Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control.

TitlePopulation genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control.
Publication TypeJournal Article
Year of Publication2010
AuthorsNeafsey, DE, Barker, BM, Sharpton, TJ, Stajich, JE, Park, DJ, Whiston, E, Hung, C-Y, McMahan, C, White, J, Sykes, S, Heiman, D, Young, S, Zeng, Q, Abouelleil, A, Aftuck, L, Bessette, D, Brown, A, FitzGerald, M, Lui, A, J Macdonald, P, Priest, M, Orbach, MJ, Galgiani, JN, Kirkland, TN, Cole, GT, Birren, BW, Henn, MR, Taylor, JW, Rounsley, SD
JournalGenome Res
Volume20
Issue7
Pagination938-46
Date Published2010 Jul
ISSN1549-5469
KeywordsBase Sequence, California, Coccidioides, DNA Transposable Elements, Evolution, Molecular, Gene Expression Regulation, Fungal, Genetic Variation, Genome, Fungal, Hybridization, Genetic, Metagenomics, Molecular Sequence Data, Mutagenesis, Insertional, Polymorphism, Single Nucleotide, Repetitive Sequences, Nucleic Acid, Sequence Analysis, DNA
Abstract

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.

DOI10.1101/gr.103911.109
Alternate JournalGenome Res.
PubMed ID20516208
PubMed Central IDPMC2892095
Grant ListHHSN266200400001C / / PHS HHS / United States
R01 AI070891 / AI / NIAID NIH HHS / United States
R01 AI071118 / AI / NIAID NIH HHS / United States
R01AI70891 / AI / NIAID NIH HHS / United States
U54-AI65359 / AI / NIAID NIH HHS / United States