Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis

G3 : Genes - Genomes - Genetics
Jeanine RefsniderErica Bree Rosenblum

Abstract

Emerging infectious diseasespose a significant threat to global health, but predicting disease outcomes for particular species can be complicated when pathogen virulence varies across space, time, or hosts. The pathogenic chytrid fungus Batrachochytrium dendrobatidis (Bd) has caused worldwide declines in frog populations. Not only do Bd isolates from wild populations vary in virulence, but virulence shifts can occur over short timescales when Bd is maintained in the laboratory. We leveraged changes in Bd virulence over multiple generations of passage to better understand mechanisms of pathogen virulence. We conducted whole-genome resequencing of two samples of the same Bd isolate, differing only in passage history, to identify genomic processes associated with virulence attenuation. The isolate with shorter passage history (and greater virulence) had greater chromosome copy numbers than the isolate maintained in culture for longer, suggesting that virulence attenuation may be associated with loss of chromosome copies. Our results suggest that genomic processes proposed as mechanisms for rapid evolution in Bd are correlated with virulence attenuation in laboratory culture within a single lineage of Bd. Moreover, these genomic pr...Continue Reading

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Citations

Apr 3, 2019·PloS One·Joana Sabino-PintoMiguel Vences
Jan 23, 2020·Genes·Himeshi SamarasingheTimothy Y James
Jun 5, 2019·Proceedings. Biological Sciences·Minjie Fu, Bruce Waldman
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Jun 8, 2021·Journal of the Indian Institute of Science·Gayathri Sreedharan, Karthikeyan Vasudevan

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Software Mentioned

R package
GATK UnifiedGenotyper
Picard
bedtools
snpEff
R scripts
GATK
KernSmooth
IndelRealigner
RealignerTargetCreator

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