Highly recombinant VGII Cryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution.
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.
Affiliation: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA email@example.com.Show MeSH
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Mentions: Polymorphisms among VGII isolates are not homogeneous along the chromosomes. In contrast with the islands of diminished polymorphism, we found SNP density was elevated locally, resulting in genomic islands of high polymorphism. For example, a region on R265 supercontig 13 located between 393 and 417 kb showed 3× to 4× more polymorphisms than the surrounding regions (Fig. 8B). This region coincides with two blocks of high linkage disequilibrium on supercontig 13 (Fig. 8A). We examined whether the increased polymorphisms were caused by the inclusion of particular VGII isolates and found that the high polymorphisms between positions 393 and 408 kb are caused by two outlying clonally related isolates (2001/935-1 and IP96/1120-1) (Fig. 8D). Removal of these two isolates reduced the polymorphism to levels identical to the genomic surroundings (red area in Fig. 8C). Similarly, the high level of polymorphism in the region from 414 to 417 kb is caused by the presence of six clonal isolates from the VGIInt group (NT3, NT7, NT8, RDH2, RDH7, and MMRL2647) (Fig. 8D). Removal of these six isolates from the analysis drastically reduced the level of polymorphism in this region (blue area in Fig. 8C).
Affiliation: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA firstname.lastname@example.org.