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bioRxiv · 10.1101/2021.11.03.467166

Two-speed genome expansion drives the evolution of pathogenicity in animal fungal pathogens

Wacker, T.·Helmstetter, N.·Wilson, D.·Fisher, M. C.·Studholme, D. J.·Farrer, R. A.
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Abstract

The origins of virulence in amphibian-infecting chytrids Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are largely unknown. Here, we use deep nanopore sequencing of Bsal and comparative genomics against 21 high-quality genome assemblies that span the fungal Chytridiomycota. Bsal has the most repeat-rich genome, comprising 40.9% repetitive elements, which has expanded to more than 3X the length of its conspecific Bd. M36 metalloprotease virulence factors are highly expanded in Bsal and 53% of the 177 unique genes are flanked by transposable elements, suggesting repeat-driven expansion. The largest M36 sub-family are mostly (84%) flanked upstream by a novel LINE element, a repeat superfamily implicated with gene copy number variations. We find that Bsal has a highly compartmentalized genome architecture, with virulence factors enriched in gene-sparse/repeat-rich compartments, while core conserved genes occur in gene-rich/repeat-poor compartments. This is a hallmark of two-speed genome evolution. Furthermore, genes with signatures of positive selection in Bd are enriched in repeat-rich regions, suggesting they are a cradle for chytrid pathogenicity evolution, and Bd also has a two-speed genome. This is the first evidence of two-speed genomes in any animal pathogen, and sheds new light on the evolution of fungal pathogens of vertebrates driving global declines and extinctions.

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Wacker, T., Helmstetter, N., Wilson, D., Fisher, M. C., Studholme, D. J., Farrer, R. A.. 2021-11-04. Two-speed genome expansion drives the evolution of pathogenicity in animal fungal pathogens. https://doi.org/10.1101/2021.11.03.467166

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