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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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Aligned read depth on supercontigs of IP96/1120-1. Read depth was approximately 2-fold higher than the genome-wide mean coverage on supercontigs 6, 13, and 14. Variation in read depth on supercontigs 6 and 13 suggests partial duplications across the region of the chromosome mapping to these supercontigs. Read depth on supercontig 14 suggests duplication of the entire region represented by this supercontig.
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fig10: Aligned read depth on supercontigs of IP96/1120-1. Read depth was approximately 2-fold higher than the genome-wide mean coverage on supercontigs 6, 13, and 14. Variation in read depth on supercontigs 6 and 13 suggests partial duplications across the region of the chromosome mapping to these supercontigs. Read depth on supercontig 14 suggests duplication of the entire region represented by this supercontig.

Mentions: Both isolates 2001/935-1 and IP96/1120-1 do not belong to an outbreak VGII subtype but do group within the VGII clade (Fig. 8D). Both isolates are of clinical origin and were isolated from HIV-positive patients from Africa. Isolate IP96/1120-1 was isolated in France from a patient who moved from Africa and isolate 2001/935-1 was isolated from a bronchoalveolar lavage sample from a Senegalese patient (20). Despite the near clonal nature of the two isolates 2001/935-1 and IP96/1120-1, we found that IP96/1120-1 likely had multiple partial and complete chromosomal duplications not found in 2001/935-1. Read depth on supercontigs 6 and 13 indicated partially duplicated regions and read depth on supercontig 14 indicated duplication of the entire region covered by this supercontig (Fig. 10). Interestingly, the introgressed region on supercontig 13 is found within a duplicated region of this supercontig. All three duplications contain only homozygous variants, suggesting the extra copies arose by duplicating the original chromosomal region represented by the supercontig, rather than through mating with a different strain, although α-α mating or autodiploidization followed by sequential chromosome loss cannot be ruled out. Duplication of chromosomes readily occurs in Cryptococcus following exposure to antifungal compounds and during sexual reproduction (9, 29). Chromosomal disomy in IP96/1120-1 isolated from an HIV+ patient may have been a direct consequence of antifungal treatment in the patient.


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)

Aligned read depth on supercontigs of IP96/1120-1. Read depth was approximately 2-fold higher than the genome-wide mean coverage on supercontigs 6, 13, and 14. Variation in read depth on supercontigs 6 and 13 suggests partial duplications across the region of the chromosome mapping to these supercontigs. Read depth on supercontig 14 suggests duplication of the entire region represented by this supercontig.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig10: Aligned read depth on supercontigs of IP96/1120-1. Read depth was approximately 2-fold higher than the genome-wide mean coverage on supercontigs 6, 13, and 14. Variation in read depth on supercontigs 6 and 13 suggests partial duplications across the region of the chromosome mapping to these supercontigs. Read depth on supercontig 14 suggests duplication of the entire region represented by this supercontig.
Mentions: Both isolates 2001/935-1 and IP96/1120-1 do not belong to an outbreak VGII subtype but do group within the VGII clade (Fig. 8D). Both isolates are of clinical origin and were isolated from HIV-positive patients from Africa. Isolate IP96/1120-1 was isolated in France from a patient who moved from Africa and isolate 2001/935-1 was isolated from a bronchoalveolar lavage sample from a Senegalese patient (20). Despite the near clonal nature of the two isolates 2001/935-1 and IP96/1120-1, we found that IP96/1120-1 likely had multiple partial and complete chromosomal duplications not found in 2001/935-1. Read depth on supercontigs 6 and 13 indicated partially duplicated regions and read depth on supercontig 14 indicated duplication of the entire region covered by this supercontig (Fig. 10). Interestingly, the introgressed region on supercontig 13 is found within a duplicated region of this supercontig. All three duplications contain only homozygous variants, suggesting the extra copies arose by duplicating the original chromosomal region represented by the supercontig, rather than through mating with a different strain, although α-α mating or autodiploidization followed by sequential chromosome loss cannot be ruled out. Duplication of chromosomes readily occurs in Cryptococcus following exposure to antifungal compounds and during sexual reproduction (9, 29). Chromosomal disomy in IP96/1120-1 isolated from an HIV+ patient may have been a direct consequence of antifungal treatment in the patient.

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