Means, motive and opportunity for biological invasions: Genetic introgression in a fungal pathogen

Invasions by fungal plant pathogens pose a significant threat to the health of agricultural ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses to crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen of soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2%-30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss the means, motive and opportunity of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographical areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.

Automated summary

Invasions by fungal plant pathogens pose a significant threat to agricultural ecosystems. Through population genomics study of Colletotrichum truncatum, a polyphagous and invasive pathogen of soybean in Brazil, it was found that the pathogen is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgressed regions, which comprise secreted protein-encoding genes, may be the targets of co-evolutionary selection. Population genomic studies can help identify high-risk geographical areas and pathogens, providing valuable information for future crop protection strategies.