Sweet potato (Ipomoea batatas L.) is the sixth most important food crop in the world. The formation and development of storage roots in sweet potato is a highly complicated and genetically programmed process. However, the underlying mechanisms of storage root development have not yet been elucidated. To better understand the molecular mechanisms involved in storage root development, a combined analysis of the transcriptome and proteome of sweet potato fibrous roots (F) and storage roots at four different stages (D1, D3, D5 and D10) was performed in the present study. A total of 26,273 differentially expressed genes were identified in a comparison between the fibrous root library and four storage root libraries, while 2558 proteins showed a 1.0-fold or greater expression difference as indicated by isobaric tags for relative and absolute quantitation (iTRAQ) analysis. The combination of the transcriptome and proteome analyses and morphological and physiological data revealed several critical pathways involved in storage root formation and development. First, genes/proteins involved in the development of meristems/cambia and starch biosynthesis were all significantly upregulated in storage roots compared with fibrous roots. Second, multiple phytohormones and the genes related to their biosynthesis showed differential expression between fibrous roots and storage roots. Third, a large number of transcription factors were differentially expressed during storage root initiation and development, which suggests the importance of transcription factor regulation in the development of storage roots. Fourth, inconsistent gene expression was found between the transcriptome and proteome data, which indicated posttranscriptional regulatory activity during the development of storage roots. Overall, these results reveal multiple events associated with storage root development and provide new insights into the molecular mechanisms underlying the regulatory networks involved in storage root development.

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.

Long non-coding RNAs (lncRNAs) have emerged as pivotal regulators in plant immune responses, yet their roles in rice resistance against Magnaporthe oryzae (M. oryzae) remain inadequately explored. In this study, we integrated translatome data with conventional genome annotations to construct an optimized protein-coding dataset. Subsequently, we developed a robust pipeline (“RiceLncRNA”) for the accurate identification of rice lncRNAs. Using strand-specific RNA-sequencing (ssRNA-seq) data from the resistant (IR25), susceptible (LTH), and Nipponbare (NPB) varieties under M. oryzae infection, we identified 9003 high-confidence lncRNAs, significantly improving identification accuracy over traditional methods. Among the differentially expressed lncRNAs (DELs), those unique to IR25 were enriched in the biosynthetic pathways of phenylalanine, tyrosine, and tryptophan, which suggests that they are associated with the production of salicylic acid (SA) and auxin (IAA) precursors, which may be involved in defense responses. Conversely, DELs specific to LTH primarily clustered within carbon metabolism pathways, indicating a metabolic reprogramming mechanism. Notably, 21 DELs responded concurrently in both IR25 and LTH at 12 h and 24 h post-inoculation, indicating a synergistic regulation of jasmonic acid (JA) and ethylene (ET) signaling while partially suppressing IAA pathways. Weighted gene co-expression network analysis (WGCNA) and competing endogenous RNA (ceRNA) network analysis revealed that key lncRNAs (e.g., LncRNA.9497.1) may function as miRNA “sponges”, potentially influencing the expression of receptor-like kinases (RLKs), resistance (R) proteins, and hormone signaling pathways. The reliability of these findings was confirmed through qRT-PCR and cloning experiments. In summary, our study provides an optimized rice lncRNA annotation framework and reveals the mechanism by which lncRNAs enhance rice blast resistance through the regulation of hormone signaling pathways. These findings offer an important molecular basis for rice disease-resistant breeding.

Long noncoding RNAs (lncRNAs) have emerged as pivotal regulators in plant immune responses, yet their roles in rice resistance against Magnaporthe oryzae (M. oryzae) remain inadequately explored. In this study, we integrated translatome data with conventional genome annotations to construct an optimized protein-coding dataset. Subsequently, we developed a robust pipeline (“RiceLncRNA”) for the accurate identification of rice lncRNAs. Using strand-specific RNA sequencing (ssRNA-seq) data from the resistant (IR25) and susceptible (LTH) and Nipponbare (NPB) varieties under M. oryzae infection, we identified 9,003 high-confidence lncRNAs, significantly improving identification accuracy over traditional methods. Among the differentially expressed lncRNAs (DELs), those unique to IR25 were enriched in the biosynthetic pathways of phenylalanine, tyrosine, and tryptophan, which suggests that they enhance the production of salicylic acid (SA) and auxin (IAA) precursors to trigger defense responses. Conversely, DELs specific to LTH primarily clustered within carbon metabolism pathways, indicating a metabolic reprogramming mechanism. Notably, 21 DELs responded concurrently in both IR25 and LTH at 12 h and 24 h post-inoculation, indicating a synergistic regulation of jasmonic acid (JA) and ethylene (ET) signaling while partially suppressing IAA pathways. Weighted gene coexpression network analysis (WGCNA) and competing endogenous RNA (ceRNA) network analysis revealed that key lncRNAs (e.g., LncRNA.9497.1) function as miRNA “sponges,” thereby indirectly modulating the expression of receptor-like kinases (RLKs), resistance (R) proteins, and hormone signaling pathways. The reliability of these findings was confirmed through qRT-PCR and cloning experiments. In summary, our study provides an optimized rice lncRNA annotation framework and reveals the mechanism by which lncRNAs enhance rice blast resistance through the regulation of hormone signaling pathways. These findings offer an important molecular basis for rice disease-resistant breeding.

Argonaute (AGO) proteins are central components of RNA silencing. While OsAGO18 is a known defense factor in antiviral immunity, its involvement in basal development and its transcriptomic behavior during fungal stress remains to be fully elucidated. In this study, based on its specific dual-localization in chloroplasts and processing bodies (P-bodies), we investigated the pleiotropic effects of OsAGO18 through transcriptomic network analysis of rice responding to the blast fungus Magnaporthe oryzae B.C. Couch. Our analysis revealed that the OsAGO18-mediated co-expression network is highly correlated with ribosome biogenesis and cell wall organization. Notably, the analyzed datasets reveal that this growth-related network is significantly suppressed upon M. oryzae challenge, highlighting a transcriptomic shift in OsAGO18 during the growth-to-defense transition. Phenotypic evaluations demonstrated that OsAGO18 overexpression accelerates early seedling growth and primary root elongation by promoting endogenous indole-3-acetic acid (IAA) accumulation, whereas ago18 mutants maintain basal growth rates without significant IAA fluctuations, reflecting robust genetic compensation within the highly redundant AGO family. Mechanistically, our integrated analysis suggests that OsAGO18 acts as a putative molecular decoy to sequester miR396d, thereby relieving the repression of the Growth-Regulating Factor OsGRF6 and triggering downstream auxin-dependent cascades. Collectively, our findings highlight OsAGO18 as a pivotal regulator of early seedling development and characterize its transcriptomic responsiveness to biotic stress, providing a plausible molecular link between post-transcriptional RNA regulation and rice growth coordination.