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Abstract The amphibian chytrid fungusBatrachochytrium dendrobatidis(Bd) is a cosmopolitan pathogen with numerous distinct lineages. The global panzootic lineage (Bd-GPL) is the most widespread and virulent lineage and is responsible for many recorded amphibian declines. Mapping the extent ofBd-GPL and other more established lineages is important for predicting disease dynamics in amphibian communities. Ecuador is the most biodiverse country per unit area for amphibian taxa and, thus, a priority for studies on genotypic diversity ofBd. In this study, we tested skin swab samples collected from 464 individual amphibians across coastal, Andean montane, and Amazonian forests, for the presence of twoBdlineages known to be present in South America: the globally-distributedBd-GPL and the Brazilian-endemicBd-Asia2/Brazil lineage. By using a discriminatory qPCR SNP assay, we found widespread prevalence ofBd-GPL in Ecuador in diverse host taxa. Genotyping efficiency was 36% in this study, meaning that one in every three swabs that tested positive forBdin infection assays were successfully genotyped. Through this study, we provide further support for the presence of a singleBdlineage in this neotropical biodiversity hotspot.
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Comparative Genomics Reveals Intra and Inter Species Variation in the Pathogenic Fungus Batrachochytrium dendrobatidis
Abstract The Global Panzootic Lineage (GPL) of Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions. Pathogen studies have benefited from three Bd-GPL strain genomes, but identifying the genetic and molecular features that distinguish the B. dendrobatidis lineages requires additional high-quality genomes from diverse lineages. We sequenced and assembled genomes with Oxford Nanopore Technologies to produce assemblies of three Bd-BRAZIL isolates and one nonpathogen outgroup species Polyrhizophydium stewartii. The Bd-BRAZIL assembly sizes ranged between 22.0 and 26.1 Mb with 8,495 to 8,620 predicted protein-coding genes. We sought to categorize the pangenome of the species by identifying homologous genes across the sampled genomes as either being core and present in all strains, or accessory and shared among strains in a lineage, an analysis that has not yet been conducted on B. dendrobatidis and its lineages. We identified a core genome consisting of 6,278 gene families, and an accessory genome of 202 Bd-BRAZIL and 172 Bd-GPL specific gene families. We discovered copy number differences in pathogenicity gene families: M36 Peptidases, Crinkler Necrosis genes, Aspartyl Peptidases, Carbohydrate-Binding Module-18 genes, and S41 Proteases, between Bd-BRAZIL and Bd-GPL strains. Comparison of B. dendrobatidis and two closely related saprophytic species identified differences in protein sequence and domain counts for M36 and CBM18 families respectively. Our pangenome analysis of lineage-specific gene content led us to explore how the selection of the reference genome affects recovery of RNAseq transcripts when comparing different strains. We tested the hypothesis that genomic variation among Bd-GPL and Bd-BRAZIL lineages can impact transcript count data by comparing results with our new Bd-BRAZIL genomes as the reference genomes. Our analysis examines the genomic variation between strains in Bd-BRAZIL and Bd-GPL and offers insights into the application of these high-quality reference genomes resources for future studies.
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- Award ID(s):
- 2215705
- PAR ID:
- 10656446
- Editor(s):
- Giraud, Tatiana
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Genome Biology and Evolution
- Volume:
- 17
- Issue:
- 6
- ISSN:
- 1759-6653
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1093/gbe/evaf114
