Chinese jujube (Ziziphus jujuba Mill.) is a native fruit crop in China. Leaf mottle and dapple fruit disease is prevalent in cultivated jujube plants grown at Aksu in Xinjiang Uygur Autonomous Region of China. Jujube yellow mottle-associated virus (JYMaV), a tentative member in the genus Emaravirus, was recently identified from mottle-diseased jujube plants grown in Liaoning Province in China, but its incidence and genetic diversity in China is unknown. In this study, the genome sequences of three JYMaV isolates from two jujube cultivars and one jujube variant were determined by high-throughput sequencing (HTS) for small RNA and rRNA-depleted RNA coupled with RT-PCR assays. Comparison of these sequences together with sequences of the viral RNA segments derived by primer set 3C/5H-based RT-PCR revealed that genetic diversity was present in the virus populations and high sequence variation occurred at the non-translational regions of each of the viral genomic segments. Field investigation confirmed the close association of the virus with leaf mottle symptoms of jujube plants. Furthermore, this study revealed that P5 encoded in the viral RNA5 displayed a nuclear localization feature differing from the plasmodesma (PD) subcellular localization of the virus movement protein (P4), and the two proteins could interact with each other in the BiFC assays. Our study provides a snapshot of JYMaV genetic diversity in its natural hosts.

A severe branch dieback and canker was observed on black walnut (Juglans nigra L.) in Yili county, Xinjiang, China, during the spring and summer, 2016. A fungus was consistently isolated from infected branches. Pathogenicity tests showed that the fungus could infect branches, and produced the same symptoms under artificial inoculation conditions as those observed in the field. The fungus was identified based on morphological and cultural characteristics as Cytospora chrysosperma. Identification was confirmed by combining multi-locus phylogenetic analyses based on the internal transcribed spacer regions (ITS 1 and 2) and intervening 5.8S nrDNA, the partial translation elongation factor (TEF-1) gene, and partial gene regions of β-tubulin (TUB 2). Morphological and cultural characteristics, as well as the sequences of the ITS, tef and β-tubulin regions and pathogenicity tests, showed that the causal agent of the disease was C. chrysosperma. This is the first report of branch dieback and canker of black walnut caused by C. chrysosperma (Pers.) Fr. worldwide.

Chinese jujube (Ziziphus jujuba Mill.) is a widely grown fruit crop at Aksu in Xinjiang Uygur Autonomous Region of China. Viral disease-like symptoms are common on jujube plants. Here, for the first time, we report a virus tentatively named persimmon ampelovirus jujube isolate (PAmpV-Ju) infecting jujube plants. The virus was identified using high-throughput sequencing from a jujube plant (ID: AKS15) and molecularly related to viruses in the family Closteroviridae. The genomic sequences of two PAmpV-Ju variants named AKS15-20 and AKS15-17 were determined by RT-PCR amplifications. The genome structure of PAmpV-Ju was identical to that of a recently reported persimmon ampelovirus (PAmpV) and consisted of seven open reading frames. The genomes of AKS15-20 and AKS15-17 shared 83.7% nt identity with each other, and the highest nt sequence identity of 79% with two variants of PAmpV. The incidence of PAmpV-Ju on Aksu jujube plants was evaluated by RT-PCR assays. The phylogenetic analysis of amplified partial sequences coding for polymerase, HSP70h, and CP revealed two phylogenetic clades represented by AKS15-20 and AKS15-17. Our study provides important evidence for understanding viruses infecting jujube plants and establishing efficient measures to prevent virus spread.

Cotton, as an economically important crop, suffers significant yield losses from infection by Fusarium oxysporum f. sp. vasinfectum race 7 (Fov7) infection. To elucidate the molecular mechanisms underlying host responses to Fov7 infection, we conducted a comprehensive transcriptional analysis of Gossypium barbadense using integrated bulk RNA sequencing (RNA-seq) and single-nucleus RNA sequencing (snRNA-seq) approaches. Our time-course study encompassed four critical infection stages (0, 2, 12, and 48 h post-inoculation) to characterize spatiotemporal transcriptomic dynamics. Bulk RNA-seq analysis revealed that the number of differentially expressed gene (DEG) numbers peaked at 2 h post-inoculation (hpi), identifying 9230 DEGs and demonstrating substantial transcriptional activation during early pathogen challenge. K-means clustering classified DEGs into six temporal expression patterns, with cluster C4 showing significant enrichment of defense-related pathways. Weighted gene co-expression network analysis (WGCNA) identified ten distinct co-expression modules, among which the turquoise module exhibited strong correlation with early infection responses. Integration of K-means clustering and WGCNA results pinpointed 1503 key defense-related genes. A single-nucleus atlas of cotton roots during Fov7 infection was constructed, comprising 32,773 nuclei, which revealed the cellular heterogeneity of cotton root tips. Functional enrichment analysis using these key genes emphasized the crucial roles of root cap and epidermal cells in pathogen perception and defense activation. Pseudotime trajectory mapping further delineated transcriptional dynamics in these cell populations during infection progression, demonstrating pathway activation in the root cap and epidermis at later infection stages. This multi-omics study establishes a valuable transcriptional resource for dissecting cotton’s resistance mechanisms against Fov7 and provides theoretical insights for developing disease-resistant cultivars through molecular breeding strategies.

Fusarium wilt, caused by Fusarium oxysporum f. sp. vasinfectum 7 (FOV7), poses a major threat to the production of elite Sea Island cotton ( Gossypium barbadense ). To uncover the molecular basis of defense FOV7 in cotton, we employed RNA sequencing to identify numerous differentially expressed genes across various stages of infection. Subsequent K-means clustering and weighted gene co-expression network analysis revealed a core module significantly enriched in defense response and abscisic acid-activated signaling pathways. A detailed examination of the gene distribution within these pathways identified 10 out of 50 genes as members of the Pathogenesis-Related 10 ( PR10 ) gene family. Evolutionary analysis of these PR10 genes uncovered a tandemly-expanded gene cluster located on chromosome 10 of the D sub-genome. In addition, root cell type maps constructed via single-nucleus RNA sequencing (snRNA-seq) enabled pinpointing FOV7 response in the root epidermis, where GbD_PR10.11 was identified as a specifically activated sentinel. Our work, by logically progressing from genome-wide patterns to a single gene in a single cell type, not only deciphers a key component of the cotton-pathogen arms race but also delivers a high-confidence target for engineering frontline resistance.