Table3_Transcriptome analysis of two pepper genotypes infected with pepper mild mottle virus.XLSX

Pepper mild mottle virus (PMMoV) poses a significant threat to pepper production because it is highly contagious and extremely persistent in soil. Despite this threat, little is known about the molecular processes that underlie plant responses to pepper mild mottle virus. Here, we performed RNA sequencing of tolerant (“17-p63”) and susceptible (“16-217”) pepper genotypes after pepper mild mottle virus or mock inoculation. Viral accumulation in systemic leaves was lower in the pepper mild mottle virus-resistant 17-p63 genotype than in the pepper mild mottle virus-sensitive 16-217 genotype, and infection symptoms were more apparent in systemic leaves of 16-217 than in those of 17-p63 at the same timepoints during the infection process. We identified 2,959 and 2,159 differentially expressed genes (DEGs) in systemic leaves of infected 16-217 and 17-p63, respectively. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes from both genotypes revealed significant enrichment of the MAPK signaling pathway, plant–pathogen interaction, and flavonoid biosynthesis. A number of differentially expressed genes showed opposite trends in relation to stress resistance and disease defense in the two genotypes. We also performed weighted gene co-expression network analysis (WGCNA) of all samples and identified modules associated with resistance to pepper mild mottle virus, as well as seven hub genes. These results identify candidate virus resistance genes and provide insight into pepper defense mechanisms against pepper mild mottle virus.

辣椒轻斑驳病毒（Pepper mild mottle virus, PMMoV）对辣椒生产构成严重威胁，因其传染性极强且在土壤中存活期极长。尽管存在此类威胁，但学界对植物应对该病毒的分子机制仍知之甚少。本研究对感染辣椒轻斑驳病毒或经模拟接种后的耐病辣椒基因型“17-p63”与感病辣椒基因型“16-217”进行了RNA测序。病毒在系统叶片中的积累量在耐病的17-p63基因型中低于感病的16-217基因型；在侵染过程的同一时间点，16-217的系统叶片上的侵染症状也比17-p63更为显著。本研究分别在受侵染的16-217与17-p63的系统叶片中鉴定出2959个和2159个差异表达基因（differentially expressed genes, DEGs）。通过对两个基因型的差异表达基因进行基因本体论（Gene Ontology, GO）与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）富集分析，发现MAPK信号通路、植物-病原体互作以及黄酮类生物合成通路均显著富集。两个基因型中，部分差异表达基因在胁迫抗性与病害防御相关过程中呈现出截然相反的表达趋势。本研究还对所有样本进行了加权基因共表达网络分析（weighted gene co-expression network analysis, WGCNA），鉴定出与辣椒轻斑驳病毒抗性相关的基因模块以及7个核心基因。本研究结果鉴定出潜在的病毒抗性候选基因，并为解析辣椒应对辣椒轻斑驳病毒的防御机制提供了新的见解。