Abstract
The Global Pandemic Lineage (GPL) of the amphibian pathogen Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions on nearly every continent. Near complete genome of three Bd-GPL strains have enabled studies of the pathogen but the genomic features that set Bd-GPL apart from other Bd lineages 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 three Bd-BRAZIL isolates and one non-pathogen outgroup species Polyrhizophydium stewartii (Ps) strain JEL0888, and compared these to genomes of previously sequenced Bd-GPL strains. The Bd-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 of Bd consists of 6278 conserved gene families, with 202 Bd-BRAZIL and 172 Bd-GPL specific gene families. We discovered gene copy number variation in pathogenicity gene families between Bd-BRAZIL and Bd-GPL strains though none were consistently expanded in Bd-GPL or Bd-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 in Bd-BRAZIL and Bd-GPL and offers insights into the application of these genomes as reference genomes for future studies.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
We have performed an analysis to enumerate expanding and contracting gene families between Bd, Ps, Hp, and Bsal. Additionally we include the Accession numbers for the Bd-BRAZIL genomes sequenced as part of this study.
Data Availability
The primary sequence data for Nanopore and Illumina DNA sequencing data are under BioProjects PRJNA987700 (Polyrhizophydium stewartii JEL0888), (Batrachochytrium dendrobatidis CLFT067 [PRJNA987741]), Batrachochytrium dendrobatidis CLFT044 [PRJNA821523], and Batrachochytrium dendrobatidis CLFT071 [PRJNA913953]. RNA sequencing data are deposited under the accession numbers GSE253912 and GSE246809. Genome assemblies for Bd strains, CLFT044, CLFT067, and CLFT071 are deposited under the Accession numbers; GCA_036783925.1, GCA_036289345.1, and GCA_029704095.1 respectively.
