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Genetic diversity of the Cryptococcus species complex suggests that Cryptococcus gattii deserves to have varieties.

Ngamskulrungroj P, Gilgado F, Faganello J, Litvintseva AP, Leal AL, Tsui KM, Mitchell TG, Vainstein MH, Meyer W - PLoS ONE (2009)

Bottom Line: The separate or combined sequence analyses of all four loci revealed seven clades with significant support for each molecular type.The sequence variation between VGI, VGIII and VGIV was similar to that between VNI/VNB and VNII.The genetic variation found among all of these haploid monophyletic lineages indicates that they warrant varietal status.

View Article: PubMed Central - PubMed

Affiliation: Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, Westmead Hospital, Westmead, New South Wales, Australia.

ABSTRACT
The Cryptococcus species complex contains two sibling taxa, Cryptococcus neoformans and Cryptococcus gattii. Both species are basidiomycetous yeasts and major pathogens of humans and other mammals. Genotyping methods have identified major haploid molecular types of C. neoformans (VNI, VNII, VNB and VNIV) and of C. gattii (VGI, VGII, VGIII and VGIV). To investigate the phylogenetic relationships among these haploid genotypes, we selected 73 strains from 2000 globally collected isolates investigated in our previous typing studies, representing each of these genotypes and carried out multigene sequence analyses using four genetically unlinked nuclear loci, ACT1, IDE, PLB1 and URA5. The separate or combined sequence analyses of all four loci revealed seven clades with significant support for each molecular type. However, three strains of each species revealed some incongruence between the original molecular type and the sequence-based type obtained here. The topology of the individual gene trees was identical for each clade of C. neoformans but incongruent for the clades of C. gattii indicating recent recombination events within C. gattii. There was strong evidence of recombination in the global VGII population. Both parsimony and likelihood analyses supported three major clades of C. neoformans (VNI/VNB, VNII and VNIV) and four major clades of C. gattii (VGI, VGII, VGIII and VGIV). The sequence variation between VGI, VGIII and VGIV was similar to that between VNI/VNB and VNII. MATa was for the first time identified for VGIV. The VNIV and VGII clades are basal to the C. neoformans or the C. gattii clade, respectively. Divergence times among the seven haploid monophyletic lineages in the Cryptococcus species complex were estimated by applying the hypothesis of the molecular clock. The genetic variation found among all of these haploid monophyletic lineages indicates that they warrant varietal status.

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Gene genealogies of the four individual loci generated by Maximum Parsimony analysis.Parsimony bootstrap support above 75 is indicated in bold. Bayesian posterior probability above 95 is indicated italicized. Phylogenetic trees are unrooted. The blue bold italic letters represent VNII-1 and VGIV-1 clades of C. neoformans and C. gattii, respectively.
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pone-0005862-g004: Gene genealogies of the four individual loci generated by Maximum Parsimony analysis.Parsimony bootstrap support above 75 is indicated in bold. Bayesian posterior probability above 95 is indicated italicized. Phylogenetic trees are unrooted. The blue bold italic letters represent VNII-1 and VGIV-1 clades of C. neoformans and C. gattii, respectively.

Mentions: For the C. neoformans taxa, the topology of the individual loci never conflicted with the phylogram of the combined loci. The analysis of the two C. neoformans var. grubii clades (VNI and VNII) confirmed their sibling relationship with the C. neoformans var. neoformans clade (VNIV) (Figure 4). Conversely, the topologies of the individual loci of C. gattii conflicted with the phylogram of the combined loci. On the PLB1, URA5 and IDE phylogenies, the VGI, VGIII and VGIV clades are clustered together and formed a sibling group with VGII. However, the phylogram generated from ACT1 has a different topology in which, VGII strains are subdivided into two subclades. The deep branches of the ACT1 phylogram did not achieve strong statistical support in the C. gattii clade, unlike the combined data set. However, both analyses generated high statistical support for the major clades, with the exception of the VGI and VGII clades of the URA5 phylogram (Figure 4).


Genetic diversity of the Cryptococcus species complex suggests that Cryptococcus gattii deserves to have varieties.

Ngamskulrungroj P, Gilgado F, Faganello J, Litvintseva AP, Leal AL, Tsui KM, Mitchell TG, Vainstein MH, Meyer W - PLoS ONE (2009)

Gene genealogies of the four individual loci generated by Maximum Parsimony analysis.Parsimony bootstrap support above 75 is indicated in bold. Bayesian posterior probability above 95 is indicated italicized. Phylogenetic trees are unrooted. The blue bold italic letters represent VNII-1 and VGIV-1 clades of C. neoformans and C. gattii, respectively.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2690690&req=5

pone-0005862-g004: Gene genealogies of the four individual loci generated by Maximum Parsimony analysis.Parsimony bootstrap support above 75 is indicated in bold. Bayesian posterior probability above 95 is indicated italicized. Phylogenetic trees are unrooted. The blue bold italic letters represent VNII-1 and VGIV-1 clades of C. neoformans and C. gattii, respectively.
Mentions: For the C. neoformans taxa, the topology of the individual loci never conflicted with the phylogram of the combined loci. The analysis of the two C. neoformans var. grubii clades (VNI and VNII) confirmed their sibling relationship with the C. neoformans var. neoformans clade (VNIV) (Figure 4). Conversely, the topologies of the individual loci of C. gattii conflicted with the phylogram of the combined loci. On the PLB1, URA5 and IDE phylogenies, the VGI, VGIII and VGIV clades are clustered together and formed a sibling group with VGII. However, the phylogram generated from ACT1 has a different topology in which, VGII strains are subdivided into two subclades. The deep branches of the ACT1 phylogram did not achieve strong statistical support in the C. gattii clade, unlike the combined data set. However, both analyses generated high statistical support for the major clades, with the exception of the VGI and VGII clades of the URA5 phylogram (Figure 4).

Bottom Line: The separate or combined sequence analyses of all four loci revealed seven clades with significant support for each molecular type.The sequence variation between VGI, VGIII and VGIV was similar to that between VNI/VNB and VNII.The genetic variation found among all of these haploid monophyletic lineages indicates that they warrant varietal status.

View Article: PubMed Central - PubMed

Affiliation: Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, Westmead Hospital, Westmead, New South Wales, Australia.

ABSTRACT
The Cryptococcus species complex contains two sibling taxa, Cryptococcus neoformans and Cryptococcus gattii. Both species are basidiomycetous yeasts and major pathogens of humans and other mammals. Genotyping methods have identified major haploid molecular types of C. neoformans (VNI, VNII, VNB and VNIV) and of C. gattii (VGI, VGII, VGIII and VGIV). To investigate the phylogenetic relationships among these haploid genotypes, we selected 73 strains from 2000 globally collected isolates investigated in our previous typing studies, representing each of these genotypes and carried out multigene sequence analyses using four genetically unlinked nuclear loci, ACT1, IDE, PLB1 and URA5. The separate or combined sequence analyses of all four loci revealed seven clades with significant support for each molecular type. However, three strains of each species revealed some incongruence between the original molecular type and the sequence-based type obtained here. The topology of the individual gene trees was identical for each clade of C. neoformans but incongruent for the clades of C. gattii indicating recent recombination events within C. gattii. There was strong evidence of recombination in the global VGII population. Both parsimony and likelihood analyses supported three major clades of C. neoformans (VNI/VNB, VNII and VNIV) and four major clades of C. gattii (VGI, VGII, VGIII and VGIV). The sequence variation between VGI, VGIII and VGIV was similar to that between VNI/VNB and VNII. MATa was for the first time identified for VGIV. The VNIV and VGII clades are basal to the C. neoformans or the C. gattii clade, respectively. Divergence times among the seven haploid monophyletic lineages in the Cryptococcus species complex were estimated by applying the hypothesis of the molecular clock. The genetic variation found among all of these haploid monophyletic lineages indicates that they warrant varietal status.

Show MeSH
Related in: MedlinePlus