Sequence capture identifies fastidious chytrid fungi directly from host tissue
Kevin P Mulder1, Anna E Savage2, Brian Gratwicke3
1Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium; Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA.
Fungal Genetics and Biology : FG & B
|December 15, 2023
Summary
This study used sequence capture technology to identify previously uncultured Batrachochytrium dendrobatidis (Bd) fungal lineages in amphibians. This method reveals hidden Bd diversity, crucial for understanding amphibian disease spread.
Area of Science:
- Mycology
- Amphibian Pathology
- Conservation Genetics
Background:
- Batrachochytrium dendrobatidis (Bd) causes chytridiomycosis, a devastating amphibian disease linked to global population declines.
- Previous research relied on culturable Bd strains, potentially missing unculturable or fastidious lineages.
- Understanding Bd diversity is critical for tracking its evolution and spread.
Purpose of the Study:
- To characterize potentially non-culturable genetic lineages of Bd.
- To employ sequence capture technology for direct DNA sequencing from host tissues and swabs.
- To expand genomic data for Bd clades, particularly in understudied regions.
Main Methods:
- DNA extraction from leopard frogs (Rana) from North America and a Japanese Giant Salamander (Andrias japonicus).
- Sequence capture technology to enrich for fungal genes from host-associated DNA.
- Phylogenetic reconstruction using sequenced fungal genes, including the ITS locus.
Main Results:
- Successfully sequenced thousands of fungal genes from both North American and Asian Bd strains.
- Phylogenetic analysis confirmed North American strains belong to the Bd-GPL clade.
- The Japanese Giant Salamander strain was placed within the Bd-Asia3 clade, expanding its known geographic range.
Conclusions:
- Sequence capture is effective for characterizing cryptic and unculturable Bd diversity.
- Recognizing hidden Bd lineages is essential for reconstructing the pathogen's evolutionary history and spatiotemporal spread.
- This approach overcomes limitations of culture-reliant methods in Bd research.
