NCM 2022: Using nanopore sequencing to investigate genome evolution in fungal symbioses: ploidy, repetitive elements, and reproduction

Symbiotic fungi perform many globally essential ecosystem services. They are fascinating research systems that expand our understanding of biological processes, including symbiont co-evolution, microbial community dynamics, and metabolite economies. Lichenised fungi, which form mutualistic relationships with algae and/or cyanobacteria, are highly specialised and are abundant and diverse in all terrestrial ecosystems. Nineteen lichen metagenomes assembled with long-read data generated on Oxford Nanopore Technologies platforms yielded some of the most complete and contiguous genomes for lichenised fungi. These data revealed that lichenised fungi can be polyploid, repetitive elements in genomes have proliferated in specific lineages, and putatively asexual lineages retain functional mating genes. Near telomere-to-telomere assemblies have also allowed for chromosome number inferences in species for which flow cytometry is challenging or impossible. Routine production of highly complete and contiguous genomes from long-read sequencing of environmental fungal samples promises to rapidly advance knowledge of fungal genome architecture and evolution.