Biology subjects

Schmey, T.

Publications and source records attributed to Schmey, T..

3 recordsLinked to original sources

bioRxiv2026

Alternaria atra from distinct ecological roles share functional genomic repertoires

Fungi, particularly ascomycetes, exhibit diverse ecological lifestyles, including endophytism, pathogenicity, and saprotrophy. Species of the genus Alternaria are taxonomically and ecologically diverse, yet the genomic determinants underlying different lifestyles remain poorly understood. Here, we investigate lifestyle-associated genomic variation in Alternaria atra using two newly collected isolates obtained as plant endophytes. We confirm their taxonomic identity and generate draft genome assemblies for both isolates. We assess their phenotypic behaviour under laboratory conditions and examine their genomic features alongside those of a previously published A. atra isolate described as pathogenic. Despite differing isolation histories, the endophytic and pathogenic isolates exhibit similar behaviour under laboratory conditions and possess highly comparable genomic repertoires, including predicted effector proteins, carbohydrate-active enzymes, and biosynthetic gene clusters. We detect no clear genomic signatures distinguishing endophytic and pathogenic origins or lifestyles. These findings suggest that A. atra harbours a shared genomic repertoire compatible with multiple ecological strategies, supporting a model of lifestyle plasticity rather than fixed genomic specialization. Our results add to growing evidence that genome content alone does not reliably predict ecological roles in ascomycete fungi.

genomics↗

bioRxiv2025

Evolutionary divergence in sympatric populations of the fungal pathogen Alternaria alternata across wild tomato hosts

Alternaria alternata is a globally distributed fungal pathogen with a broad host range, increasingly affecting both tomato crops and wild tomato relatives. The genomic basis of this ecological breadth in A. alternata remains poorly understood. Here we leverage the opportunity of wild pathosystems to study pathogen evolution and diversity beyond agricultural settings. We sampled isolates from wild tomato species across a 2,500 km range in South America, producing highly contiguous genomes, to investigate population structure. Our comparative genomics analyses reveal that A. alternata sensu stricto consists of two divergent clades. Strikingly, this divergence is not linked to host species, geography, or habitat type. Transposable elements contribute to variation within clades but do not explain their separation. Although some signs of recombination are present, reproductive mode appears stable across clades. Notably, global reference isolates cluster with one clade, while the other, more diverse clade is only found in wild populations. We hypothesize that these wild populations may act as reservoirs of evolutionary potential. These findings challenge prevailing assumptions about the population structure of necrotrophic pathogens and raise new questions about how genetic divergence can persist without ecological or geographic isolation. Media summary (lay abstract)The fungus Alternaria alternata is an emerging threat on tomato and potato crops. In a previous study, we found that it also infects wild tomato plants over a large range in Chile and Peru. Here we sequenced and compared full genomes of the fungi. Surprisingly, they formed two distinct groups that do not reflect different host plant species, geographical locations, or environments. One of those groups is related more closely to global reference samples, while the other group is more diverse. This suggests wild plants may quietly harbour forms of the fungus that could affect crops in the future.

genomics↗

bioRxiv2022

Small-spored Alternaria spp. (section Alternaria) are common on wild tomato species

The wild relatives of modern tomato crops are native to South America. These plants occur in habitats as different as the Andes and the Atacama Desert and are to some degree all susceptible to fungal pathogens of the genus Alternaria. Alternaria is a large genus. On tomato, several species cause early blight, leaf spot, and other diseases. We collected Alternaria-like infection lesions from the leaves of eight wild tomato species from Chile and Peru. Using molecular barcoding markers, we characterized the pathogens. The infection lesions were caused predominantly by small-spored species of Alternaria of the section Alternaria, like A. alternata, but also by Stemphylium spp., Alternaria spp. from the section Ulocladioides, and other related species. Morphological observations and an infection assay confirmed this. Comparative genetic diversity analyses show a larger diversity in this wild system than in studies of cultivated Solanum species. As A. alternata has been reported to be an increasing problem on cultivated tomato, investigating the evolutionary potential of this pathogen is not only interesting to scientists studying wild plant-pathosystems. It could also inform crop protection and breeding programs to be aware of potential epidemics caused by species still confined to South America.

microbiology↗