The infection by a single-stranded DNA virus, Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1), causes hypovirulence, a reduced growth rate, and other colony morphological changes in its host Sclerotinia sclerotiorum strain DT-8. However, the mechanisms of the decline are still unclear. Using digital RNA sequencing, a transcriptome analysis was conducted to elucidate the phenotype-related genes with expression changes in response to SsHADV-1 infection. A total of 3110 S. sclerotiorum differentially expressed genes (DEGs) were detected during SsHADV-1 infection, 1741 of which were up-regulated, and 1369 were down-regulated. The identified DEGs were involved in several important pathways. DNA replication, DNA damage response, carbohydrate and lipid metabolism, ribosomal assembly, and translation were the affected categories in S. sclerotiorum upon SsHADV-1 infection. Moreover, the infection of SsHADV-1 also suppressed the expression of antiviral RNA silencing and virulence factor genes. These results provide further detailed insights into the effects of SsHADV-1 infection on the whole genome transcription in S. sclerotiorum.

Verticillium wilt is a disastrous disease caused by Verticillium dahliae that severely damages the production of cotton in China. Even under homogeneous conditions, the same cotton cultivar facing V. dahliae tends to either stay healthy or become seriously ill and die. This binary outcome may be related to the interactions between microbiome assembly and plant health. Understanding how the rhizosphere microbiome responds to V. dahliae infection is vital to controlling Verticillium wilt through the manipulation of the microbiome. In this study, we evaluated the healthy and diseased rhizosphere microbiome of two upland cotton cultivars that are resistant to V. dahliae, Zhong 2 (resistant) and Xin 36 (susceptible), using 16S rRNA and ITS high-throughput sequencing. The results showed that the healthy rhizosphere of both resistant cultivar and susceptible cultivar had more unique bacterial ASVs than the diseased rhizosphere, whereas fewer unique fungal ASVs were found in the healthy rhizosphere of resistant cultivar. There were no significant differences in alpha diversity and beta diversity between the resistant cultivar and susceptible cultivar. In both resistant cultivar and susceptible cultivar, bacterial genera such as Pseudomonas and Acidobacteria bacterium LP6, and fungal genera such as Cephalotrichum and Mortierella were both highly enriched in the diseased rhizosphere, and Pseudomonas abundance in diseased rhizospheres was significantly higher than that in the healthy rhizosphere regardless of the cultivar type. However, cultivar and V. dahliae infection can cause composition changes in the rhizosphere bacterial and fungal communities, especially in the relative abundances of core microbiome members, which varied significantly, with different responses in the two cotton cultivars. Analysis of co-occurrence networks showed that resistant cultivar has a more complex network relationship than susceptible cultivar in the bacterial communities, and V. dahliae has a significant impact on the bacterial community structure. These findings will further broaden the understanding of plant-rhizosphere microbiome interactions and provide an integrative perspective on the cotton rhizosphere microbiome, which is beneficial to cotton health and production.

As a common disease, canker seriously affects the yield and quality of fragrant pear due to the lack of effective control measures. Some fungi have been reported to harbor rich reservoirs of viral resources, and some mycoviruses can be used as biocontrol agents against plant diseases. In this study, 199 isolates were obtained from diseased branches of fragrant pear in the main production areas of Xinjiang. Among them, 134 belonged to Valsa spp., identified using morphological and molecular biological techniques, in which V. mali was the dominant species. The mycoviruses in Valsa spp. were further identified using metatranscriptomic sequencing and RT-PCR. The results revealed that a total of seven mycoviruses were identified, belonging to Botourmiaviridae, Endornaviridae, Fusariviridae, Hypoviridae, Mitoviridae, and Narnaviridae, among which Phomopsis longicolla hypovirus (PlHV) was dominant in all the sample collection regions. The Cryphonectria hypovirus 3-XJ1 (CHV3-XJ1), Botourmiaviridae sp.-XJ1 (BVsp-XJ1), and Fusariviridae sp.-XJ1 (Fvsp-XJ1) were new mycoviruses discovered within the Valsa spp. More importantly, compared with those in the virus-free Valsa spp. strain, the growth rate and virulence of the VN-5 strain co-infected with PlHV and CHV3-XJ1 were reduced by 59% and 75%, respectively, and the growth rate and virulence of the VN-34 strain infected with PlHV were reduced by 42% and 55%, respectively. On the other hand, the horizontal transmission efficiency of PlHV decreased when PlHV was co-infected with CHV3-XJ1, indicating that PlHV and CHV3-XJ1 were antagonistic. In summary, the mycoviruses in Valsa spp. were identified in Xinjiang for the first time, and three of them were newly discovered mycoviruses, with two strains yielding good results. These results will offer potential biocontrol resources for managing pear canker disease and provide a theoretical basis for the control of fruit tree Valsa canker disease.

Phelipanche aegyptiaca Pers. is a holoparasitic plant that causes tremendous losses of agricultural crops worldwide. The initiation and development of the haustoria (special intrusive organs) is a key step in the growth of parasitic plants. The initiation of haustorium is largely dependent on haustorium-inducing factors (HIFs) secreted from host roots. Although HIFs of many semi-parasitic plants have been identified and reported, HIFs of the obligate parasitic plant P. aegyptiaca are largely unknown. This work demonstrated that the root exudates of the host plant Cucumis melo L. contain allelochemicals displaying haustorium-inducing activity on P. aegyptiaca germinating seeds, and there are significant differences in the induction effects of the resistant and susceptible C. melo cultivars of P. aegyptiaca (KR1326 and K1076). Ultra-performance liquid chromatography–mass spectrometry (UPLC-MS/MS) technology was used to identify and analyze the metabolites in root exudates of KR1326 and K1076. Cluster and PCA analyses showed significant differences between the metabolites in the KR1326 and K1076 root exudates. The determination of the haustorium induction effects of some metabolites screened from the differential metabolites indicated that scopoletin, quercetin, IAA, and DMBQ had relatively high haustorium induction activity. The results provide clues for finding HIFs of obligate parasitic plants and shed new light on the control of P. aegyptiaca by regulating haustorium development.

Introduction: Verticillium dahliae causes a serious decline in cotton yield and quality, posing a serious threat to the cotton industry. However, the mechanism of resistance to V. dahliae in cotton is still unclear, which limits the breeding of resistant cultivars.Methods: To analyze the defense mechanisms of cotton in response to V. dahliae infection, we compared the defense responses of two upland cotton cultivars from Xinjiang (JK1775, resistant; Z8,susceptible) using transcriptome sequencing at different infection stages.Results: The results revealed a significant differential expression of genes in the two cotton cultivars post V. dahliae infection, with the number of DEGs in JK1775 being higher than that in Z8 at different infection stages of V. dahliae. Interestingly, the DEGs of both JK1775 and Z8 were enriched in the MAPK signaling pathway in the early and late stages of infection. Importantly, the upregulated DEGs in both cultivars were significantly enriched in all stages of the phenylpropanoid metabolic pathway. Some of these DEGs were involved in the regulation of lignin and coumarin biosynthesis, which may be one of the key factors contributing to the resistance of upland cotton cultivars to V. dahliae in Xinjiang. Lignin staining experiments further showed that the lignin content increased in both resistant and susceptible varieties after inoculation with V. dahliae.Discussion: This study not only provides insights into the molecular mechanisms of resistance to Verticillium wilt in Xinjiang upland cotton but also offers important candidate gene resources for molecular breeding of resistance to Verticillium wilt in cotton.

Verticillium wilt, a prevalent soil-borne disease, poses a significant challenge to cotton production in Xinjiang, China. Continuous cotton monoculture has increased disease incidence and affected soil microbial diversity in Xinjiang, while crop rotation is recognized as an effective strategy for soil pathogen control. This study investigates how a one-year maize rotation affects Verticillium wilt incidence and soil microbiome composition in cotton fields across northern and southern Xinjiang. The results demonstrated that short-term rotation significantly reduced Verticillium wilt occurrence in both northern and southern Xinjiang. Using high-throughput sequencing of fungal ITS and bacterial 16S rRNA regions, microbial community analysis revealed minimal changes in alpha-diversity but significant structural reorganization between continuous cropping (CC) and rotation (CR) systems, particularly in fungal and bacterial genera composition, with distinct spatial patterns between northern and southern fields. Crop rotation promoted beneficial taxa such as Sphingomonas and Pseudogymnoascus, while reducing the abundance of pathogens such as Verticillium dahliae. LEfSe study suggested Tepidisphaerales and Lasiosphaeriaceae as biomarkers for CR systems, whereas Hypocreales and Blastocatellia dominated in CC soils. Co-occurrence network analysis revealed more bacterial connectivity and modularity under CR, suggesting better microbial interactions and ecological resilience. The increased structural complexity of bacterial networks under CR indicates their greater contribution to soil health maintenance and ecosystem resilience. Our findings demonstrate that short-term crop rotation not only effectively reduces Verticillium wilt incidence but also restructures soil microbial communities, providing an actionable strategy for sustainable cotton cultivation in Xinjiang.