Assembly and polishing of repeat-rich fungal genomes, exemplified by the chytrid Batrachochytrium salamandrivorans

Amphibian declines are a threat to global biodiversity and part of Earth’s sixth mass extinction. Amphibian extinctions and extirpations are caused by a variety of factors, including the Chytridiomycosis panzootic and its causative agents: the batrachochytrids Batrachochytrium salamandrivorans (Bsal) and Batrachochytrium dendrobatidis (Bd). Until recently, the genomic basis for the batrachochytrids’ evolution and their virulence was largely unknown. To investigate their virulence and evolution, high-quality genome assemblies were needed. Prior to 2022, only a highly fragmented short-read assembly of Bsal’s genome assembly had been generated and made available, largely owing to its repeat-richness. In 2022, a new assembly based on deep nanopore long-read sequencing provided a much-needed improvement in both contiguity and completeness. The new assembly revealed that Bsal has undergone a repeat-driven genome expansion and has a highly compartmentalized genome architecture. Here, the road map to assembling and polishing a highly repeat-rich chytrid fungus genome using both long and short reads is described, detailing the methodology for each step, and explaining the rationales underpinning those steps. Considerations for tailoring this methodology to other similar genome assemblies are illustrated. Additionally, we describe how a high-quality assembly can be analysed to provide insight into the genomic architecture and the underlying evolutionary processes