Alternaria atra from distinct ecological contexts share functional genomic repertoires

Abstract 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 whether isolates of Alternaria atra originating from different ecological contexts differ in their genomic repertoires. We generated draft genome assemblies for two newly collected isolates obtained as putative endophytes from asymptomatic plant tissue. 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; i.e. extracted from symptomatic plant tissue. Despite differing ecological origins, the 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 detected no clear genomic signatures associated with isolates originating from asymptomatic or symptomatic plant tissue. These findings suggest that the currently available A. atra genomes share a largely conserved genomic repertoire despite contrasting ecological origins . This observation is consistent with a model of lifestyle plasticity rather than fixed genomic specialization. Although our conclusions are based on a limited number of available genomes, our results further support the growing view that genome content alone may not reliably predict ecological behaviour in ascomycete fungi.