PPI network analysis of differentially expressed mRNA in the roots of tobacco varieties resistant to Meloidogyne incongnita (Kofold&White) Chitwood

doi:10.16178/j.issn.0528-9017.20221179

Abstract

Abstract:

Based on the differentially expressed genes among varieties, tobacco disease resistant variety K326 and susceptible variety Changbohuang were selected as experimental materials, and key genes related to infection resistance were screened using bioinformatics analysis methods, this article used Protein Protein Interaction (PPI) and Gene Ontology (GO) functional classification analysis (including Biological Process analysis and KEGG pathway analysis) to annotate the biological functions of differentially expressed genes, identify important genes and genes with consistent pathways in the PPI network, analyze these genes to clarify the resistance mechanism of tobacco varieties to Meloidogyne incongnita (Kofold&White) Chitwood, and provide theoretical basis for studying the molecular mechanism of tobacco resistance to Meloidogyne incongnita (Kofold&White) Chitwood. The results showed that differentially expressed genes were significantly enriched in 9 pathways related to anti-infection, including cell metabolism, intracellular transport, and RNA mediated gene silencing. Seven key factor genes that simultaneously formed the PPI network were identified, including Fab1b, Fab1c, Fab1d, Glu1, Dcl1, Dcl2 and Dcl4.

Key words: tobacco, Meloidogyne incongnita (Kofold&White) Chitwood, protein protein interaction, gene ontology (GO) functional classification analysis, key genes

CLC Number:

S572

Xiaoxiang CHEN, Wenjun ZHANG, Zhengguang ZHAI, Zhiqiang XU, Huabing LIU, Yongjian ZHONG, Zhimin JIANG. PPI network analysis of differentially expressed mRNA in the roots of tobacco varieties resistant to Meloidogyne incongnita (Kofold&White) Chitwood[J]. Journal of Zhejiang Agricultural Sciences, 2024, 65(2): 395-400.

Figures/Tables 4

References 33

[1]	祝明亮, 李天飞, 夏振远, 等. 云南省烟草根结线虫发病土壤生态因子分析[J]. 中国烟草学报, 2003, 9(4): 30-34.
[2]	邱雪柏. 烟草根结线虫生物防治研究进展[J]. 贵州农业科学, 2010, 38(7):121-124.
[3]	王袁, 邢雪霞, 李晓辉, 等. 烟草品种对南方根结线虫抗性鉴定及抗性指标筛选[J]. 中国农业科技导报, 2017, 19(8):124-131.
[4]	吴宝山. 豫西烟区烟草根结线虫种类鉴定及其损失估计研究[D]. 长沙: 湖南农业大学, 2013.
[5]	孔凡玉, 王静. 烟草根结线虫病研究进展[J]. 沈阳农业大学学报, 2001, 32(3):232-235.
[6]	王袁. 烟草品种抗南方根结线虫机制研究[D]. 郑州: 河南农业大学, 2018.
[7]	AMMIRAJU J, VEREMIS J, HUANG X, et al. The heat-stable root-knot nematode resistance gene Mi-9 from Lycopersicon peruvianum is localized on the short arm of chromosome 6[J]. Theoretical and Applied Genetics, 2003, 106(3): 478-484.
[8]	DJIAN-CAPORALINO C, PIJAROWSKI L, FAZARI A, et al. High-resolution genetic mapping of the pepper (Capsicum annuum L.) resistance loci Me3 and Me 4 conferring heat-stable resistance to root-knot nematodes (Meloidogyne spp.)[J]. Theoretical and Applied Genetics, 2001, 103(4): 592-600.
[9]	MORTAZAVI A, WILLIAMS B A, MCCUE K, et al. Mapping and quantifying mammalian transcriptomes by RNA-seq[J]. Nature Methods, 2008, 5(7): 621-628.
[10]	李国栋, 刘志明, 陆秀红, 等. 烟草品种对南方根结线虫的抗性鉴定[J]. 广西农业科学, 2010, 41(3):233-235.
[11]	喻盛甫, 白万明, 胡先奇, 等. 烟草品种对常见根结线虫抗性鉴定的研究[J]. 中国农业科学, 1999, 32(5):55-61.
[12]	沈显生. 生命科学概论[M]. 北京: 科学出版社, 2007.
[13]	顾小辉, 魏建和, 王国全, 等. 虫害诱导植物合成防御性次生代谢产物的研究进展[J]. 生命科学研究, 2017, 21(5):458-465, 470.
[14]	KISSEN R, WINGE P, TRAN D H T, et al. Transcriptional profiling of an Fd-GOGAT1/GLU1 mutant in Arabidopsis thaliana reveals a multiple stress response and extensive reprogramming of the transcriptome[J]. BMC Genomics, 2010, 11:190.
[15]	杨欣, 徐艳红, 魏建和, 等. 几种重要植物次生代谢防御反应物质的生物合成途径及分子调控机制研究进展[J]. 生物技术通讯, 2013, 24(2):285-289.
[16]	田培, 李晓辉, 贺文俊, 等. 南方根结线虫侵染烟草抗感品种前后的代谢组学分析[J]. 中国烟草学报, 2019, 25(4): 81-92.
[17]	MELLMAN I. Endocytosis and molecular sorting[J]. Annual Review of Cell and Developmental Biology, 1996, 12:575-625.
[18]	SERRAZINA S, DIAS F V, MALHÓ. Characterization of FAB1 phosphatidylinositol kinases in Arabidopsis pollen tube growth and fertilization[J]. New Phytologist, 2014, 203(3):784-793.
[19]	HIRANO T, STECKER K, MUNNIK T, et al. Visualization of phosphatidylinositol 3,5-bisphosphate dynamics by a tandem ML1N-based fluorescent protein probe in Arabidopsis[J]. Plant and Cell Physiology, 2017, 58(7): 1185-1195.
[20]	SOUSA E, KOST B, MALHÓ R. Arabidopsis phosphatidylinositol-4-monophosphate 5-kinase 4 regulates pollen tube growth and polarity by modulating membrane recycling[J]. The Plant Cell, 2008, 20(11):3050-3064.
[21]	哀建国, 杨勇. RNA介导的植物基因沉默作用及其应用[J]. 浙江林学院学报, 2005, 22(1): 123-128.
[22]	FIRE A, XU S Q, MONTGOMERY M K, et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans[J]. Nature, 1998, 391(6669): 806-811.
[23]	FIRE A. RNA-triggered gene silencing[J]. Trends in Genetics, 1999, 15(9):358-363.
[24]	HANNON G J. RNA interference[J]. Nature, 2002, 418(6894):244-251.
[25]	HAMMOND S M, BERNSTEIN E, BEACH D, et al. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells[J]. Nature, 2000, 404(6775):293-296.
[26]	BASS B L. Double-stranded RNA as a template for gene silencing[J]. Cell, 2000, 101(3):235-238.
[27]	DUNOYER P, HIMBER C, VOINNET O. DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal[J]. Nature Genetics, 2005, 37(12):1356-1360.
[28]	DU Q S, DUAN C G, ZHANG Z H, et al. DCL4 targets cucumber mosaic virus satellite RNA at novel secondary structures[J]. Journal of Virology, 2007, 81(17):9142-9151.
[29]	WU Y Y, HOU B H, LEE W C, et al. DCL2- and RDR6-dependent transitive silencing of SMXL4 and SMXL5 in Arabidopsis dcl4 mutants causes defective phloem transport and carbohydrate over-accumulation[J]. The Plant Journal, 2017, 90(6): 1064-1078.
[30]	KUNG Y J, LIN P C, YEH S D, et al. Genetic analyses of the FRNK motif function of turnip mosaic virus uncover multiple and potentially interactive pathways of cross-protection[J]. Molecular Plant-Microbe interactions: MPMI, 2014, 27(9):944-955.
[31]	JAKUBIEC A, YANG S W, CHUA N H. Arabidopsis DRB4 protein in antiviral defense against turnip yellow mosaic virus infection[J]. The Plant Journal, 2012, 69(1):14-25.
[32]	GASCIOLLI V, MALLORY A C, BARTEL D P, et al. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs[J]. Current Biology, 2005, 15(16):1494-1500.
[33]	MLOTSHWA S, PRUSS G J, PERAGINE A, et al. DICER-LIKE2 plays a primary role in transitive silencing of transgenes in Arabidopsis[J]. PLoS One, 2008, 3(3):e1755.

通路	差异性	占比/ %	差异基因数量
regulation of cellular metabolic process	7.80×10^-12	17.78	8
endosomal transport	2.40×10^-4	14.04	8
jasmonic acid mediated signaling pathway	1.20×10^-28	7.18	74
heterocycle metabolic process	7.80×10^-12	17.78	8
gene silencing by RNA	2.40×10^-17	7.40	25
innate immune response	2.10×10^-12	7.12	24
sugar mediated signaling pathway	7.40×10^-5	17.50	7
hormone-mediated signaling pathway	1.20×10^-14	6.47	54
response to salt stress	2.60×10^-6	6.18	35

通路	差异性	占比/ %	差异基因数量
regulation of cellular metabolic process	7.80×10^-12	17.78	8
endosomal transport	2.40×10^-4	14.04	8
jasmonic acid mediated signaling pathway	1.20×10^-28	7.18	74
heterocycle metabolic process	7.80×10^-12	17.78	8
gene silencing by RNA	2.40×10^-17	7.40	25
innate immune response	2.10×10^-12	7.12	24
sugar mediated signaling pathway	7.40×10^-5	17.50	7
hormone-mediated signaling pathway	1.20×10^-14	6.47	54
response to salt stress	2.60×10^-6	6.18	35

基因ID号	基因编码蛋白	蛋白相互作用程度	来源
AT1G36160	ACC1	18	Subnetwork1
AT5G53460	GLT1	18	Subnetwork1
AT4G24190	SHD	17	Subnetwork1
AT5G04140	GLU1	15	Subnetwork1
AT2G40030	NRPE1	15	Subnetwork1

基因ID号	基因编码蛋白	蛋白相互作用程度	来源
AT1G36160	ACC1	18	Subnetwork1
AT5G53460	GLT1	18	Subnetwork1
AT4G24190	SHD	17	Subnetwork1
AT5G04140	GLU1	15	Subnetwork1
AT2G40030	NRPE1	15	Subnetwork1