Genomic insights are provided into the ecological adaptation and pathogenic potential of JDA-12, while revealing environmental conditions favorable for SCR development, facilitating the development of effective disease management strategies.
Abstract
Strawberry crown rot (SCR) disease poses a significant threat to strawberry production in Zhejiang Province, China. In our previous study, we identified Colletotrichum siamense strain JDA-12 as the dominant causal agent of SCR disease in samples collected from Zhejiang. However, the factors associated with this phenomenon remain unclear. In this study, a comparative analysis of JDA-12 and other documented Colletotrichum species revealed that the gene families AbiEii and CBM24-GH71, together with two annotated RiPP-like secondary metabolite biosynthetic clusters, are specifically expanded or uniquely present in JDA-12. These lineage-specific genomic features may represent genomic signatures associated with ecological adaptation and host-associated interactions of JDA-12. Additionally, we assessed the pathogenicity of JDA-12 on major strawberry cultivars grown in Zhejiang. The findings demonstrated that ‘Benihoppe’ exhibited high susceptibility, while ‘Fenyu No.1′ showed comparatively strong resistance. Furthermore, we evaluated the impact of environmental factors on pathogenicity and found that short-day conditions (10L:14D), high temperature (~30 °C), and high humidity (≥90%) constitute the optimal environment for JDA-12 infection in strawberries, at least under conditions representative of Zhejiang. This study provides genomic insights into the ecological adaptation and pathogenic potential of JDA-12, while revealing environmental conditions favorable for SCR development, facilitating the development of effective disease management strategies.
The first comprehensive pangenome of D. dadantii is constructed by integrating complete PacBio HiFi sequencing of a representative strain with resequencing of 32 Chinese isolates and 23 global strains, revealing that geographic isolation and host adaptation drive genetic differentiation.
Meng Fan, Xia-Wei Ding, Qian-Yu Shi et al.· Journal of Agricultural and...· 0 citations
Peanut root-knot nematode (RKN) disease caused by Meloidogyne hapla is among the most destructive soil-borne diseases threatening peanut production worldwide. We isolated Trichoderma harzianum strain Snef3255 from peanut rhizosphere soil, which exhibited high virulence against second-stage juveniles, with a mortality rate of 86.08%. Field trials demonstrated that TC and TS provided control efficacies of 70.85% and 61.88%, respectively, while boosting peanut yields by 18.15% and 13.61%. We report a high-quality chromosome-level genome assembly of T. harzianum Snef3255 using Oxford Nanopore, Illumina and high-throughput chromatin conformation capture (Hi-C) sequencing data. This assembly comprised seven chromosomes (40,811,729 bp) with a BUSCO completeness of 99.31%. A total of 13,611 protein-coding genes were predicted. Systematic comparative genomic analysis of T. harzianum Snef3255 with other Trichoderma species was performed, and putative functional gene clusters were investigated. Furthermore, we identified two candidate secreted proteins, ThCP1 and ThLysM1, and screened their interacting proteins in peanut, respectively. This study demonstrated the potential of Snef3255 as a biocontrol agent for peanut RKN disease and provided a genomic basis for understanding Trichoderma–peanut interactions.
India contributes 26% of global banana production, yet cultivation is severely threatened by Fusarium wilt (Fusarium oxysporum f. sp. cubense, Foc), necessitating sustainable, eco-friendly management strategies. This study evaluated the biocontrol potential of endophytic bacteria isolated from Foc-resistant and -susceptible banana cultivars. Isolates from the pseudostem, corm, and root of the resistant cultivar showed significantly greater inhibitory activity than those from the susceptible cultivar, underscoring the role of host genotype in shaping functionally competent endophytic communities. Among all isolates, Bacillus sp. from the corm of cv. Rose (AB) showed the highest mycelial inhibition of Foc (70.37–76.54%) in vitro. GC-MS-based metabolite profiling revealed a chemically diverse array of secondary metabolites, fatty acid esters, steroids, terpenoids, siloxanes, and nitrogenous compounds. Corm-associated endophytes exhibited membrane-disruptive and cytotoxic activity, while root-associated endophytes contributed protective, defense-modulatory effects. Halomonas sp. RoRo2 and B. subtilis RoC1 showed the highest inhibition in both agar-well and in planta assays, with unsaturated fatty acids and organic acid derivatives implicated as key antifungal effectors acting through multiple biochemical pathways. These findings identify metabolically versatile endophytes as promising candidates for developing efficient, environmentally compatible bioinoculants as sustainable alternatives to chemical control of Fusarium wilt in banana.
D. P. Mohite, Kavino Mathiyazhagan, Nakkeeran Sevugapperumal et al.· Pathogens· 0 citations
Chia (Salvia hispanica L.) is an emerging crop in Bangladesh valued for its medicinal properties and economic significance. In March 2024, target spot-like symptoms were observed in an experimental chia field (24.75° N, 90.50° E) at Bangladesh Agricultural University in Mymensingh, Bangladesh, with disease incidence ranged from 23% to 47% across approximately 0.25 ha. Initially appearing as brick-red spots, these symptoms developed into target-shaped concentric rings, affecting leaves, stems, and inflorescences. A total of 24 fungal isolates were recovered from infected tissue; two representative isolates (BGECh-3 and BGECh-4) were randomly selected for detailed characterization. Pathogen identity was established through morphological traits, multilocus phylogenetic analysis of internal transcribed spacer (ITS) and elongation factor 1-alpha (TEF-1α) gene sequences identifying the causal agent as Corynespora cassiicola. Pathogenicity was confirmation through Koch’s postulates, and the isolates demonstrated a broad host range and were pathogenic to brinjal, chili, bottle gourd, country bean, tomato, and soybean. In vitro fungicide sensitivity assays with seven commercial fungicides showed that both isolates were highly sensitive to Goldazim (50% carbendazim), which caused 98.05 ± 2.88% mycelial growth inhibition at 10 µg mL − ¹ and complete inhibition at higher concentrations, with the lowest EC50 (0.76 µg mL − ¹). Conza (10% Hexaconazole) and Amistar top (18.2% azoxystrobin + 11.4% difenoconazole) also exhibited high efficacy, achieving 86.17 ± 1.31% and 67.77 ± 1.34% inhibition, respectively, at the same concentration, with EC50 values of 1.34 and 1.09 µg mL − ¹, respectively. Tilt (25% propiconazole) showed moderate activity (59.30 ± 2.08% inhibition at 10 µg mL − ¹; EC50 = 4.75 µg mL − ¹), whereas the remaining fungicides exhibited comparatively lower efficacy and did not produce reliable EC50 estimates. This study represents the first report of target spot disease of chia caused by C. cassiicola in Bangladesh and provides insights for effective disease management strategies.
Avi Kumar Badhon, D. R. Gupta, Swapan Kumar Paul et al.· PLoS ONE· 0 citations
The results show that FOLac populations in Spain are epidemiologically and biologically heterogeneous and highlight the need to integrate molecular tools and pathogenicity assays for race surveillance, breeding programs, and disease management.
Moises Bernal De Leon, Daniel Palmero, Laura Gálvez· Plant Disease· 0 citations
Apple bitter rot, caused by Colletotrichum species, is a major constraint to apple production in Korea. This study investigated the nationwide distribution and fungicide resistance of Colletotrichum species collected from five major apple-producing regions over 10 years (2015-2024). Among 319 isolates, C. fructicola (54%) and C. siamense (37%) were identified as the predominant species through multi-locus phylogenetic analysis and species-specific PCR. A distinct geographical pattern was observed: C. siamense predominated in northern regions, while C. fructicola was more prevalent in southern regions, although the frequency of C. fructicola has recently increased in the north. Fungicide sensitivity assays revealed that C. fructicola isolates exhibited high dual resistance to pyraclostrobin and benomyl, whereas C. siamense remained sensitive to both. Molecular analysis confirmed that resistance was associated with G143A mutations in the cyt b gene and E198A mutations in the tub2 gene, respectively. Field fitness evaluations, including mycelial growth, pathogenicity, and sporulation at various temperatures, showed no significant differences between the two species. These results demonstrate a clear fungicide-driven species replacement, where the ecological success of C. fructicola is attributed to its dual resistance rather than physiological superiority. This study provides critical evidence of how long-term selection pressure reshapes pathogen population dynamics, necessitating a re-evaluation of current management strategies.
Abdulkareem Abdullahi, S. An, Soobin Park et al.· Plant Pathology Journal· 0 citations
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