Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a newly discovered group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27 to 393 kb and last shared a common ancestor ca. 400 Ma. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize four additional Starships whose activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager’s activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first dedicated agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.

Ten morphological groups of plant-parasitic nematodes (spiral, lesion, lance, dagger, stunt, pin, ring, stubby-root, cyst, and miscellaneous tylenchids) were detected in corn fields in Ohio, but the presence and population density of these groups varied among fields. Binary and ordinal logistic regression models were fitted to the data to estimate the odds of each group being present, and the lesion, lance, spiral, and pin nematode population densities being at moderate-high risk levels based on soil region, cropping sequence, tillage, and soil pH, silt content, and electrical conductivity. All covariates were associated with at least one nematode group, but soil region had the greatest and most consistent effect. Dagger and ring nematodes were more likely to be present in region 6 than in any of the other regions, whereas lance, stunt, pin, stubby-root, and spiral nematodes were more likely to be present in regions 1 to 5 than 6. Spiral, lance, and pin nematode population densities were more likely to be at moderate-high risk levels in regions 3 and 4 than in region 6. Fields under conservation tillage were two times more likely to have moderate-high risk lance nematode population densities than fields under conventional tillage. Similarly, pin nematode population densities were two times more likely to be at moderate-high risk levels in fields under rotation than in continuous corn. For every unit increase in soil pH, the odds of the spiral nematode population density being at moderate-high risk levels increased by 43%, but the odds of the lesion and pin nematode population densities being at the same risk level decreased by 63 and 29%, respectively. The predicted probability of lesion and lance population densities being at moderate-high risk levels decreased as the silt content of the soil increased. These finding will be useful for developing future nematode sampling protocols and for assessing the risk associated with nematodes in corn fields in Ohio.

Soil samples were collected from 425 corn fields in 28 Ohio counties between growth stages V3 and V6 during the 2013 and 2014 growing seasons. Ten morphological groups of plant-parasitic nematodes, namely spiral, lesion, lance, dagger, stunt, pin, ring, stubby-root, cyst, and “tylenchids” (several genera morphologically similar to members of the subfamily Tylenchinae [NCBI Taxonomy] including Cephelenchus, Filenchus, Malenchus, and Tylenchus) were identified. Eight species belonging to six of these groups were characterized. Spiral, tylenchids, lesion, pin, lance, stunt, and dagger nematodes were detected in 94, 96, 80, 57, 48, 48, and 37% of the fields, respectively, whereas the stubby-root, cyst, and ring nematodes were present in fewer than 14% of the samples. Averaged across fields, the spiral, tylenchids, and pin nematodes had the highest mean population densities. For all groups, incidence and population density varied among counties, and in some cases, among soil regions and cropping practices. Both population parameters were heterogeneous at multiple spatial scales, with the lowest heterogeneity among soil regions and the highest among fields within county and soil region. Estimated variances at the soil region level were not significantly different from zero for most of the nematodes evaluated. Stunt and lance were two of the most variable groups at all tested spatial scales. In general, the population densities were significantly more heterogeneous at the field level than at the county level. Findings from this study will be useful for developing sampling protocols and establishing on-farm trials to estimate losses and evaluate nematode management strategies.

Los nematodos fitoparásitos se encuentran entre los patógenos de plantas más perjudiciales a través del mundo, afectando el crecimiento y rendimiento de los cultivos. La respuesta de las plantas al daño ocasionado por los nematodos está estrechamente relacionada con su ubicación donde se alimentan, como ectoparásitos o endoparásitos, y los tipos de daño celular que producen, tales como la destrucción de células ocasionada por especies de Pratylenchus y Radopholus; la sincitia, por especies de Heterodera y Globodera; y la formación de células gigantes, por especies de Meloidogyne. El objetivo de esta revisión es analizar el alcance de los resultados de investigaciones sobre el entendimiento de las implicaciones fisiológicas que tiene la interacción de la planta con nematodos fitoparásitos, principalmente los que destruyen la célula, forman sincitia y células gigantes. En general, los nematodos reducen la absorción de agua a través de las raíces de las plantas y crean un desbalance de macro y micronutrimentos que inducen cambios fisiológicos en estas y en los procesos fotosintéticos. Los nematodos fitoparásitos incluidos en esta revisión, independiente del tipo de daño que ocasionan, reducen las funciones fisiológicas de las raíces y de la parte aérea produciendo pérdidas considerables en rendimiento. Se requiere más investigación que relacione el estado nutricional de las plantas con las prácticas de nutrición edáfica y foliar, que conlleve a una mejor respuesta fisiológica del hospedante, lo cual permitiría un menor impacto del parasitismo de los nematodos en las plantas, contribuyendo al manejo integrado de estos

Knowledge of the factors structuring populations of pathogenic fungi is fundamental to disease management efforts and basic biology. However, this crucial information is missing for many important pathogens, including broad-host-range and drought-associated pathogens from the globally distributed Macrophomina genus. The objectives of this work were to evaluate the evidence for host specialization, geographic adaptation, and recombination using a global survey of Macrophomina isolates from diverse geographic, temporal, and host sources. We obtained high-quality short-read sequence data for 463 Macrophomina spp. isolates, representing four putative species, collected from 91 host plant species and soil in 23 countries. Analysis of bi-allelic, single-nucleotide polymorphisms revealed high diversity, admixture, and equal mating type ratios, suggesting ongoing recombination. Although most tested isolates asymptomatically colonized strawberry, only strawberry-derived isolates caused disease on this host. These isolates were all in a single lineage, suggesting that the ability to cause disease on strawberry is not widespread among M. phaseolina. Significant associations were also found between isolations from soybean plants and specific population clusters, suggesting that specialization for virulence or reproduction has also occurred for soybean. Geography × isolate genotype associations were weak, suggesting that Macrophomina spp. were frequently trafficked between regions. Reference-free whole-genome comparisons support current boundaries among four Macrophomina species, and new molecular markers were designed to specifically identify each species. Contrary to expectations, M. phaseolina should be considered a single species with both specialist and generalist populations in which meiosis can maintain genetic diversity. [ ] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Phytophthora is a long-established, well-known, and globally important genus of plant pathogens. Phylogenetic evidence has shown that the biologically distinct, obligate biotrophic downy mildews evolved from Phytophthora at least twice. Because, cladistically, this renders Phytophthora “paraphyletic,” it has been proposed that Phytophthora evolutionary clades be split into multiple genera ( Crous et al. 2021 ; Runge et al. 2011 ; Thines 2023 , 2024 ). In this letter, we review arguments for the retention of the generic name Phytophthora with a broad circumscription made by Brasier et al. (2022) and by many delegates at an open workshop organized by The American Phytopathological Society. We present our well-considered responses to the genus splitting proposals, both in general terms and in terms of the specific proposals for new genera, alongside new information regarding the biological properties and mode of origin of the Phytophthora clades. We consider that the proposals are mostly non-rigorous and not supported by the scientific evidence. Further, given (i) the apparent lack of any distinguishing biological characteristics (synapomorphies) between the Phytophthora clades; (ii) the fundamental monophyly of Phytophthora in the original Haeckelian sense ( Haeckel 1877 ); (iii) the fact that paraphyly is not a justification for taxonomic splitting; and (iv) the considerable likely damage to effective scientific communication and disease management from an unnecessary breakup of the genus, we report that workshop delegates voted unanimously in favor of preserving the current generic concept and for seeking endorsement of this view by a working group of the International Commission on the Taxonomy of Fungi. [ ] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .