Integrated analysis of transcriptome sequencing and metabolomics provides insights into the molecular response of Solanum tuberosum cv. Cooperation 88 to Potato virus S
The results suggest that the flavonoid biosynthesis pathway in potatoes plays a key role in responding to PVS infection and promotes the selection and utilization of disease-resistant varieties.
Abstract
Introduction Potato virus S (PVS), is an important member of the genus Carlavirus in the family Betaflexiviridae, is a significant pathogen in potatoes worldwide. Previous studies have found it to be the most frequently detected virus in potatoes in China. However, research data on the response mechanisms of potatoes to PVS remain extremely scarce. Methods Here, comparative transcriptomics and metabolomics were performed on potato (Solanum tuberosum cv. Cooperation 88) leaves to elucidate the response mechanisms underlying the infection of Potato virus S to Solanum tuberosum cv. Cooperation 88 at the molecular level. Results A total of 588 significantly differentially expressed genes (SDEGs) were identified post-infection, including 161 upregulated genes and 427 downregulated genes, primarily enriched in biological processes such as the MAPK signaling pathway, plant hormone signal transduction, phenylpropanoid metabolism, and DNA replication. Metabolomic analysis revealed 1,313 and 880 differential metabolites detected in positive and negative ion modes, respectively, with flavonoids showing a significant accumulation trend. Integrated analysis indicated that the phenylpropanoid metabolic pathway (particularly the flavonoid biosynthesis pathway) plays a central regulatory role in antiviral responses. Real-time quantitative PCR validation further confirmed that the expression patterns of key genes (e.g., PAL, C4H, 4CL) were positively correlated with metabolite accumulation. Conclusion The results suggest that the flavonoid biosynthesis pathway in potatoes plays a key role in responding to PVS infection. This study not only helps to deeply understand the interaction mechanism between PVS and potatoes, but also promotes the selection and utilization of disease-resistant varieties.
The combined transcriptome and metabolome analysis revealed that plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis were significantly enriched in resistant rice varieties, providing valuable information on the molecular mechanisms by which rice defends against U. virens infection.
Rongtao Fu, Huan Li, Xi Luo et al.· BMC Plant Biology· 0 citations
Tomato mottle mosaic virus (ToMMV) is an emerging tobamovirus causing severe losses in tomato production. To elucidate host resistance mechanisms, we compared two tomato cultivars with contrasting responses to ToMMV using integrated transcriptomic, metabolomic, and functional analyses. The resistant line (R) carried resistance gene Tm‑2² at extremely low levels, while the susceptible line (S) did not; both lines highly expressed susceptibility gene tm-2. R plants exhibited minimal viral accumulation and maintained chlorophyll levels, whereas S plants showed high viral load and chlorophyll degradation. Multi-omics revealed that in S, ToMMV primarily disrupted chlorophyll biosynthesis and photosynthesis, while activating multiple defense pathways, including plant-pathogen interaction, phenylpropanoid/flavonoid biosynthesis, and MAPK signaling. In R, a broader activation of plant-pathogen interaction and phosphatidylinositol signaling pathways was observed, alongside early upregulation of SlSN2. The abundance of phenolic acids, notably caffeic acid, ferulic acid, and sinapic acid, was significantly higher in R than in S. Integrated transcriptomic and metabolomic analyses showed that both differential genes and metabolites were co-enriched in the phenylpropanoid biosynthesis pathway. Functional assays demonstrated that SlSN2 overexpression suppressed ToMMV accumulation and infection, likely via enhanced lignin biosynthesis. These findings suggest a potential role for SlSN2 in contributing to ToMMV resistance, independent of the known Tm‑2² pathway. This work identifies SlSN2 as a candidate factor for further evaluation in the prevention of ToMMV.
Tobacco is a model plant as well as an important economic crop. Black shank disease, caused by Phytophthora nicotianae, severely undermines tobacco yield and quality, yet the molecular basis of differential cultivar resistance remains incompletely understood. Here, we compared the resistant cultivar, 'Xiangyan 7' (X7) and the susceptible cultivar 'Honghuadajinyuan' (HD), after inoculation with P. nicotianae race 0. Disease evaluation showed that X7 had a significantly lower disease index than HD. Transcriptomic and metabolomic analyses were performed on leaves collected at 0, 1, 2, 4, 8, and 12 days post-inoculation (dpi). RNA-seq identified extensive transcriptional responses in both cultivars; the inter-cultivar differentially expressed gene (DEG) number peaked at 8 dpi with 14,160 DEGs (7057 up-regulated and 7103 down-regulated). Widely targeted metabolomics detected 1092 metabolites, and the inter-cultivar differentially accumulated metabolite (DAM) number peaked at 12 dpi with 355 DAMs (95 up-regulated and 260 down-regulated). Weighted Gene Co-expression Network Analysis (WGCNA) identified 593 hub genes from three resistance-associated modules (Coral3, Lightblue3, and Lavender). Integrated Kyoto Encyclopedia of Genes and Genomes (KEGG) co-enrichment analysis revealed that phenylpropanoid biosynthesis, biosynthesis of secondary metabolites, and plant hormone signal transduction were common transcriptional-metabolic pathways enriched in X7, together with early calcium-related signaling in the plant-pathogen interaction pathway. These results suggest that the stronger resistance to P. nicotianae by X7 is associated with rapid coordination of defense-related transcription, phenylpropanoid and flavonoid metabolism, hormone signaling, and suppression of photosynthesis and primary metabolism. Our study provides multi-omics resources and candidate genes, including Nitab4.5_0000101g0110, Nitab4.5_0000101g0120, Nitab4.5_0001915g0140, and Nitab4.5_0002942g0040, for improving tobacco resistance to black shank disease.
Guo Li, Changjiang Zhang, Bei Yu et al.· Plant physiology and biochem...· 0 citations
Rice (Oryza sativa L.) is a crucial global cereal crop, severely threatened by the brown planthopper (BPH), which causes extensive damage through direct feeding and virus transmission. To elucidate the resistance mechanism mediated by the BPH-resistance gene Bph6, metabolic responses to BPH infestation were compared between the resistant rice line G6 and the susceptible cultivar Nipponbare using LC-MS-based metabolomics combined with quantitative real-time PCR analysis. The Bph6 gene conferred both antixenotic and antibiotic resistance to BPH. A total of 673 metabolites were identified across all samples. BPH infestation induced more pronounced metabolic alterations in susceptible Nipponbare than in the resistant G6 line. Compared with Nipponbare, G6 exhibited a more coordinated defense response characterized by enhanced accumulation of amino acid-derived metabolites, flavonoids, and serotonin-associated compounds. Consistently, the expression levels of key biosynthetic genes, including TDC and CYP71A1 involved in serotonin biosynthesis and CHS and F3H associated with flavonoid biosynthesis, were significantly upregulated in G6. These findings demonstrate that Bph6 mediates a more stable and effective defense metabolism in rice through coordinated regulation of primary and secondary metabolism, particularly flavonoid- and serotonin-related pathways.
Jiajiao Zhang, Qian Zhang, Yinhua Ma et al.· Functional Plant Biology· 0 citations
These findings provide the first comprehensive evidence that alkaloid metabolism, particularly the isoquinoline alkaloid pathway, are transcriptionally and metabolically reprogrammed during blister blight infection, suggesting a potential role in tea’s defense against this pathogen.
Yanglongyu Chen, Ping Li, Yuqing Ma et al.· Frontiers in Plant Science· 0 citations
Magnoliae Flos (MF)
, the dried flower buds of
Magnolia denudata
Desr.,
Magnolia biondii
Pamp., and
Magnolia sprengeri
Pamp., is a crucial East Asian medicinal herb used to treat allergic rhinitis and other ailments. However, the molecular basis for its quality differences remains unclear.
This study integrates GC-MS-based volatile metabolomics, high-throughput RNA sequencing, and RT-qPCR validation to elucidate the terpenoid metabolic differences and their regulatory mechanisms among the three
MF
varieties.
The metabolomic analysis screened 55 differential terpenoids (15 key markers) that distinguish the
MF
varieties, with terpenoids being the primary metabolic category and the
M. sprengeri
vs.
M. biondii
group exhibiting the most differential metabolites. The transcriptomic analysis revealed
TPS26
as key candidate genes involved in monoterpene synthesis, while IMPMBI2G0000034954 and IMPMBI2G0000034957 were identified as candidate genes for sesquiterpene synthesis. The expression abundances of these genes exhibited significant linear correlations with the accumulation levels of differential terpenoids, though such coordinated variation does not confirm direct causal regulation.
Collectively, this work reveals the molecular basis of terpenoid diversity in
MF
, and provides theoretical references for germplasm discrimination, quality evaluation and genetic improvement of medicinal magnolia resources.
Rui Ma, Hong-Dan Liu, Weimeng Feng et al.· Frontiers in Plant Science· 0 citations