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Highly recombinant VGII Cryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution.

Billmyre RB, Croll D, Li W, Mieczkowski P, Carter DA, Cuomo CA, Kronstad JW, Heitman J - MBio (2014)

Bottom Line: We found that VGIIa/b/c populations show evidence of clonal expansion in the PNW.We also found that the genomes of two basal VGII isolates from HIV(+) patients contain an introgression tract spanning three genes.This work shows that multiple processes can contribute to the emergence of an outbreak.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA heitm001@duke.edu.

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Related in: MedlinePlus

Whole-genome allele compatibility test shows evidence for prolific recombination at the population level. (A) An example of a paired allele compatibility test from the VGII population. Alternative SNPs are depicted in red and the reference in white. Evidence for recombination is provided by any pairwise comparison of two loci in which strains are present where red-red, white-white, red-white, and white-red combinations are all found (AB, Ab, aB, and ab) satisfying the allele compatibility test, providing evidence for recombination. (B) One hundred random SNPs were selected from the VGII data set and collapsed into 46 unique allele patterns. The reference nucleotide is indicated by white and the variant by red. A pairwise comparison of all 46 unique loci is shown, with green shading indicating a positive result and evidence for recombination.
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fig7: Whole-genome allele compatibility test shows evidence for prolific recombination at the population level. (A) An example of a paired allele compatibility test from the VGII population. Alternative SNPs are depicted in red and the reference in white. Evidence for recombination is provided by any pairwise comparison of two loci in which strains are present where red-red, white-white, red-white, and white-red combinations are all found (AB, Ab, aB, and ab) satisfying the allele compatibility test, providing evidence for recombination. (B) One hundred random SNPs were selected from the VGII data set and collapsed into 46 unique allele patterns. The reference nucleotide is indicated by white and the variant by red. A pairwise comparison of all 46 unique loci is shown, with green shading indicating a positive result and evidence for recombination.

Mentions: In addition to the shared genomic islands, use of a paired allele compatibility test based on SNP information (AB × ab giving rise to AB, ab, Ab, or αB) provided evidence for sexual reproduction and recombination (Fig. 7A). One hundred random loci were selected using the Genome Analysis Toolkit (GATK) SelectVariants walker out of the 262,614 polymorphic sites in the data set. These loci were collapsed into unique and informative allele combinations, leaving 46 loci, and then compared. This test showed evidence for mating and meiosis occurring between a number of different isolates at the whole-genome level, both with and without the involvement of the three sequenced MATa isolates in this study. In particular, all of the 46 loci tested showed evidence for recombination with at least 13 of the 45 other loci (29%) and as many as 40 out of 45 (89%) (Fig. 7B). Recombination provides strong evidence for the involvement of the sexual cycle in the production of these C. gattii strains, and given the paucity of a isolates in the environment, we hypothesize this involved both a-α bisexual and α-α unisexual reproduction.


Highly recombinant VGII Cryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution.

Billmyre RB, Croll D, Li W, Mieczkowski P, Carter DA, Cuomo CA, Kronstad JW, Heitman J - MBio (2014)

Whole-genome allele compatibility test shows evidence for prolific recombination at the population level. (A) An example of a paired allele compatibility test from the VGII population. Alternative SNPs are depicted in red and the reference in white. Evidence for recombination is provided by any pairwise comparison of two loci in which strains are present where red-red, white-white, red-white, and white-red combinations are all found (AB, Ab, aB, and ab) satisfying the allele compatibility test, providing evidence for recombination. (B) One hundred random SNPs were selected from the VGII data set and collapsed into 46 unique allele patterns. The reference nucleotide is indicated by white and the variant by red. A pairwise comparison of all 46 unique loci is shown, with green shading indicating a positive result and evidence for recombination.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4128362&req=5

fig7: Whole-genome allele compatibility test shows evidence for prolific recombination at the population level. (A) An example of a paired allele compatibility test from the VGII population. Alternative SNPs are depicted in red and the reference in white. Evidence for recombination is provided by any pairwise comparison of two loci in which strains are present where red-red, white-white, red-white, and white-red combinations are all found (AB, Ab, aB, and ab) satisfying the allele compatibility test, providing evidence for recombination. (B) One hundred random SNPs were selected from the VGII data set and collapsed into 46 unique allele patterns. The reference nucleotide is indicated by white and the variant by red. A pairwise comparison of all 46 unique loci is shown, with green shading indicating a positive result and evidence for recombination.
Mentions: In addition to the shared genomic islands, use of a paired allele compatibility test based on SNP information (AB × ab giving rise to AB, ab, Ab, or αB) provided evidence for sexual reproduction and recombination (Fig. 7A). One hundred random loci were selected using the Genome Analysis Toolkit (GATK) SelectVariants walker out of the 262,614 polymorphic sites in the data set. These loci were collapsed into unique and informative allele combinations, leaving 46 loci, and then compared. This test showed evidence for mating and meiosis occurring between a number of different isolates at the whole-genome level, both with and without the involvement of the three sequenced MATa isolates in this study. In particular, all of the 46 loci tested showed evidence for recombination with at least 13 of the 45 other loci (29%) and as many as 40 out of 45 (89%) (Fig. 7B). Recombination provides strong evidence for the involvement of the sexual cycle in the production of these C. gattii strains, and given the paucity of a isolates in the environment, we hypothesize this involved both a-α bisexual and α-α unisexual reproduction.

Bottom Line: We found that VGIIa/b/c populations show evidence of clonal expansion in the PNW.We also found that the genomes of two basal VGII isolates from HIV(+) patients contain an introgression tract spanning three genes.This work shows that multiple processes can contribute to the emergence of an outbreak.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA heitm001@duke.edu.

Show MeSH
Related in: MedlinePlus