Trunk canker poses a major threat to the production of Chinese hickory tree (Carya cathayensis Sarg.), which is primarily determined by Botryosphaeriaceae. In our previous work, we identified Botryosphaeria dothidea as the predominant pathogen of this disease. However, it is still unclear about corresponding gene families and mechanisms associated with B. dothidea’s pathogenicity on Chinese hickory tree. Here, we present a comparative analysis of high-quality genome assemblies of Botryosphaeria dothidea and other isolated pathogens, showing highly syntenic relationships between B. dothidea and its closely related species and the conservative evolution of the Botryosphaeriaceae family. Higher GC contents were found in the genomes of B. dothidea and three other isolated pathogens (Botryshaeria cortices, Botryshaeria fabicerciana, and Botryshaeria qingyuanensis) compared to Macrophomina phaseolina, Neofusicoccum parvum, Diplodia corticola, and Lasiodiplodia theobromae. An investigation of genes specific to or expanded in B. dothidea revealed that one secreted glucanase, one orsellinic acid biosynthesis enzyme, and two MFS transporters positively regulated B. dothidea’s pathogenicity. We also observed an overrepresentation of viral integrase like gene and heterokaryon incompatibility proteins in the B. dothidea’s genome. In addition, we observed one LRR-domain-containing protein and two Sec-domain-containing proteins (Sec_1 and Sec_7) that underwent positive selection. This study will help to understand B. dothidea’s pathogenicity and potential influence on the infection of Chinese hickory, which will help in the development of disease control and ensure the security of Chinese hickory production.

Rice false smut caused by Ustilaginoidea virens is one of the most devastating diseases in rice worldwide, which results in serious reductions in rice quality and yield. As an airborne fungal disease, early diagnosis of rice false smut and monitoring its epidemics and distribution of its pathogens is particularly important to manage the infection. In this study, a quantitative loop-mediated isothermal amplification (q-LAMP) method for U. virens detection and quantification was developed. This method has higher sensitivity and efficiency compared to the quantitative real-time PCR (q-PCR) method. The species-specific primer that the UV-2 set used was designed based on the unique sequence of the U. virens ustiloxins biosynthetic gene (NCBI accession number: BR001221.1). The q-LAMP assay was able to detect a concentration of 6.4 spores/mL at an optimal reaction temperature of 63.4 °C within 60 min. Moreover, the q-LAMP assay could even achieve accurate quantitative detection when there were only nine spores on the tape. A linearized equation for the standard curve, y = −0.2866x + 13.829 (x is the amplification time, the spore number = 10^0.65y), was established for the detection and quantification of U. virens. In field detection applications, this q-LAMP method is more accurate and sensitive than traditional observation methods. Collectively, this study has established a powerful and simple monitoring tool for U. virens, which provides valuable technical support for the forecast and management of rice false smut, and a theoretical basis for precise fungicide application.

Rice bakanae disease (RBD) is a typical seed-borne fungal disease caused by Fusarium fujikuroi. Prochloraz is a sterol demethylation inhibitor, which is among the most important classes of active ingredients for the management of RBD. In 2022, the total resistance frequency of F. fujikuroi to prochloraz in Zhejiang Province was 62.67%. The fitness of the prochloraz-resistant population was lower than that of the susceptible population, but its pathogenicity was slightly stronger. The S312T and F511S double mutations of Ffcyp51b were detected in the resistant isolates. Loop-mediated isothermal amplification (LAMP) technology based on S312T was established to rapidly determine prochloraz resistance in F. fujikuroi. LAMP primer mismatch design was performed based on the cyp51b gene, and 100–300 bp sequences containing a mutation at codon 312 were amplified. In a 25 µL reaction tube, 1 pg/µL DNA of F. fujikuroi could be detected. The detection limit for the frequency of prochloraz resistance was 0.498% using this method. We performed LAMP detection on rice seedlings inoculated with prochloraz-sensitive and -resistant isolates and treated them with prochloraz. Prochloraz demonstrated good control in rice seedlings. A chromogenic reaction was observed in seedlings treated with prochloraz-resistant isolates, and the results were verified using electrophoresis. It has been demonstrated that LAMP technology based on the S312T genotype can quickly and specifically detect prochloraz-resistant isolates in rice seedlings.

Rice spikelet rot disease (RSRD) affects the production and market price of rice, and can be harmful to humans and livestock. In this study, 51 strains of Fusarium spp. were isolated from rice spikelets in the Lin’an, Yuhang, and Fuyang regions. The isolates comprised four composite species: Fusarium incarnatum-equiseti species complex (FIESC), Fusarium asiaticum species complex (FSAMSC), Fusarium fujikuroi species complex (FFSC), Fusarium commune species complex (FNSC), and five species of Fusarium spp. (F. luffae, F. sulawesiense, F. asiaticum, F. fujikuroi, and F. commune). The separation rate of F. sulawesiense was the highest (41.2%), followed by F. asiaticum at 37.3%. The results of this study, compared with those of other studies, found that the newly discovered species of Fusarium spp. associated with RSRD were FSAMSC (F. asiaticum) and FNSC (F. commune). Temperature is one of the important factors causing RSRD; the optimal growth temperature for F. sulawesiense and F. commune was 30 °C, and the optimal growth temperature for other species was 25 °C. A high temperature of 35 °C did not inhibit the growth of Fusarium, as F. commune and F. fujikuroi could grow at this temperature. At 20–30 °C, the growth rate of F. asiaticum was higher than those of other strains. To determine whether the occurrence of RSRD is related to the correlation between Fusarium and other fungi in rice spikelets under different health conditions, the genetic diversity of fungi in rice spikelets was analyzed by amplicon Internal Transcribed Spacer (ITS) sequencing, and the correlations between strains of Fusarium spp. were measured. The results showed that the fungal diversity of diseased rice spikelets (RD) was higher than that of relatively healthy rice spikelets (RH). Curvularia spp., which was affected by the condition of the spikelets, was negatively correlated with Fusarium spp. in RH and positively correlated with Fusarium spp. in RD. Therefore, Fusarium spp. and Curvularia spp. can jointly cause the occurrence of RSRD. The results of the study are significant for understanding the occurrence of RSRD and formulating prevention and control measures.

Strawberry black spot, caused by Alternaria spp., is an emerging disease that threatens both leaves and fruits during strawberry growth and postharvest storage. This study investigated the boscalid sensitivity of 49 Alternaria isolates collected from symptomatic strawberry leaves. Boscalid has been widely used to control diseases in strawberry in China for several years. The EC₅₀ values for the tested isolates ranged from 0.0884 to 266.3289 µg/mL, indicating that most isolates exhibited varying levels of resistance to boscalid based on resistance ratio values. A substitution of SDHC-H134R was detected from most high-resistance isolates. Fitness cost assessment revealed that highly resistant isolates had a reduced conidial germination rate; however, their mycelial growth and conidia production were increased. No significant virulence deficiency was observed, suggesting low fitness cost in resistant isolates. Furthermore, the highly resistant isolates exhibited positive cross-resistance to fluopyram and fluxapyroxad. Molecular docking analysis revealed that the SDHC-H134R mutation reduced the binding affinity between boscalid and mitochondrial complex II. These findings suggest that resistance management strategies, such as fungicide rotation or combinations of fungicides with different action modes, should be implemented to control strawberry diseases, minimizing the development of fungicide resistance and improving overall disease control efficacy.

Botryosphaeria dothidea is the causative agent of Chinese hickory trunk canker, which poses significant threat to the production of Chinese hickory (Carya cathayensis Sarg.). Previous studies reported that endophytic–pathogenic phase transition, also referred to as latent infection, plays an important role in the interaction of Botryosphaeria dothidea with various host plants, including Chinese hickory. However, the mechanism underlying this phase transition is not well understood. Here, we employed RNA-Seq to investigate transcriptional changes in B. dothidea during its phase transition upon interaction with Chinese hickory. A co-expression network was generated based on 6391 differentially expressed genes (DEGs) identified from different infection stages and temperature treatments. One co-expressed module was found that highly correlated with temperature treatments which simulated conditions of B. dothidea latent infection in the field. Subsequently, 53 hub genes were detected, and gene ontology (GO) enrichment analysis revealed three categories of enriched GO terms: transmembrane transport or activity, ion homeostasis or transport, and carbohydrate metabolism. One PacC transcriptional factor (BDLA_00001555, an ambient pH regulator), and one endo-β-1,3-glucanase (BDLA_00010249) were specifically upregulated under temperature treatments that corresponded with the activation stage of B. dothidea’s pathogenic state. The knockout mutant strain of BDLA_00001555 demonstrated defective capability upon the activation of the pathogenic state. This confirmed that BDLA_00001555, the PacC transcriptional factor, plays an important role in the latent infection phase of B. dothidea. Our findings provide insights into the pathogenic mechanism of Chinese hickory trunk canker disease.