Comparative genomics reveals intra and inter species variation in the pathogenic fungusBatrachochytrium dendrobatidis

Abstract

AbstractThe Global Pandemic Lineage (GPL) of the amphibian pathogenBatrachochytrium dendrobatidis(Bd) has been described as a main driver of amphibian extinctions on nearly every continent. Near complete genome of threeBd-GPL strains have enabled studies of the pathogen but the genomic features that setBd-GPL apart from otherBdlineages is not well understood due to a lack of high-quality genome assemblies and annotations from other lineages. We used long-read DNA sequencing to assemble high-quality genomes of threeBd-BRAZIL isolates and one non-pathogen outgroup speciesPolyrhizophydium stewartii(Ps) strain JEL0888, and compared these to genomes of previously sequencedBd-GPL strains. TheBd-BRAZIL assemblies range in size between 22.0 and 26.1 Mb and encode 8495-8620 protein-coding genes for each strain. Our pan-genome analysis provided insight into shared and lineage-specific gene content. The core genome ofBdconsists of 6278 conserved gene families, with 202Bd-BRAZIL and 172Bd-GPL specific gene families. We discovered gene copy number variation in pathogenicity gene families betweenBd-BRAZIL andBd-GPL strains though none were consistently expanded inBd-GPL orBd-BRAZIL strains. Comparison within the Batrachochytrium genus and two closely related non-pathogenic saprophytic chytrids identified variation in sequence and protein domain counts. We further test these new Bd-BRAZIL genomes to assess their utility as reference genomes for transcriptome alignment and analysis. Our analysis examines the genomic variation between strains inBd-BRAZIL andBd-GPL and offers insights into the application of these genomes as reference genomes for future studies.