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<p>The bud rot pathogen <i>Phytophthora palmivora</i> poses a major threat to global coconut production. The lack of effective management strategies is largely due to limited knowledge of its pathogenic mechanisms and the absence of resistant cultivars. To address this gap, we performed dual RNA-seq analyses at three time points (12, 24, and 36&#xa0;h post-inoculation) using the in vitro assay, standardized to track transcriptional regulation and system-wide host responses to <i>P. palmivora</i>. Differential gene expression analysis between control and infected samples revealed extensive modulation of stress-responsive genes in coconut, while <i>P. palmivora</i> exhibited differential expression of genes encoding effectors and carbohydrate-active enzymes. KEGG pathway enrichment analysis revealed the upregulation of genes associated with plant-pathogen interactions, mitogen-activated protein kinase (MAPK) signaling, and plant hormone signal transduction in coconut. These pathways are critical in stress responses, immune defense, and growth regulation. To validate these findings, we quantified the expression of 10 differentially expressed genes from coconut and <i>P. palmivora</i> using quantitative real-time PCR (qRT-PCR) across the same time points. The qRT-PCR results aligned with the dual RNA-seq data, reinforcing the reliability of our transcriptional analysis. This study highlights the significant regulation of stress-related genes in coconut and the activation of effector and carbohydrate-active enzyme genes in <i>P. palmivora</i> during infection. Notably, dual RNA-seq revealed that <i>P. palmivora</i> activation began before 12 hpi, whereas coconut’s molecular defense was initiated early but exhibited complete activation at 24 hpi. Our findings provide crucial insights into the molecular interactions governing the coconut–<i>P. palmivora</i> pathosystem and offer a foundation for developing targeted disease management strategies.</p>

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Decoding the coconut–Phytophthora conflict: insights from dual RNA-seq analysis

  • 期刊论文

  • 发表日期：

    2025年9月12日

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  • K. P. Gangaraj,
  • M. K. Rajesh,
  • Ashok Kumar Jangam,
  • V. H. Prathibha,
  • S. V. Ramesh,
  • Ginny Antony,
  • Jasmin Habeeb,
  • K. T. K. Amritha,
  • K. S. Muralikrishna,
  • P. B. Rajitha,
  • N. Hemalatha

摘要

The bud rot pathogen Phytophthora palmivora poses a major threat to global coconut production. The lack of effective management strategies is largely due to limited knowledge of its pathogenic mechanisms and the absence of resistant cultivars. To address this gap, we performed dual RNA-seq analyses at three time points (12, 24, and 36 h post-inoculation) using the in vitro assay, standardized to track transcriptional regulation and system-wide host responses to P. palmivora. Differential gene expression analysis between control and infected samples revealed extensive modulation of stress-responsive genes in coconut, while P. palmivora exhibited differential expression of genes encoding effectors and carbohydrate-active enzymes. KEGG pathway enrichment analysis revealed the upregulation of genes associated with plant-pathogen interactions, mitogen-activated protein kinase (MAPK) signaling, and plant hormone signal transduction in coconut. These pathways are critical in stress responses, immune defense, and growth regulation. To validate these findings, we quantified the expression of 10 differentially expressed genes from coconut and P. palmivora using quantitative real-time PCR (qRT-PCR) across the same time points. The qRT-PCR results aligned with the dual RNA-seq data, reinforcing the reliability of our transcriptional analysis. This study highlights the significant regulation of stress-related genes in coconut and the activation of effector and carbohydrate-active enzyme genes in P. palmivora during infection. Notably, dual RNA-seq revealed that P. palmivora activation began before 12 hpi, whereas coconut’s molecular defense was initiated early but exhibited complete activation at 24 hpi. Our findings provide crucial insights into the molecular interactions governing the coconut–P. palmivora pathosystem and offer a foundation for developing targeted disease management strategies.