Transcriptome and metabolome analyses revealed the response mechanism of pepper roots to Phytophthora capsici infection.

Phytophthora root rot caused by the oomycete Phytophthora capsici is the most devastating disease in pepper production worldwide, and current management strategies have not been effective in preventing this disease. Therefore, the use of resistant varieties was regarded as an important part of disease management of P. capsici. However, our knowledge of the molecular mechanisms underlying the defense response of pepper roots to P. capsici infection is limited. A comprehensive transcriptome and metabolome approaches were used to dissect the molecular response of pepper to P. capsici infection in the resistant genotype A204 and the susceptible genotype A198 at 0, 24 and 48 hours post-inoculation (hpi). More genes and metabolites were induced at 24 hpi in A204 than A198, suggesting the prompt activation of defense responses in the resistant genotype, which can attribute two proteases, subtilisin-like protease and xylem cysteine proteinase 1, involved in pathogen recognition and signal transduction in A204. Further analysis indicated that the resistant genotype responded to P. capsici with fine regulation by the Ca2+- and salicylic acid-mediated signaling pathways, and then activation of downstream defense responses, including cell wall reinforcement and defense-related genes expression and metabolites accumulation. Among them, differentially expressed genes and differentially accumulated metabolites involved in the flavonoid biosynthesis pathways were uniquely activated in the resistant genotype A204 at 24 hpi, indicating a significant role of the flavonoid biosynthesis pathways in pepper resistance to P. capsici. The candidate transcripts may provide genetic resources that may be useful in the improvement of Phytophthora root rot-resistant characters of pepper. In addition, the model proposed in this study provides new insight into the defense response against P. capsici in pepper, and enhance our current understanding of the interaction of pepper-P. capsici.

Lei G ，Zhou KH ，Chen XJ ，Huang YQ ，Yuan XJ ，Li GG ，Xie YY ，Fang R ... -  《BMC GENOMICS》

The dynamic transcriptome of pepper (Capsicum annuum) whole roots reveals an important role for the phenylpropanoid biosynthesis pathway in root resistance to Phytophthora capsici.

Phytophthora root rot, caused by the soilborne oomycete pathogen Phytophthora capsici (Leon.), is a devastating disease causing significant losses in pepper production worldwide. To uncover the mechanism of root-mediated resistance to P. capsici we elucidated the dynamic transcriptome of whole pepper roots of the resistant accession CM334 and the susceptible accession NMCA10399 after P. capsici infection at 0, 12 and 36 hpi using RNA-Seq method. We detected that the roots of the resistant CM334 and the susceptible NMCA10399 had different transcriptional responses to P. capsici, suggesting the former activated a response to P. capsici earlier than the latter. KEGG enrichment analysis showed the pathways involved in the synthesis of secondary metabolites were those in which the most DEGs were enriched. Focusing on the gene regulation of phenylpropanoid biosynthesis-related genes, we found genes related to the key enzyme phenylalanine ammonia-lyase (PAL) were activated earlier with greater changes in the resistant accession than in the susceptible one. Moreover, genes related to cinnamoyl-CoA reductase (CCR1) were also upregulated in resistant roots but downregulated with great folder changes in susceptible roots. Briefly, we inferred that the phenylpropanoid biosynthesis pathway, especially cinnamaldehyde and lignin derived from its branches, played significant roles in pepper root resistance to P. capsici. These results provide new insight into root-mediated resistance to P. capsici in pepper.

Li Y ，Yu T ，Wu T ，Wang R ，Wang H ，Du H ，Xu X ，Xie D ，Xu X ... -  《-》

Transcriptional regulation of hormone signalling genes in black pepper in response to Phytophthora capsici.

Black pepper (Piper nigrum L.) is a non-model spice crop of significant agricultural and biological importance. The 'quick wilt' disease caused by the oomycete Phytophthora capsici is a major threat, leading to substantial crop loss. The molecular mechanisms governing the plant immune responses to this pathogen remain unclear. This study employs RNA sequencing and transcriptome analysis to explore the defense mechanisms of P. nigrum against P. capsici. Two-month-old P. nigrum plantlets were subjected to infection with P. capsici, and leaf samples were collected at 6- and 12-hours post-inoculation. RNA was extracted, sequenced, and the resulting data were processed and assembled. Differential gene expression analysis was conducted to identify genes responding to the infection. Additionally, the study investigated the involvement of Salicylic acid (SA), Jasmonic acid (JA), and Ethylene (ET) signalling pathways. Our transcriptome assembly comprised 64,667 transcripts with 96.7% completeness, providing valuable insights into the P. nigrum transcriptome. Annotation of these transcripts identified functional categories and domains, provided details on molecular processes. Gene expression analysis identified 4,714 transcripts at 6 h post-infection (hpi) and 9,416 at 12 hpi as differentially expressed, revealing dynamic regulation of immune-related genes. Furthermore, the study investigated key genes involved in biosynthesis pathways of Salicylic acid, Jasmonic acid, and Ethylene signalling. Notably, we found differential regulation of critical genes associated with these pathways while comparing data before and after infection, thereby shedding light on their roles in defense mechanism in P. nigrum defense. This comprehensive transcriptome analysis of P. nigrum response to P. capsici attack provides valuable insights into the plant defense mechanisms. The dynamic regulation of innate immunity and the involvement of key signalling pathways highlight the complexity of the plant-pathogen interaction. This study contributes to our understanding of plant immunity and offers potential strategies for enhancing P. nigrum resistance to this harmful pathogen.

Mahadevan C ，Shafi KM ，Nagarathnam B ，Sakuntala M ，Sowdhamini R ... -  《BMC GENOMICS》

De novo transcriptome sequencing of black pepper (Piper nigrum L.) and an analysis of genes involved in phenylpropanoid metabolism in response to Phytophthora capsici.

Hao C ，Xia Z ，Fan R ，Tan L ，Hu L ，Wu B ，Wu H ... -  《BMC GENOMICS》

Comparative Transcriptome and Metabolome Analysis of Resistant and Susceptible Piper Species Upon Infection by the Oomycete Phytophthora Capsici.

Phytophthora capsici is a destructive oomycete pathogen that causes devastating disease in black pepper, resulting in a significant decline in yield and economic losses. Piper nigrum (black pepper) is documented as susceptible to P. capsici, whereas its close relative Piper flaviflorum is known to be resistant. However, the molecular mechanism underlying the resistance of P. flaviflorum remains obscure. In this study, we conducted a comparative transcriptome and metabolome analysis between P. flaviflorum and P. nigrum upon P. capsici infection and found substantial differences in their gene expression profiles, with altered genes being significantly enriched in terms relating to plant-pathogen interaction, phytohormone signal transduction, and secondary metabolic pathways, including phenylpropanoid biosynthesis. Further metabolome analysis revealed the resistant P. flaviflorum to have a high background endogenous ABA reservoir and time-course-dependent accumulation of ABA and SA upon P. capsici inoculation, while the susceptible P. nigrum had a high background endogenous IAA reservoir and time-course-dependent accumulation of JA-Ile, the active form of JA. Investigation of the phenylpropanoid biosynthesis metabolome further indicated the resistant P. flaviflorum to have more accumulation of lignin precursors than the susceptible P. nigrum, resulting in a higher accumulation after inoculation. This study provides an overall characterization of biologically important pathways underlying the resistance of P. flaviflorum, which theoretically explains the advantage of using this species as rootstock for the management of oomycete pathogen in black pepper production.

Fan R ，Tao XY ，Xia ZQ ，Sim S ，Hu LS ，Wu BD ，Wang QH ，Hao CY ... -  《Frontiers in Plant Science》