Tapping Culture Collections for Fungal Endophytes: First Genome Assemblies for Three Genera and Five Species in the Ascomycota

The Ascomycota form the largest phylum in the fungal kingdom and show a wide diversity of lifestyles, some involving associations with plants. Genomic data are available for many ascomycetes that are pathogenic to plants, but endophytes, which are asymptomatic inhabitants of plants, are relatively understudied. Here, using short- and long-read technologies, we have sequenced and assembled genomes for 15 endophytic ascomycete strains from CABI's culture collections. We used phylogenetic analysis to refine the classification of taxa, which revealed that 7 of our 15 genome assemblies are the first for the genus and/or species. We also demonstrated that cytometric genome size estimates can act as a valuable metric for assessing assembly completeness, which can easily be overestimated when using BUSCOs alone and has broader implications for genome assembly initiatives. In producing these new genome resources, we emphasise the value of mining existing culture collections to produce data that can help to address major research questions relating to plant-fungal interactions.

Automated summary

The Ascomycota, the largest phylum in the fungal kingdom, exhibit diverse lifestyles, including associations with plants. This study focuses on the relatively understudied endophytic ascomycetes, which are asymptomatic inhabitants of plants. By sequencing and assembling genomes for 15 endophytic ascomycete strains and using phylogenetic analysis, the researchers refined the classification of taxa and provided valuable insights into plant-fungal interactions. They also demonstrated the importance of cytometric genome size estimates in assessing assembly completeness.