UC Riverside

Batrachochytrium dendrobatidis (Bd) is unique among the fungal phylum Chytridiomycota. Bd and its relative species Batrachochytrium salamandrivorans (Bsal) are the only known species of this phylum known to cause disease in vertebrates. Bd causes the devastating amphibian disease, chytridiomycosis, a disease that contributed to the extinctions of nearly seven percent of all known frog species. Bd is a diverse species divided into distinct lineages; Global Panzootic Lineage (Bd-GPL), Bd-BRAZIL, Bd-ASIA, Bd-CAPE. Importantly Bd-GPL is the only lineage that is globally distributed while the others are restricted geographically. In this thesis I utilize comparative genomics and transcriptomics to examine how the genomes of Bd differ by lineage and establish a pangenome of Bd. I further employ these comparative strategies to investigate the presence of Endogenous Viral Elements (EVEs) in Bd and other fungal species. In Chapter one, I illustrate the genomic diversity of Bd strains from the Bd-BRAZIL and Bd-GPL lineages. Here I compare the genomic repertoire of pathogenicity genes between strains from these two lineages and explain the potential pitfalls when relying on a single Bd reference genome for transcriptomic analysis. Using these and other genomic resources, we discovered a novel endogenous DNA mycovirus, Batrachochytrium dendrobatidis DNA virus 1 (BdDV-1), present in the enzootic Bd lineages but absent in Bd-GPL. In chapter two I investigate the evolutionary history of BdDV-1 and its relationship with Bd. I describe Bd as an EVE derived from the family Circoviridae. BdDV-1 was associated with differential gene expression between two closely related EVE positive (EVE+) and EVE negative (EVE-) strains. My collaborators at the University of Michigan found a correlation between Bd’s virulence and the presence of BdDV-1. They found that frogs infected with EVE+ Bd strains displayed increased mortality, succumbing to chytridiomycosis faster than frogs infected with EVE- strains. In chapter three I perform a wide-scale search for EVEs in the fungal kingdom. I report the presence of 1210 unique EVEs in 333 genomes from eight phyla.