Jessica Allen: Using nanopore sequencing to investigate genome evolution in fungal symbioses

Symbiotic fungi perform many globally essential ecosystem services. They are fascinating
research systems that expand our understanding of biological processes, including symbiont coevolution, microbial community dynamics, and metabolite economies. Lichenized fungi, which form mutualistic relationships with algae and/or cyanobacteria, are highly specialized 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 lichenized fungi. These data revealed that lichenized 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.