Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii

MBio
Rhys A FarrerChristina A Cuomo

Abstract

Cryptococcus gattii is a fungal pathogen of humans, causing pulmonary infections in otherwise healthy hosts. To characterize genomic variation among the four major lineages of C. gattii (VGI, -II, -III, and -IV), we generated, annotated, and compared 16 de novo genome assemblies, including the first for the rarely isolated lineages VGIII and VGIV. By identifying syntenic regions across assemblies, we found 15 structural rearrangements, which were almost exclusive to the VGI-III-IV lineages. Using synteny to inform orthology prediction, we identified a core set of 87% of C. gattii genes present as single copies in all four lineages. Remarkably, 737 genes are variably inherited across lineages and are overrepresented for response to oxidative stress, mitochondrial import, and metal binding and transport. Specifically, VGI has an expanded set of iron-binding genes thought to be important to the virulence of Cryptococcus, while VGII has expansions in the stress-related heat shock proteins relative to the other lineages. We also characterized genes uniquely absent in each lineage, including a copper transporter absent from VGIV, which influences Cryptococcus survival during pulmonary infection and the onset of meningoencephalitis. T...Continue Reading

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Datasets Mentioned

BETA
CBS10090
AAFP01000000
ATAL01000000
AZGX01000000
ASCQ01000000
ATAM01000000
AVEY01000000
AZGW01000000
ASCM01000000
AAFP02000000

Methods Mentioned

BETA
Illumina sequencing
glycosylation
PCA

Software Mentioned

GeneWise
RepeatMasker
Pilon
SAMtools54
BWA
BLASTz
Picard
RAxML
MEM
HMMER3

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