蛋白基因MaZAT10的克隆及表达分析[J].分子植物育种, 17(14): 4551-4559.
(Wang J Y, Liu J H, Jia C H, et al.2019. Clone and expression of the C2H2-type zinc finger transcription factor gene MaZAT10 in banana[J]. Molecular Plant Breeding, 17(14): 4551-4559.)
[10] 张舒. 2017. 黄瓜基因组内锌指蛋白的鉴定及特征分析[D]. 硕士学位论文, 中国农业科学院, 导师: 张忠华, pp. 1-1.
(Zhang S.2017. Genome-wide identification and characterization of zinc finger proteins in cucumber[D]. Thesis for M.S., Chinese Academy of Agricultural Sciences, Supervisor: Zhang Z H, pp. 1-1.)
[11] Abu-Romman S.2014. Molecular cloning and expression analysis of zinc finger-homeodomain transcription factor TaZFHD1 in wheat[J]. South African Journal of Botany, 91: 32-36.
[12] Ariel F D, Manavella P A, Dezar C A, et al.2007. The true story of the HD-Zip family[J]. Trends in Plant Science, 12(9): 419-426.
[13] Bailey T L, Boden M, Buske F A, et al.2009. MEME SUITE: Tools for motif discovery and searching[J]. Nucleic Acids Research, 37(suppl_2): W202-W208.
[14] Chen C J, Xia R, Chen H, et al.2018. TBtools, a toolkit for biologists integrating various biological data handling tools with a user-friendly interface[J]. Bio Rxiv, 289660.
[15] Finn R D, Clements J, Eddy S R.2011. HMMER web server: Interactive sequence similarity searching[J]. Nucleic Acids Research, 39(suppl_2): W29-W37.
[16] Finn R D, Coggill P, Eberhardt R Y, et al.2015. The Pfam protein families database: Towards a more sustainable future[J]. Nucleic Acids Research, 44(D1): D279-D285.
[17] Han G L, Wei X C, Dong X X, et al.2020. Arabidopsis ZINC FINGER PROTEIN1 acts downstream of GL2 to repress root hair initiation and elongation by directly suppressing bHLH genes[J]. The Plant Cell, 32(1): 206-225.
[18] He F, Li H G, Wang J J, et al.2019. PeSTZ1, a C2H2-type zinc finger transcription factor from Populus euphratica, enhances freezing tolerance through modulation of ROS scavenging by directly regulating PeAPX2[J]. Plant Biotechnology Journal, 17(11): 2169-2183.
[19] Hichri I, Muhovski Y, Žižková E, et al.2014. The solanum lycopersicum zinc finger2 cysteine-2/histidine-2 repressor-like transcription factor regulates development and tolerance to salinity in tomato and Arabidopsis[J]. Plant Physiology, 164(4): 1967-1990.
[20] Hu W, Ma H.2006. Characterization of a novel putative zinc finger gene MIF1: Involvement in multiple hormonal regulation of Arabidopsis development[J]. The Plant Journal, 45(3): 399-422.
[21] Hu W, DePamphilis C W, Ma H.2008. Phylogenetic analysis of the plant-specific zinc finger-homeobox and mini zinc finger gene families[J]. Journal of Integrative Plant Biology, 50(8): 1031-1045.
[22] Jain M, Tyagi A K, Khurana J P.2008. Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice[J]. The FEBS Journal, 275(11): 2845-2861.
[23] Jin J P, Tian F, Yang D C, et al.2016. PlantTFDB 4.0: Toward a central hub for transcription factors and regulatory interactions in plants[J]. Nucleic Acids Research, 45(Database issue): D1040-D104.
[24] Ke A, Mathias J R, Vershon A K, et al.2002. Structural and thermodynamic characterization of the DNA binding properties of a triple alanine mutant of MATα2[J]. Structure, 10(7): 961-971.
[25] Khatun K, Nath U K, Robin A H K, et al.2017. Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato[J]. BMC Genomics, 18(1): 695.
[26] Kluska K, Adamczyk J, Krężel A.2018. Metal binding properties, stability and reactivity of zinc fingers[J]. Coordination Chemistry Reviews, 367: 18-64.
[27] Letunic I, Doerks T, Bork P.2011. SMART 7: Recent updates to the protein domain annotation resource[J]. Nucleic Acids Research, 40(D1): D302-D305.
[28] Liu M Y, Wang X X, Sun W J, et al.2019. Genome-wide investigation of the ZF-HD gene family in tartary buckwheat (Fagopyrum tataricum)[J]. BMC Plant Biology, 19(1): 248.
[29] Muthuramalingam P, Krishnan S R, Saravanan K, et al.2018. Genome-wide identification of major transcription factor superfamilies in rice identifies key candidates involved in abiotic stress dynamism[J]. Journal of Plant Biochemistry and Biotechnology, 27(3): 300-317.
[30] Park H C, Kim M L, Lee S M, et al.2007. Pathogen-induced binding of the soybean zinc finger homeodomain proteins GmZF-HD1 and GmZF-HD2 to two repeats of ATTA homeodomain binding site in the calmodulin isoform 4 (GmCaM4) promoter[J]. Nucleic Acids Research, 35(11): 3612-3623.
[31] Sun Z X, Liu R H, Guo B, et al.2019. Ectopic expression of GmZAT4, a putative C2H2-type zinc finger protein, enhances PEG and NaCl stress tolerances in Arabidopsis thaliana[J]. 3 Biotech, 9(5): 166.
[32] Tan Q K G, Irish V F.2006. The Arabidopsis zinc finger-homeodomain genes encode proteins with unique biochemical properties that are coordinately expressed during floral development[J]. Plant Physiology, 140(3): 1095-1108.
[33] Tran L S P, Nakashima K, Sakuma Y, et al.2007. Co-expression of the stress-inducible zinc finger homeodomain ZFHD1 and NAC transcription factors enhances expression of the ERD1 gene in Arabidopsis[J]. The Plant Journal, 49(1): 46-63.
[34] Wang H, Yin X J, Li X Q, et al.2014. Genome-wide identification, evolution and expression analysis of the grape (Vitis vinifera L.) zinc finger-homeodomain gene family[J]. International Journal of Molecular Sciences, 15(4): 5730-5748.
[35] Wang W L, Wu P, Li Y, et al.2016. Genome-wide analysis and expression patterns of ZF-HD transcription factors under different developmental tissues and abiotic stresses in Chinese cabbage[J]. Molecular Genetics and Genomics, 291(3): 1451-1464.
[36] Wang Y P, Tang H B, DeBarry J D, et al.2012. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity[J]. Nucleic Acids Research, 40(7): e49-e49.
[37] Windhövel A, Hein I, Dabrowa R, et al.2001. Characterization of a novel class of plant homeodomain proteins that bind to the C4 phosphoenolpyruvate carboxylase gene of Flaveria trinervia[J]. Plant Molecular Biology, 45(2): 201-214.