Ivanovic, Z. | bioRxiv Science

bioRxiv2025

Distribution and Shared Pathogenicity of Small-Spored Alternaria on Solanaceous Crops in Europe

Small-spored Alternaria species such as A. alternata and A. arborescens are frequently isolated from diseased potato and tomato plants. However, their respective host ranges and pathogenic behaviours remain poorly resolved, and it is unclear whether their occurrence across hosts reflects true specialisation or ecological opportunism. Limited genetic differentiation among these closely related taxa further complicates their classification as primary necrotrophs or secondary colonisers. In this study, we analysed natural populations of small-spored Alternaria from Germany, Poland, and Serbia using molecular phylogenetics, morphological characterisation, and controlled infection assays to clarify species identity, host associations, and pathogenic potential. Both A. alternata and A. arborescens were detected across all regions and hosts, indicating broad distribution and ecological overlap. The two species were consistently isolated from foliar lesions and were each capable of causing characteristic Alternaria Brown-Spot (ABS) symptoms, thereby fulfilling Kochs postulates. Phylogenetic analyses based on Alt A1 and RPB2 loci resolved two well-supported species clades and revealed extensive haplotype sharing across more than 1300 km, multiple hosts, and diverse climates, suggesting high gene flow and limited population structure. The consistent co-occurrence and comparable pathogenicity of A. alternata and A. arborescens underscore their equal ecological relevance and redefine their roles in ABS epidemiology. These findings indicate that perceived differences in host specialisation may be overstated and that both species contribute equally to Alternaria Brown-Spot epidemics in solanaceous crops.

microbiology↗

bioRxiv2021

Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani

Early blight of potato is caused by the fungal pathogen Alternaria solani and is an increasing problem worldwide. The primary strategy to control the disease is applying fungicides such as succinate dehydrogenase inhibitors (SDHI). SDHI-resistant strains, showing reduced sensitivity to treatments, appeared in Germany in 2013, five years after the introduction of SDHIs. Two primary mutations in the Sdh complex (SdhB-H278Y and SdhC-H134R) have been frequently found throughout Europe. How these resistances arose and spread, and whether they are linked to other genomic features, remains unknown. We performed whole-genome sequencing for A. solani isolates from potato fields across Europe (Germany, Sweden, Belgium, and Serbia) to better understand the pathogens genetic diversity in general and understand the development and spread of the genetic mutations that lead to SDHI resistance. We used ancestry analysis and phylogenetics to determine the genetic background of 48 isolates. The isolates can be grouped into 7 genotypes. These genotypes do not show a geographical pattern but appear spread throughout Europe. The Sdh mutations appear in different genetic backgrounds, suggesting they arose independently, and the observed admixtures might indicate a higher adaptive potential in the fungus than previously thought. Our research gives insights into the genetic diversity of A. solani on a genome level. The mixed occurrence of different genotypes and apparent admixture in the populations indicate higher genomic complexity than anticipated. The conclusion that SDHI tolerance arose multiple times independently has important implications for future fungicide resistance management strategies. These should not solely focus on preventing the spread of isolates between locations but also on limiting population size and the selective pressure posed by fungicides in a given field to avoid the rise of new mutations in other genetic backgrounds.

evolutionary biology↗