基于RNA-seq的番茄青枯病响应基因鉴定与表达分析

doi:10.7668/hbnxb.20192621

摘要/Abstract

摘要：

为了挖掘番茄青枯病抗性基因,对青枯菌侵染前后的不同番茄自交系进行转录组测序(RNA-seq)。结果发现,在12个样本中共获得75.02 Gb的高质量数据,以差异倍数(FC)≥2且错误发现率(FDR)<0.01为标准,在抗、感番茄中分别获得970,695个差异表达基因(DEGs),共计1 312个,占基因总数的3.71%。其中,上调基因数目分别为457,450个,共计693个;下调基因数目分别为513,245个,共计621个。这些DEGs中,有836个材料特异DEGs。通过GO和KEGG注释,这些DEGs主要分为代谢、调控、响应、结合和催化等47个功能组和DNA复制、次生物质合成、植物-病原物互作、信号转导等88个代谢通路,涉及4个NBS类抗病基因、6个植病互作基因、11个植物激素信号转导基因、22个防御反应基因、32个蛋白激酶、65个转录因子和多个其他重要功能基因,表明这些基因在响应Rs方面扮演着重要角色。启动子分析发现,这些基因含有多个防御与胁迫响应相关元件。选取50个代表基因进行RT-qPCR验证,发现超过1/2的基因表达变化趋势与RNA-seq结果一致。Solyc02g086980.3和Solyc04g011670.3可能参与抗病反应,Solyc01g073985.1、Solyc09g092580.4、Solyc09g098100.4和Solyc10g081300.1可能参与感病反应。这些基因表达谱有助于认识番茄青枯病抗性分子基础,进而加快基因改良和分子育种应用。

关键词: 番茄, 青枯菌, 转录组, 差异表达基因, 基因注释, 定量表达

Abstract:

To explore bacterial wilt resistance genes,RNA sequencing was used to characterize the transcriptomes of resistant and susceptible tomato inbred lines with Ralstonia solanacearum inoculation(RsI).The results showed that a total of 75.02 Gb high-quality data were generated in 12 libraries.With the fold change(FC)≥2 and false discovery rate(FDR)<0.01 as the standard,970 and 695 differentially expressed genes(DEGs)were identified in the two tomato lines,respectively.The 1 312 DEGs accounted for 3.71% of the total.Among them,the numbers of up-regulated genes were 457 and 450,respectively,totaling 693;the numbers of down-regulated genes were 513 and 245,respectively,totaling 621.Among these DEGs,836 genotype-specific DEGs were highlighted.These DEGs were mainly divided into 47 functional groups such as metabolism,regulation,response,binding,and catalysis,and 88 metabolic pathways such as DNA replication,secondary metabolite synthesis,plant-pathogen interaction,and signal transduction by GO and KEGG annotation.Specifically,4 NBS resistance genes,6 plant-pathogen interaction genes,11 plant hormone signal transduction genes,22 defense response genes,32 protein kinases,65 transcription factors,and several other important functional genes were involved,indicating that they played important roles in response to Rs.Promoter analysis revealed that these genes possessed multiple defense and stress response elements.The output was confirmed using RT-qPCR for 50 representative genes.It was found that more than half of the genes were consistent with RNA-seq in expression.Solyc02g086980.3 and Solyc04g011670.3 might be involved in the resistance response,whereas Solyc01g073985.1,Solyc09g092580.4,Solyc09g098100.4,and Solyc10g081300.1 might be the opposite.Together,these gene expression profiles serve as fundamental information to understand the potential molecular basis in the response to Rs in tomato,and facilitate the application of related resistance genes in breeding.

Key words: Tomato, Ralstonia solanacearum, Transcriptome, Differentially expressed genes, Gene annotation, Quantitative expression

史建磊, 熊自立, 苏世闻, 王克磊, 宰文珊. 基于RNA-seq的番茄青枯病响应基因鉴定与表达分析[J]. 华北农学报, 2022, 37(2): 171-182. doi: 10.7668/hbnxb.20192621.

SHI Jianlei, XIONG Zili, SU Shiwen, WANG Kelei, ZAI Wenshan. Identification and Expression Analysis of Bacterial Wilt Response Genes Based on RNA-seq in Tomato[J]. Acta Agriculturae Boreali-Sinica, 2022, 37(2): 171-182. doi: 10.7668/hbnxb.20192621.

http://www.hbnxb.net/CN/Y2022/V37/I2/171

图/表 11

表1 部分RT-qPCR引物

Tab.1 Part of the primers used for RT-qPCR

基因 Gene	正向引物(5'—3') Forward primer	反向引物(5'—3') Reverse primer
SlRPL2	GTCATCCTTTCAGGTACAAGCA	CGTTACAAACAACAGCTCCTTC
Solyc01g073985.1	GTTGGCTCGTGGAGGATGAT	TGCTGGCTGCTTCACTTCA
Solyc02g086980.3	GCGTTGAGTTAGGCAGTAAGG	CTAGAAGATGATCCAGTGAGTGAGA
Solyc04g011670.3	CATTATCGTTGATGGTTGCCTGAA	GCGTTCTGCTGATGTCTTCC
Solyc09g092580.4	CAAGCCGCCACTTCACAA	GCCAACATTTCTTCCGTCACT
Solyc09g098100.4	GCGAACAAGTCAAGTGCCATAC	TTCACCTCATTCCACCAAGATTCT
Solyc10g081300.1	TCCAAGCCTAAATTCATCCCACAT	TCCTCCAACATCTTCACATTCTTCA

表2 番茄各样本RNA测序数据统计

Tab.2 RNA sequencing data statistics of tomato libraries

样本 Libraries	净读数 Clean reads	净碱基数/Gb Clean bases	GC含量/% GC content	Q30/%
RC02	40 564 140	6.07	43.72	94.82
RC13	46 173 674	6.90	43.73	94.81
RC14	48 085 886	7.18	43.79	95.01
RT06	45 753 134	6.83	43.74	94.56
RT17	41 260 090	6.17	43.27	94.97
RT18	39 092 480	5.84	43.79	94.61
SC04	41 490 160	6.21	44.17	94.98
SC15	43 627 624	6.51	44.10	94.40
SC16	38 440 746	5.74	43.78	94.85
ST08	38 380 600	5.73	43.97	94.13
ST19	39 741 206	5.94	43.78	94.78
ST20	39 487 202	5.90	44.09	94.57

表3 番茄各样本Clean reads与参考基因组比对

Tab.3 Comparing Clean reads onto the reference genome in each tomato library

样本 Libraries	比对读数 Mapped reads	唯一比对读数 Uniquely mapped reads	多比对读数 Multiple mapped reads	峰值片段大小/bp Insert size peak
RC02	38 673 468 (95.34%)	37 000 978 (91.22%)	1 672 490 (4.12%)	298
RC13	43 965 762 (95.22%)	42 226 315 (91.45%)	1 739 447 (3.77%)	298
RC14	45 679 708 (95.00%)	43 498 262 (90.46%)	2 181 446 (4.54%)	292
RT06	43 520 979 (95.12%)	41 628 854 (90.99%)	1 892 125 (4.14%)	298
RT17	39 471 364 (95.66%)	38 040 850 (92.20%)	1 430 514 (3.47%)	286
RT18	37 279 419 (95.36%)	35 490 584 (90.79%)	1 788 835 (4.58%)	298
SC04	39 648 351 (95.56%)	37 777 814 (91.05%)	1 870 537 (4.51%)	298
SC15	41 661 217 (95.49%)	39 393 711 (90.30%)	2 267 506 (5.20%)	298
SC16	37 020 893 (96.31%)	35 358 525 (91.98%)	1 662 368 (4.32%)	281
ST08	36 769 537 (95.80%)	34 961 451 (91.09%)	1 808 086 (4.71%)	298
ST19	38 083 435 (95.83%)	36 273 601 (91.27%)	1 809 834 (4.55%)	298
ST20	37 682 695 (95.43%)	35 757 215 (90.55%)	1 925 480 (4.88%)	298

表4 生物学重复样本的相关性

Tab.4 Correlation between biological replicates

样本 Libraries	RC02	RC13	RC14	RT06	RT17	RT18	SC04	SC15	SC16	ST08	ST19	ST20
RC02	1.000
RC13	0.982	1.000
RC14	0.992	0.960	1.000
RT06	0.959	0.928	0.969	1.000
RT17	0.947	0.940	0.943	0.964	1.000
RT18	0.952	0.907	0.968	0.993	0.947	1.000
SC04	0.975	0.949	0.968	0.947	0.907	0.942	1.000
SC15	0.966	0.915	0.982	0.957	0.892	0.963	0.969	1.000
SC16	0.985	0.951	0.987	0.955	0.918	0.953	0.989	0.987	1.000
ST08	0.960	0.916	0.971	0.985	0.927	0.986	0.969	0.977	0.972	1.000
ST19	0.957	0.914	0.969	0.990	0.948	0.991	0.951	0.968	0.963	0.991	1.000
ST20	0.968	0.921	0.978	0.981	0.934	0.986	0.967	0.983	0.979	0.993	0.993	1.000

表5 差异表达基因数目

Tab.5 Number of differentially expressed genes

差异表达基因集 DEG set	DEG数目 DEG number	上调基因 Up-regulated DEGs	下调基因 Down-regulated DEGs
RC vs RT	970	457	513
SC vs ST	695	450	245
RC vs SC	741	225	516
RT vs ST	644	316	328

表6 差异表达基因的模式分布

Tab.6 Pattern distribution of differentially expressed genes

基因表达模式 Gene expression pattern	RC vs RT Up	RC vs RT Down	RC vs RT Normal
SC vs ST Up	214	2	216
SC vs ST Down	0	137	104
SC vs ST Normal	198	316	125

图1 差异表达基因GO注释
1.代谢过程;2.细胞过程;3.单生物体过程;4.生物调控;5.刺激响应;6.定位;7.细胞组成与发生;8.信号;9.发育过程 ;10.多细胞生物体过程;11.生殖过程;12.生物群体过程;13.生长;14.繁殖;15.免疫系统过程;16.细胞死亡;17.节律过程;18.移动;19.生物粘附;20.细胞;21.细胞部分;22.膜;23.细胞器;24.膜部分;25.细胞器部分;26.大分子复合物;27.膜内腔;28.胞间区;29.细胞连接;30.共质体;31.胞间区部分;32.颗粒;33.颗粒部分;34.类核;35.结合;36.催化活性;37.转运活性;38.核酸结合转录因子活性;39.结构分子活性;40.电子载体活性;41.分子传导活性;42.信号传导活性;43.抗氧化活性;44.转录因子活性-蛋白结合;45.养分存储活性;46.蛋白质标签;47.金属伴侣活性。

Fig.1 GO annotation of differentially expressed genes
1.Metabolic process;2.Cellular process;3.Single-organism process;4.Biological regulation;5.Response to stimulus;6.Localization;7.Cellular component organization or biogenesis;8.Signaling;9.Developmental process;10.Multicellular organismal process;11.Reproductive process;12.Multi-organism process;13.Growth;14.Reproduction;15.Immune system process;16.Cell killing;17.Rhythmic process;18.Locomotion;19.Biological adhesion;20.Cell;21.Cell part;22.Membrane;23.Organelle;24.Membrane part;25.Organelle part;26.Macromolecular complex;27.Membrane-enclosed lumen;28.Extracellular region;29.Cell junction;30.Symplast;31.Extracellular region part;32.Virion;33.Virion part;34.Nucleoid;35.Binding;36.Catalytic activity;37.Transporter activity;38.Nucleic acid binding transcription factor activity;39.Structural molecule activity;40.Electron carrier activity;41.Molecular transducer activity;42.Signal transducer activity;43.Antioxidant activity;44.Transcription factor activity, protein binding;45.Nutrient reservoir activity;46.Protein tag;47.Metallochaperone activity.

图2 差异表达基因KEGG注释(A)与富集(B)

Fig.2 KEGG annotation(A)and enrichment(B)of differentially expressed genes

图3 植病互作通路差异表达基因KEGG富集

Fig.3 KEGG enrichment of differentially expressed genes in the plant-pathogen interaction pathway

图4 74个DEGs启动子响应元件
A.已知基因;B.新基因。

Fig.4 Promoter responsive elements in 74 selected differentially expressed genes
A.Known genes;B.New genes.

图5 抗感番茄6个DEGs青枯菌侵染下的相对表达量
R和S分别表示抗病和感病番茄。不同大小写字母分别表示0.01和0.05水平下的差异显著性。

Fig.5 Relative expression levels of six vital DEGs in the resistant and susceptible tomato lines with RsI
R and S represent resistant and susceptible tomato lines,respectively.Different upper and lowercase letters indicate statistically significant differences at the 0.01 and 0.05 level,respectively.

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