烟草抗感南方根结线虫品种根部差异表达mRNA的PPI网络分析

doi:10.16178/j.issn.0528-9017.20221179

浙江农业科学 ›› 2024, Vol. 65 ›› Issue (2): 395-400.DOI: 10.16178/j.issn.0528-9017.20221179

烟草抗感南方根结线虫品种根部差异表达mRNA的PPI网络分析

陈小翔¹(), 张文军², 翟争光², 徐志强¹, 刘化冰¹, 钟永健¹, 江智敏¹^,^*()

1.浙江中烟工业有限责任公司技术开发分公司,浙江杭州 310008
2.湖南省烟草公司长沙市公司,湖南长沙 410000

收稿日期:2022-11-18 出版日期:2024-02-11 发布日期:2024-02-28
通讯作者: 江智敏(1972—),男,本科,工程师,研究方向为烟草原料生产与加工,E-mail:jiangzhimin@zjtobacco.com。
作者简介:江智敏(1972—),男,本科,工程师,研究方向为烟草原料生产与加工,E-mail:jiangzhimin@zjtobacco.com。
陈小翔(1966—),男,浙江江山人,本科,工程师,研究方向为烟叶生产与加工,E-mail:chenxx@zjtobacco.com。
基金资助:
中国烟草总公司河南省公司重点项目(2021410000240021);河南省烟草公司许昌市公司重点项目(2020411000240069);贵州省烟草公司贵阳市公司重点项目(2020-07);湖南省烟草公司长沙市公司重点项目(21-23A04);广西壮族自治区烟草公司百色市公司(202145100020165);福建省烟草公司南平市公司(NYK2021-09-03)

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

Xiaoxiang CHEN¹(), Wenjun ZHANG², Zhengguang ZHAI², Zhiqiang XU¹, Huabing LIU¹, Yongjian ZHONG¹, Zhimin JIANG¹^,^*()

1. Technology Development Branch, China Tobacco Zhejiang Industrial Co., Ltd., Hangzhou 310008, Zhejiang
2. Changsha Branch of Hunan Provincial Tobacco Company, Changsha 410000, Hunan

Received:2022-11-18 Online:2024-02-11 Published:2024-02-28
Contact: Zhimin JIANG

摘要/Abstract

摘要：

基于品种间的差异表达基因,选取烟草抗病品种K326与感病品种长脖黄为试验材料,利用生物信息学分析方法筛选出与抗感染相关的关键基因,通过蛋白互作网络分析(Protein-Protein Interaction,PPI)以及 Gene Ontology(GO)功能分类分析(包括Biological Process分析与 KEGG 通路分析)对差异表达基因进行生物学功能注释,并找出PPI网络中的重要基因以及作用通路一致的基因,并对这些基因加以解析,以明确抗南方根结线虫烟草品种抗性机制,为研究烟草抗南方根结线虫的分子机制提供理论依据。结果表明,差异表达基因主要在细胞代谢、胞内体转运、RNA介导的基因沉默等9条与抗感染相关的通路中显著富集,并且筛选出Fab1b、Fab1c、Fab1d、Glu1、Dcl1、Dcl2、Dcl4共7个同时构成PPI网络的关键基因。

关键词: 烟草, 南方根结线虫, PPI网络分析, GO分类, 关键基因

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

中图分类号:

S572

陈小翔, 张文军, 翟争光, 徐志强, 刘化冰, 钟永健, 江智敏. 烟草抗感南方根结线虫品种根部差异表达mRNA的PPI网络分析[J]. 浙江农业科学, 2024, 65(2): 395-400.

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.

图/表 4

表1 GO功能(BP)分类中差异基因显著富集通路Top9

Table 1 Significant enrichment pathway of differential genes in GO function (BP) classification Top9

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

图1 PPI网络中的subnetwork1 红色节点代表上调蛋白,绿色节点代表下调蛋白;颜色间差异代表基因表达水平差异程度,其中颜色越深代表基因表达水平差异越大; 面积的大小代表互作程度的高低,其中面积越大表示互作程度越高。

Fig.1 Subnetwork1 in PPI network

图2 PPI Subentwork1功能模块分析 “P-value”表示模块的显著性,P<0.05表示差异显著,不同的“COLOR”表示不同的模块。

Fig.2 PPI Subentwork1 functional module analysis

表2 Subnetwork中蛋白互作程度最高的5个Hub node

Table 2 The 5 Hub nodes with the highest degree of protein interaction in the subnetwork

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

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烟草抗感南方根结线虫品种根部差异表达mRNA的PPI网络分析

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

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