Red rot disease reduces sugarcane yield and impacts the sugar quality, posing an important threat to the sugarcane industry in Florida. Although Colletotrichum falcatum, the causal agent of red rot in Florida, was first reported in 1984 based on morphology, molecular and pathological data have remained limited, highlighting the critical need for comprehensive characterization. Thirteen isolates were obtained from three local sugarcane varieties in Belle Glade, Florida. Phylogenetic analyses of five genetic markers (ITS, ACT, TUB2, GAPDH, and CHS-1) confirmed all the strains as C. falcatum. In addition, the study documented the disease progression at the cellular level and assessed the pathogenicity of representative strains using the leaf sheath and whole-seedling inoculation methods. The varieties CP96-1252 and CP89-2143 showed greater host resistance. These findings represent the first report of C. falcatum causing red rot in southern Florida, offer valuable insights for/into red rot management, and provide a basis for future breeding programs to enhance sugarcane resistance to red rot disease.

The transition from manual to mechanical planting in Florida has raised concerns about the impact of mechanical harvesting on seed cane integrity, increasing the potential for infection by naturally occurring soilborne pathogens. Surveys conducted during the 2023 and 2024 planting seasons identified Thielaviopsis sp. and Fusarium sp. in 43 and 38% of the 569 sampled seed cane, respectively. Statistical analyses revealed a positive correlation between muck soils and Thielaviopsis; however, Fusarium incidence appeared to be independent of soil type. Among sugarcane varieties, CP07-2320 exhibited negative correlation to Thielaviopsis but was positively correlated to Fusarium. In contrast, CP96-1252 was particularly correlated to Thielaviopsis and negatively correlated to Fusarium. Of particular interest to growers, CPCL05-1201 demonstrated moderate correlation to both pathogens. Spatial analyses using kernel density estimation highlighted pathogen hotspots, aligning with varietal correlation trends to the two pathogens. This study provides insights for local growers, enabling more informed decisions for targeted disease management, particularly in optimizing variety selection and field practices to mitigate disease risks. These contributions support the sustainable transition to mechanical planting in sugarcane production while offering broader implications for managing soilborne diseases in other agricultural systems.

Colletotrichum sublineola Henn. causes anthracnose disease on grain, forage, and sweet sorghum [Sorghum bicolor (L.) Moench], and on the related weed Johnsongrass [S. halepense (L.) Pers.]. Previous genetic fingerprinting studies using neutral markers indicated C. sublineola in the southeastern United States comprises two divergent populations mostly associated with the Sorghum host species. In the current study, we further characterized these populations by evaluating restriction fragment length polymorphisms (RFLPs) in fourteen putative pathogenicity-related genes (twelve small secreted-protein effector genes and two secondary metabolite-associated protein genes), and by sequencing polymorphic regions of a subset of these genes. These analyses identified three clades: one (clade A) corresponded to the previously defined population isolated mostly from S. bicolor; the other two (clades B and C) revealed further subdivision within the population recovered mostly from S. halepense. Evidence for reticulation among the gene trees suggested that the three clades correspond to genetically distinct subpopulations within C. sublineola. In greenhouse pathogenicity assays, representatives of the A clade caused disease only on S. bicolor, while clade B members caused disease only on S. halepense, and isolates belonging to clade C were pathogenic to both host species. Estimates of genetic variation indicated that the B clade was the most diverse. Members of the three subpopulations were morphologically similar but could be differentiated by single-nucleotide polymorphisms (SNPs) within a subset of the pathogenicity gene alleles, and several phylogenetic sequence markers. These SNPS could be used to identify members of the three subpopulations for future diagnostic, breeding, and research purposes.

Celery leaf curl, or anthracnose, is characterized by leaf curling, leaf spots, and stem lesions, leading to stunted growth and plant death. Colletotrichum fioriniae has been reported as the main causal agent of anthracnose in celery. In the fall of 2022, 2023, and 2024, anthracnose symptoms were observed on 5 to 20% of celery plants in commercial farms in southern Florida. Eighteen strains were collected and, based on phylogenetic analysis of the glyceraldehyde-3-phosphate dehydrogenase ( GAPDH ), chitin synthase 1 ( CHS-1 ), and β-tubulin ( TUB2 ) genes, 17 of them were identified as C. theobromicola and one as C. fioriniae . Four genetically and phenotypically representative strains were selected to spray-inoculate two celery cultivars, Duda 71 and M9, and they confirmed Koch’s postulates by reproducing symptoms and reisolating the same species. However, spots caused by C. theobromicola were generally larger than those caused by C. fioriniae , whereas leaf curl was more pronounced in plants inoculated with C. fioriniae . Although some symptom overlap was observed, C. theobromicola consistently produced petiole lesions, whereas C. fioriniae was uniquely associated with crown necrosis. This study represents the first report of C. fioriniae causing celery anthracnose in Florida and of C. theobromicola causing the disease worldwide. These findings enhance our understanding of the distribution and diversity of Colletotrichum species in Florida and provide a foundation for developing effective disease management strategies for growers in southern Florida.

Chitinases have been demonstrated to enhance plant resistance to fungi in various pathosystems. Although there is evidence of the effectiveness of these proteins in coffee–fungus interactions, no genome-wide identification or characterization of coffee chitinases has been performed. In this study, we employed phylogenetic analysis, domain architecture, gene structure analysis, and subcellular localization to identify and characterize putative genes and proteins in the genomes of Coffea arabica and its progenitors, Coffea canephora and Coffea eugenioides. A total of 113, 47, and 69 putative chitinase proteins were identified in C. arabica, C. canephora, and C. eugenioides, respectively. These chitinases were classified according to their catalytic domains, GH18 and GH19, and into Classes I, II, III, IV, and V, as determined through phylogenetic analysis based on the Arabidopsis thaliana classification. Furthermore, based on orthologous analysis, we identified ten, six, and seven putative chitinases associated with fungal defense responses in C. arabica, C. canephora, and C. eugenioides, respectively. These findings are valuable for future studies focusing on coffee chitinases, particularly on genetic programs involved in plant pathogen resistance.

Pineapple sett rot, caused by Thielaviopsis species, constrains sugarcane production worldwide. Mechanical planting systems facilitate pathogen infection through increased wounding of planting material, exacerbating disease incidence. In Florida's Everglades Agricultural Area, the recent transition from manual to mechanical planting has intensified pineapple sett rot problems, threatening the United States' most important sugarcane-growing region. This study characterized Thielaviopsis isolates from symptomatic sugarcane billets collected during the 2023-2024 Florida planting season to establish species identity, virulence, and baseline fungicide sensitivity. Phylogenetic analysis of concatenated ITS and tef1-α sequences confirmed all 93 isolates as Thielaviopsis ethacetica, representing the first molecular characterization from North American sugarcane. Phylogenetic analysis resolved the Florida population in study into the two previously described intraspecific lineages of T. ethacetica, one isolate assigned to the African lineage and 11 to the South American lineage; the latter exhibited intra-lineage polymorphism resolvable into at the least three subclades. MAT1-1 mating type idiomorphs were detected in 38.7% of isolates; MAT1-2 could not be confirmed due to primer amplification failure. Virulence testing on cultivars CP96-1252 and CPCL05-1201 revealed that all representative isolates were highly pathogenic, reducing survival by 50-98% and plant height by 64-96% at 38 days after inoculation. Among the tested cultivars, CPCL05-1201 displayed higher quantitative resistance to T. ethacetica. Baseline propiconazole sensitivity testing of 14 representative isolates spanning the phylogenetic diversity observed in the population showed uniform susceptibility, with EC₅₀ values from 0.0081 to 0.0115 μg/mL (mean = 0.0095 μg/mL, CV = 12.2%). These values were substantially lower than typical field application rates, suggesting strong propiconazole efficacy. These findings provide critical baseline data for proactive resistance management and breeding programs targeting pineapple sett rot in sugarcane.