Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control.
We have sequenced the genomes of 18 isolates of the closely related human pathogenic fungi Coccidioides immitis and Coccidioides posadasii to more clearly elucidate population genomic structure, bringing the total number of sequenced genomes for each species to 10. Our data confirm earlier microsatellite-based findings that these species are genetically differentiated, but our population genomics approach reveals that hybridization and genetic introgression have recently occurred between the two species. The directionality of introgression is primarily from C. posadasii to C. immitis, and we find more than 800 genes exhibiting strong evidence of introgression in one or more sequenced isolates. We performed PCR-based sequencing of one region exhibiting introgression in 40 C. immitis isolates to confirm and better define the extent of gene flow between the species. We find more coding sequence than expected by chance in the introgressed regions, suggesting that natural selection may play a role in the observed genetic exchange. We find notable heterogeneity in repetitive sequence composition among the sequenced genomes and present the first detailed genome-wide profile of a repeat-induced point mutation (RIP) process distinctly different from what has been observed in Neurospora. We identify promiscuous HLA-I and HLA-II epitopes in both proteomes and discuss the possible implications of introgression and population genomic data for public health and vaccine candidate prioritization. This study highlights the importance of population genomic data for detecting subtle but potentially important phenomena such as introgression.
Neafsey
Daniel E
DE
Broad Institute, Cambridge, Massachusetts 02142, USA. neafsey@broadinstitute.org
Barker
Bridget M
BM
Sharpton
Thomas J
TJ
Stajich
Jason E
JE
Park
Daniel J
DJ
Whiston
Emily
E
Hung
Chiung-Yu
CY
McMahan
Cody
C
White
Jared
J
Sykes
Sean
S
Heiman
David
D
Young
Sarah
S
Zeng
Qiandong
Q
Abouelleil
Amr
A
Aftuck
Lynne
L
Bessette
Daniel
D
Brown
Adam
A
FitzGerald
Michael
M
Lui
Annie
A
Macdonald
J Pendexter
JP
Priest
Margaret
M
Orbach
Marc J
MJ
Galgiani
John N
JN
Kirkland
Theo N
TN
Cole
Garry T
GT
Birren
Bruce W
BW
Henn
Matthew R
MR
Taylor
John W
JW
Rounsley
Steven D
SD
D001483:Base Sequence; D002140:California; D003045:Coccidioides / Q000235:genetics*; D004251:DNA Transposable Elements / Q000502:physiology*; D019143:Evolution, Molecular; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D014644:Genetic Variation; D016681:Genome, Fungal; D006824:Hybridization, Genetic / Q000235:genetics*; D056186:Metagenomics; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional / Q000502:physiology; D020641:Polymorphism, Single Nucleotide; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017422:Sequence Analysis, DNA
D004251:DNA Transposable Elements