基于RNA-seq的番茄响应根结线虫MiPDCD6蛋白的SA信号通路基因鉴定与表达分析

doi:10.7668/hbnxb.20193473

摘要/Abstract

摘要：

为了揭示南方根结线虫MiPDCD6蛋白抑制番茄PTI免疫的分子机理,以番茄品种新金丰1号 MiPDCD6超表达苗为试验材料,以番茄品种新金丰1号组培苗为对照,通过转录组测序技术分别对番茄MiPDCD6超表达苗和对照苗进行转录组测序。以番茄栽培品种Heinz 1706基因组作为参考基因组进行对比,利用FPKM法计算基因表达量,设定参数(|log₂ FC|>1且P<0.05)筛选差异表达基因。利用Gene Ontology(GO)数据库进行差异表达基因GO功能富集分析,统计每个GO term中的差异表达基因数目,计算出基因富集的显著性,找出富集显著的功能条目。利用KEGG数据库对差异表达基因进行Pathway富集分析,超几何分布检验方法计算每个Pathway中差异表达基因富集的显著性。以FDR和基因数量来衡量KEGG的富集程度。结合基因差异表达分析和功能富集分析,研究MiPDCD6蛋白对番茄PTI免疫相关通路基因的影响。结果发现:在超表达MiPDCD6番茄植株中,与野生型番茄相比,MiPDCD6过表达番茄植株中有2 366个差异表达基因(DEGs),其中1 354个上调基因,1 012个下调基因。这些DEGs中,通过GO和KEGG注释,植物激素信号转导(sly04075)、植物-病原互作(sly04626)、植物MAPK信号通路(sly04016)和丙环素生物合成(sly00940)等KEGG通路中富集到大量的差异表达基因。SA生物合成途径包括ICS和PAL,MiPDCD6过表达番茄植株中SA合成通路PAL1和PAL-like基因以及SA信号转导途径TGA9、TGA10-like和PR1a2基因均显著下调,表明MiPDCD6基因可能抑制SA合成,从而抑制植物PTI免疫。

关键词: 番茄, 根结线虫, 转录组, 差异表达基因, SA信号通路, MiPDCD6

Abstract:

In order to reveal the molecular mechanism of MiPDCD6 protein suppressing tomato PTI immunity,the MiPDCD6 overexpression seedlings of tomato variety Xinjinfeng 1 were used as experimental materials,and the tissue culture seedlings of tomato variety Xinjinfeng 1 were used as control.Transcriptome sequencing was performed on tomato MiPDCD6 overexpressing seedlings and control seedlings,respectively.With tomato cultivars Heinz 1706,comparing the genome as a reference genome,FPKM method was used to calculate quantity of gene expression,set parameters(|log₂FC|>1 and P<0.05)in screening the differentially expressed genes(DEGs).Gene ontology(GO)database was used to analyze the GO functional enrichment of DEGs,count the number of DEGs in each GO term,calculate the significance of gene enrichment,and find out the functional term with significant enrichment.KEGG database was used for Pathway enrichment analysis of DEGs,and hypergeometric distribution test was used to calculate the significance of enrichment of DEGs in each Pathway.The enrichment degree of KEGG was measured by FDR and gene number.Combined with gene differential expression analysis and functional enrichment analysis,the effect of MiPDCD6 protein on tomato PTI immune-related pathway genes was studied.The results showed that there were 2 366 DEGs in MiPDCD6 overexpressed tomato plants compared with wild-type tomato,including 1 354 up-regulated genes and 1 012 down-regulated genes.In these DEGs,a large number of differentially expressed genes were concentrated in KEGG pathways such as plant hormone signal transduction(sly4075),plant-pathogen interaction(sly04626),plant MAPK signal pathway(sly04016)and procycloid biosynthesis(sly00940)through GO and KEGG annotation.SA biosynthesis pathways included ICS and PAL.In the MiPDCD6 overexpressed tomato plants,PAL1 and PAL-like genes in SA synthesis pathways and TGA9,TGA10-like and PR1a2 genes in SA signal transduction pathways were significantly down-regulated,suggesting that MiPDCD6 may inhibit SA synthesis thus inhibiting plant PTI immunity.

Key words: Tomato, Root knot nematode, Transcriptome, Differentially expressed genes, SA signal transduction pathways, MiPDCD6

邓小大, 袁永强, 蔡书静, 郑礼军, 徐春玲, 王新荣. 基于RNA-seq的番茄响应根结线虫MiPDCD6蛋白的SA信号通路基因鉴定与表达分析[J]. 华北农学报, 2023, 38(1): 184-195. doi: 10.7668/hbnxb.20193473.

DENG Xiaoda, YUAN Yongqiang, CAI Shujing, ZHENG Lijun, XU Chunling, WANG Xinrong. Identification and Expression Analysis of Tomato SA Signaling Pathway Genes in Response to Root Knot Nematode MiPDCD6 Protein Based on RNA-seq[J]. Acta Agriculturae Boreali-Sinica, 2023, 38(1): 184-195. doi: 10.7668/hbnxb.20193473.

http://www.hbnxb.net/CN/Y2023/V38/I1/184

图/表 14

表1 RT-qPCR引物

Tab.1 Primers used for RT-qPCR

基因名称 Gene name	引物序列(5'—3') Primer sequences(5'—3')	参考文献 References
PAL1	F: GTCAAGGCAGCTCAGAAGCT	[23]
	R: GCAAGGAATTGAAGTTCTGAGC
TGA9	F: ACGAGCAAAGCAGACGAAGA	本研究
	R: AAACTTGCCAGGGTACCACC
TGA10-like	F: GGCTTTGTTAGACAGGCGGA	本研究
	R: TATTCATGTCGAGGCCGAGC
WRKY33B	F: AATGGCTTCTTCAGGTGGAAA	本研究
	R: AAGGCGAAGCAGGTGATGTT
RIN4	F: ACCACTTCACCCCAATTCCC	本研究
	R: TCATTGTCATCCCATCCGCC
β-Actin	F: TGTCCCTATTTACGAGGGTTATGC	[24]
	R: CAGTTAAATCACGACCAGCAAGAT

表2 南方根结线虫MiPDCD6基因过表达番茄转录组测序数据统计

Tab.2 Transcriptome sequencing data of MiPDCD6 overexpression tomato

样本名 Sample name	净读数 Clean reads	序列长度/bp Sequence length	GC含量/% GC	Q20/%	Q30/%
WT1	24 143 599	150	42	99.991 20	98.645 45
WT2	23 297 585	150	42	99.991 13	98.709 50
OE1	16 287 433	150	42	99.988 38	98.524 16
OE2	19 089 630	150	42	99.990 79	98.501 17

表3 南方根结线虫MiPDCD6过表达番茄转录组测序基因数量统计分析

Tab.3 Statistical analysis of transcriptome sequencing genes from MiPDCD6 overexpressed tomato

样本 Sample	已知基因数 Number of known genes	新基因数 Number of novel genes	已知转录本数 Number of known transcripts	新转录本数 Number of novel transcripts
WT1	22 490	1 791	31 497	13 337
WT2	22 473	1 774	31 296	13 129
OE1	22 556	1 811	31 929	13 100
OE2	23 024	1 824	32 884	13 114

图1 南方根结线虫MiPDCD6过表达番茄转录组测序基因表达水平检测 A.基因表达水平FPKM值5个范围内基因表达数量;B.4个样品间基因表达水平的log₂(FPKM+1)值箱线图。

Fig.1 Detection of gene expression level of transcriptome from MiPDCD6 overexpression tomato A.The number of gene expression within five ranges of FPKM value of gene expression level;B.Boxplot of log₂(FPKM+1)values of gene expression levels among 4 samples.

图2 南方根结线虫MiPDCD6过表达番茄转录组测序4个样本相关性分析 A.Spearman相关性热图;B.Pearson相关性热图。

Fig.2 Correlation analysis of transcriptome sequences from four samples related to MiPDCD6 overexpression tomato A.Spearman correlation heat map;B.Pearson correlation heat map.

图3 南方根结线虫MiPDCD6过表达番茄转录组测序差异表达基因分析 A.差异表达基因统计柱状图。B.差异表达基因火山图:红色表示上调基因,蓝色表示下调基因,灰色表示无显著性差异表达的基因,每一个点表示一个基因,横坐标为某一个基因在两样品中表达量差异倍数的对数值(log₂(FC));纵坐标为基因表达量变化的统计学显著性的负对数值(-log₁₀(P-value))。C.差异基因聚类分析,每一列表示一个样品,每一行表示一个DEG,橙色表示上调,蓝色表示下调。

Fig.3 Analysis of differentially expressed genes of transcriptome from MiPDCD6 overexpression tomato A.Statistical histogram of differentially expressed genes.B.Volcano map of differentially expressed genes:red represents up-regulated genes,blue represents down regulated genes,gray represents genes with no significant differential expression,each point represents a gene,and the abscissa is the logarithm of the difference multiple of the expression of a certain gene in the two samples(log₂ (FC));the ordinate is the negative logarithm(-log₁₀(P-value))of the statistical significance of the change in gene expression.C.For differential gene cluster analysis,each column represents a sample,each row represents a DEG,orange represents up regulation,and blue represents down regulation.

图4 南方根结线虫MiPDCD6过表达番茄转录组差异表达基因GO term分析

Fig.4 GO term analysis of different expressed genes in the transcriptom from MiPDCD6 overexpressed tomato

表4 南方根结线虫MiPDCD6过表达番茄植株DEG的KEGG通路富集分析

Tab.4 Results of KEGG pathway enrichment analysis of DEG from MiPDCD6 overexpression tomato plant

通路号 KO ID	通路名称 Pathway name	基因比例 Gene ratio	校正后P值 P-adjust
sly00196	光合作用-天线蛋白	21/934	0.000 000 000 487 6
sly00195	光合作用	41/934	0.000 000 003 452 6
sly04016	植物MAPK信号通路	67/934	0.000 000 190 593 6
sly04626	植物-病原互作	70/934	0.000 007 169 939 6
sly04075	植物激素信号转导	72/934	0.003 692 774 659 5
sly00860	卟啉和叶绿素代谢	18/934	0.024 461 163 393 7
sly00561	甘油酯代谢	24/934	0.059 662 578 388 4
sly00940	苯丙酸生物合成	56/934	0.060 904 395 160 7
sly00564	甘油磷脂代谢	29/934	0.068 028 570 366 4
sly00270	半胱氨酸和蛋氨酸代谢	31/934	0.153 741 213 184 3
sly00073	角质、软木脂和蜡的生物合成	12/934	0.153 741 213 184 3
sly00910	氮代谢	11/934	0.227 817 972 577 2
sly00400	苯丙氨酸酪氨酸和色氨酸	14/934	0.325 873 798 172 2
sly00906	类胡萝卜素生物合成	11/934	0.338 278 128 256 7
sly00920	硫代谢	11/934	0.338 278 128 256 7
sly03440	同源重组	15/934	0.338 278 128 256 7
sly00500	淀粉和蔗糖代谢	35/934	0.345 821 690 083 9
sly00450	硒化合物代谢	6/934	0.430 445 770 585 5

图5 南方根结线虫MiPDCD6过表达番茄差异表达基因KEGG 通路分析差异表达基因KEGG Pathway功能分析点图;P-adjust是校正后的P-value,P-adjust值越小表示富集越显著。

Fig.5 Analysis of KEGG pathway of differential expression gene from MiPDCD6 overexpressed tomato plant Functional analysis point diagram of differentially expressed gene KEGG pathway;P-adjust is the corrected P-value,the smaller the P-adjust value the more significant the enrichment.

图6 MiPDCD6过表达番茄植物-病原互作途径DEG热图

Fig.6 DEG heat map of plant pathogen interaction pathway in MiPDCD6 overexpression tomato

图7 MiPDCD6过表达番茄苯丙氨酸、酪氨酸和色氨酸生物合成途径DEG热图

Fig.7 DEG heat map of biosynthesis pathway of phenylalanine,tyrosine and tryptophan in MiPDCD6 overexpressed tomato

图8 MiPDCD6过表达番茄苯丙酸生物合成KEGG途径DEG热图

Fig.8 DEG heat map of phenylpropionic acid biosynthesis KEGG pathway in overexpressing MiPDCD6 tomato

图9 MiPDCD6过表达番茄植物激素信号转导途径DEG热图

Fig.9 DEG heat map of hormone signaling pathways in MiPDCD6 overexpressed tomato

图10 MiPDCD6过表达番茄差异表达基因RT-qPCR验证数据采用SPSS软件进行显著性分析,a、b和c表示在P<0.05水平上差异显著(Duncan's test)。

Fig.10 RT-qPCR of some differently expressed genes from MiPDCD6 overexpression tomato Data were analyzed by SPSS software for significance;a,b and c indicated significant difference at P<0.05(Duncan's test).

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