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

被引：135

作者：

Neafsey, Daniel E. ^{[1
]}

Barker, Bridget M. ^{[2
]}

Sharpton, Thomas J. ^{[3
]}

Stajich, Jason E. ^{[4
]}

Park, Daniel J. ^{[1
]}

Whiston, Emily ^{[5
]}

Hung, Chiung-Yu ^{[6
]}

McMahan, Cody ^{[6
]}

White, Jared ^{[1
]}

Sykes, Sean ^{[1
]}

Heiman, David ^{[1
]}

Young, Sarah ^{[1
]}

Zeng, Qiandong ^{[1
]}

Abouelleil, Amr ^{[1
]}

Aftuck, Lynne ^{[1
]}

Bessette, Daniel ^{[1
]}

Brown, Adam ^{[1
]}

FitzGerald, Michael ^{[1
]}

Lui, Annie ^{[1
]}

Macdonald, J. Pendexter ^{[1
]}

Priest, Margaret ^{[1
]}

Orbach, Marc J. ^{[7
]}

Galgiani, John N. ^{[8
]}

Kirkland, Theo N. ^{[9
]}

Cole, Garry T. ^{[6
]}

Birren, Bruce W. ^{[1
]}

Henn, Matthew R. ^{[1
]}

Taylor, John W. ^{[5
]}

Rounsley, Steven D. ^{[7
]}

机构：

[1] Broad Inst, Cambridge, MA 02142 USA

[2] Montana State Univ, Dept Vet Mol Biosci, Bozeman, MT 59717 USA

[3] Gladstone Inst Cardiovasc Dis, San Francisco, CA 94158 USA

[4] Univ Calif Riverside, Riverside, CA 92521 USA

[5] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA

[6] Univ Texas San Antonio, Dept Biol, San Antonio, TX 78249 USA

[7] Univ Arizona, Sch Plant Sci, Tucson, AZ 85721 USA

[8] Univ Arizona, Valley Fever Ctr Excellence, Tucson, AZ 85724 USA

[9] Univ Calif San Diego, Dept Pathol, La Jolla, CA 92093 USA

来源：

GENOME RESEARCH | 2010年 / 20卷 / 07期

关键词：

POSADASII; GENE; ALIGNMENT; SOFTWARE; VACCINES; IMMITIS; MICE;

D O I：

10.1101/gr.103911.109

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 degrees 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.

引用

页码：938 / 946

页数：9

共 40 条

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