Citrus Huanglongbing (HLB), caused by the phloem-inhibiting bacterium Candidatus Liberibacter asiaticus (CLas), is the most devastating citrus disease, intimidating citrus production worldwide. Although commercially cultivated citrus cultivars are vulnerable to CLas infection, HLB-tolerant attributes have, however, been observed in certain citrus varieties, suggesting a possible pathway for identifying innate defense regulators that mitigate HLB. By adopting transcriptome and small RNAome analysis, the current study compares the responses of HLB-tolerant lemon (Citrus limon L.) with HLB-susceptible Shatangju mandarin (Citrus reticulata Blanco cv. Shatangju) against CLas infection. Transcriptome analysis revealed significant differences in gene expression between lemon and Shatangju. A total of 1751 and 3076 significantly differentially expressed genes were identified in Shatangju and lemon, respectively. Specifically, CLas infected lemon tissues demonstrated higher expressions of genes involved in antioxidant enzyme activity, protein phosphorylation, carbohydrate, cell wall, and lipid metabolism than Shatangju. Wet-lab experiments further validated these findings, demonstrating increased antioxidant enzyme activity in lemon: APX (35%), SOD (30%), and CAT (64%) than Shatangju. Conversely, Shatangju plants exhibited higher levels of oxidative stress markers like H₂O₂ (44.5%) and MDA content (65.2%), alongside pronounced ion leakage (11.85%), than lemon. Moreover, microscopic investigations revealed that CLas infected Shatangju phloem exhibits significantly more starch and callose accumulation than lemon. Furthermore, comparative sRNA profiles revealed the potential defensive regulators for HLB tolerance. In Shatangju, increased expression of csi-miR166 suppresses the expression of disease-resistant proteins, leading to inadequate defense against CLas. Conversely, reduced expression of csi-miR166 in lemon plants enables them to combat HLB by activating disease-resistance proteins. The above findings indicate that when infected with CLas, lemon exhibits stronger antioxidative activity and higher expression of disease-resistant genes, contributing to its enhanced tolerance to HLB. In contrast, Shatangju shows lower antioxidative activity, reduced expression of disease-resistant genes, significant ion leakage, and extensive callose deposition, possibly related to damage to plant cell structure and blockage of phloem sieve tubes, thereby promoting the development of HLB symptoms.

Verticillium wilt, caused by Verticillium dahliae, is a devastating disease that severely threatens cotton production worldwide. The long-term survival of the pathogen in soil and the limited availability of resistant cultivars make effective control strategies challenging. Although the fungal cross-kingdom RNA VdsR-1 has been reported to delay floral transition and prolong vegetative growth, the underlying plant regulatory mechanisms remain largely unclear. Here, we show that the transcription factor AtTOE1, a target of ath-miR172b-3p, displays altered expression in response to changes in ath-miR172b-3p levels during V. dahliae inoculation, coinciding with coordinated changes in plant immune-related and developmental responses. Increased AtTOE1 expression is correlated with enhanced disease resistance, reduced pathogen colonization, and delayed floral transition. Furthermore, our results indicate that the VdsR-1/AtSPL13A module is associated with modulation of AtTOE1 expression via ath-miR172b-3p, suggesting the involvement of a cross-kingdom RNA-related regulatory framework linking plant immunity and development. Notably, this regulatory relationship is also observed in cotton, indicating evolutionary conservation across plant species. Together, our findings highlight TOE1 as a potential integrator of defense and growth-related processes during pathogen challenge and provide insights that may inform strategies to improve resistance to V. dahliae in cotton and other crops.