Erica M. Goss

Black pod rot caused by Phytophthora megakarya is a major disease impacting cacao ( Theobroma cacao L.) production in West Africa. Resistance is influenced by genetic variation in both host and pathogen populations. While genomic prediction approaches have been widely applied in plant breeding, most studies incorporate only host genomic information. The value of explicitly modeling pathogen genomic relatedness in quantitative disease prediction remains largely unknown. We genotyped 947 clones from the International Cacao Collection at CATIE using a 10K-SNP panel and characterized 67 P. megakarya isolates by sequencing 3,505 virulence-associated genes and 2,774 SNP loci. Cacao clones were extensively admixed, while isolates formed three geographically structured subpopulations. Mixed linear models were fitted to lesion diameters on detached pods of 350 genotyped clones inoculated with 58 isolates in 30 bioassays, covering 5% of possible clone-by-isolate combinations. Differences among isolates explained a larger share of lesion-size variation than differences among clones (0.34 and 0.27 of phenotypic variance, respectively). After accounting for broad pathogen subpopulation structure, incorporating within-subpopulation genomic relatedness among isolates improved neither model fit nor prediction, whereas incorporating genomic relationships among cacao clones improved model fit and enabled prediction of phenotypically untested clones with a predictive ability of 0.41. Clone rankings were stable across pathogen subpopulations (genomic correlation 0.86 ± 0.06), whereas clone-by-isolate interactions accounted for little phenotypic variation and were not resolved with confidence in the sparse design. An exploratory ancestry analysis associated several Upper Amazon ancestry components with smaller predicted lesions. These are the first genomic predictions of resistance to P. megakarya in cacao. In this strongly structured host-pathogen system, genomic relationships among hosts carried most of the predictable signal beyond broad pathogen subpopulation effects, and the predictions provide a starting point for prioritizing screening and selection efforts.

The reported genome represents a nearly complete reference assembly of the mammalian pathogenic oomycete Pythium insidiosum , generated from clinical isolates collected from animals in the southern United States. Genome assembly was performed from combined long- and short-read sequencing data obtained with the Oxford Nanopore Technologies and Illumina MiSeq platforms.

The management of bacterial spot of tomato is challenged by the widespread occurrence of copper resistance among its causal pathogens. In Xanthomonas euvesicatoria pv. perforans , a major causal agent, copper resistance is conferred by cop genes organized in an operon located on either the chromosome or plasmid. In the United States, copper resistance is predominantly chromosomally encoded. Plasmid-borne resistance is limited to a few phylogenetic groups but is prevalent in other bacterial spot pathogens. We hypothesized that plasmid-encoded copper resistance genes exhibit higher expression than chromosomally encoded genes but may be unstable in the absence of selective pressure for resistance. To test this hypothesis, we examined how the chromosomal versus plasmid-borne cop operon influences gene copy number and expression, as well as plasmid stability. Relative to strains with only chromosomal resistance, strains carrying plasmid-encoded resistance exhibited an increased copy number of copB , a key gene in the operon, while strains carrying both chromosomal and plasmid-encoded resistance showed an even greater increase in gene copy number. Correspondingly, copB expression was elevated in both groups. During in vitro growth without copper, partial or complete plasmid loss occurred in a subset of strains, and genome sequencing of colonies with reduced plasmid size revealed transposase-mediated plasmid rearrangements. These findings demonstrate that plasmid-borne copper resistance increases gene copy number and expression of copper resistance genes but can be unstable without copper selection in some strain backgrounds, highlighting the role of mobile genetic elements in shaping Xanthomonas euvesicatoria pv. perforans adaptation to changing copper environments. IMPORTANCE: Plasmids are key players in the dissemination of antimicrobial resistance. Although copper resistance is widespread among Xanthomonas euvesicatoria pv. perforans strains, copper-based bactericides remain at the forefront of disease management. We previously demonstrated that distinct genetic elements, including plasmid- and chromosomally encoded genomic islands, contribute to the acquisition of copper resistance and the occurrence of multicopy resistance in X. euvesicatoria pv. perforans . Here, we show that the localization of copper resistance genes on a plasmid, chromosome, or both influences gene copy number and expression of copper resistance genes. Furthermore, rearrangements between co-resident plasmids affect plasmid stability, leading to the loss of copper resistance in X. euvesicatoria pv. perforans . These findings highlight how plasmid dynamics can shape bacterial evolvability and adaptation to selective environments.

A draft genome sequence of the mammalian pathogenic oomycete Paralagenidium karlingii was generated from canine clinical isolate samples collected in the Eastern United States. Genome assembly was performed from a combination of long- and short-read sequencing data, followed by annotation of a 16,944 predicted protein-coding genes data set.

: Black pod disease is a major threat to global cacao ( Theobroma cacao L.) production. It is caused by multiple Phytophthora species with geographic ranges from regionally restricted to pantropical, and developing resistant cultivars requires screening against the diversity of these pathogens. This study evaluated the response of 25 cacao clones to 13 isolates of P. palmivora (eight), P. megakarya (two), and P. theobromicola (three) by nonwounding inoculation of detached pods. Lesion size and lesion expansion status were evaluated 4 days after inoculation. The linear mixed model included 178 combinations among 17 clones and 12 isolates, each represented by at least two biological replicate pods. Lesion size differed among clones (F _{(16, 449.2)} = 25.16) and among isolates (F _{(11, 416.0)} = 32.90), and the clone by isolate interaction was significant (F _{(150, 465.4)} = 1.72; all P < 0.001). PENTAGONA-17 had the smallest estimated marginal lesion size (9.3 mm) and fitted values of 3.8 to 16.9 mm across 11 isolates representing all three species. ARF-31, ICS-47, POUND-7, and PMCT-73 had the next four smallest estimates, whereas NA-246 had the largest (36.7 mm). Isolate estimates varied more than fourfold, from 9.6 to 42.0 mm. Despite a marginal estimate of 12.9 mm, POUND-7 had a fitted estimate of 49.2 mm with P. megakarya GH34. The probability of lesion expansion also differed among clones and isolates (both P < 0.001). Together, these findings identify candidates for further resistance evaluation and show that multi-isolate screening provides a stronger basis for selecting materials for black pod resistance breeding.

Bacterial spot of tomato and pepper (BST/P) is an economically devastating disease caused by four distinct Xanthomonas pathogens: X. euvesicatoria pv. euvesicatoria ( Xe ), X. euvesicatoria pv. perforans ( Xp ), X. hortorum pv. gardneri ( Xg ), and X. vesicatoria ( Xv ). A key component of virulence in these pathogens is the type III secretion system (T3SS), which delivers type III effector (T3E) proteins into host plant cells. To comprehensively characterize T3E repertoires and assess the stability of core effectors at a population scale, we evaluated a global dataset comprising 1,037 quality-filtered genomes, including 585 Xp , 350 Xe , 69 Xg , and 33 Xv strains. Across this collection, genes for six effectors were present in 100% of the examined genomes (XopK, XopL, XopM, XopN, XopX, and XopZ1) and an additional four effectors in ≥95% of genomes (XopK, XopL, XopM, XopN, XopX, and XopZ1). Xp and Xe populations maintained large total effector repertoires with extensive allelic variation, displaying exceptional polymorphism within XopD and XopAD. In contrast, Xg and Xv exhibited highly stable effector profiles with markedly reduced allelic diversification across geographic regions and decades. Disruptive mutations, including early stop codons and frameshifts mutations, in genes for XopAZ, XopAF, and XopAR were prevalent across specific pathogens pointing to ongoing pseudogenization and targeted gene loss. These findings provide a high-resolution characterization of the conserved and variable components of the BST/P pathogen effector arsenal and serve as a foundation for monitoring population evolution and breeding durable disease resistance to multiple pathogens.

In the bacterial spot of tomato disease complex, Xanthomonas euvesicatoria pv. perforans (Xep) is known to outcompete X. euvesicatoria pv. euvesicatoria (Xee). The result, over time in tomato production systems where both pathogens are present, is the anticipated displacement of Xee by Xep. In this study, we characterized the population of recovered strains from grower fields in response to a bacterial spot of tomato outbreak in east and central Oklahoma in 2018 and 2019. Tomato and pepper strains sampled in earlier years were included to provide additional context. Phenotypic and genome-based analyses showed marked differences in race and species composition in recovered strains. All pre-2018 (2001 to 2014) tomato bacterial spot strains were Xep race T3, except one T4 strain. Tomato bacterial spot strains in 2018 consisted of Xee race T1 and Xep T3, whereas strains recovered in 2019 from the same locations were exclusively Xep T4 strains. The 2019 Xep T4 strains form the same cluster with the 2014 Xep T4 strain on the phylogenetic tree, suggesting the same population. Only the Xep race T4 strains did not elicit a hypersensitive reaction on pepper. The recovered strains were also variable in copper sensitivity and effector content. We additionally recovered nonbacterial spot xanthomonads, one of which belongs to the new species Xanthomonas oklahomensis sp. nov. These results contribute to novel insights in understanding genomic heterogeneity and seasonal population flux between competing bacterial genotypes during disease outbreaks and can be considered when developing disease-management strategies.

Decomposition of plant litter, facilitated primarily by microbial decomposers, plays a critical role in biogeochemical cycling and ecosystem function. The rate of litter decomposition can determine its environmental impact, where accelerated decomposition alters the timing and rate of nutrient release and may promote nutrient leaching, whereas slowed decomposition can result in litter accumulation, which impacts seedling recruitment, fire regimes, perennation of microbial communities, and slows nutrient release. Mutualistic endophytes are known to slow litter decomposition, but less is known about the impact that plant pathogens, present in diseased litter, have on decomposition rates. We compared litter decomposition of the invasive annual grass Microstegium vimineum with Bipolaris leaf spot symptoms, a fungal disease, to litter without symptoms of the disease in a year‐long common garden experiment. We found leaf tissue with disease symptoms decomposed later in the year compared to litter without symptoms. By summer, 54% of leaf tissue from healthy sites remained compared to 80% of leaf material from diseased litter. Fungal infection did not impact the lignin or C:N content of the litter. There were significant differences in fungal community composition between infected and healthy litter at the start of the experiment that persisted until the end of summer. Disease epidemics prior to senescence contributed to the persistence of infected tissue, which could slow the return of nutrients to the environmental pool and promote the survival and dispersal of pathogen inoculum the following season.

Xanthomonas spp. are increasingly recognized as a global threat to agriculture, impacting a broad range of economically important crops. We report the whole-genome sequences of six Xanthomonas strains isolated from tomato and pepper plants in Turkey that were experiencing symptoms of bacterial spot disease. Phylogenomic analysis with representative Xanthomonas genomes from each species revealed that three of these strains belonged to Xanthomonas perforans , two to Xanthomonas euvesicatoria and one to Xanthomonas campestris . We then analysed the phylogenomic relatedness of these strains with other strains from these respective species and characterized their type III secreted effector content. These genomic data represent a valuable resource for understanding the genetic diversity and local epidemiology of bacterial spot disease in Turkey.