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Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii.

Farrer RA, Desjardins CA, Sakthikumar S, Gujja S, Saif S, Zeng Q, Chen Y, Voelz K, Heitman J, May RC, Fisher MC, Cuomo CA - MBio (2015)

Bottom Line: By identifying syntenic regions across assemblies, we found 15 structural rearrangements, which were almost exclusive to the VGI-III-IV lineages.In addition, we found evidence for recent transcontinental spread, mitochondrial genetic exchange, and positive selection in multidrug transporters.Our results suggest that gene expansion/contraction and positive selection are diversifying the mechanisms of pathogenicity across this species complex.

View Article: PubMed Central - PubMed

Affiliation: Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

No MeSH data available.


Related in: MedlinePlus

RAxML phylogeny of 53 nuclear genomes of C. gattii. All sites that were homozygous in all isolates and had an SNP in ≥1 isolate were used (1,432,518 sites, or 8.3% of the total length). Isolate names are colored according to geographic origin (blue, Pacific Northwest [PNW]; red, South America; green, Australia) and labeled. Isolates labeled USA are non-PNW. The asterisk indicates 100% bootstrap support using 1,000 replicates. The branch site model (BSM) of selection in Codeml was employed across 17 subclades highlighted in the table (to the right of the tree) to identify genes under selection across the internal branches within each subclade. Multiple testing correction was performed using both the Storey-Tibshirani and Benjamini-Hochberg methods (requiring q values of <0.05 for each). The number of genes identified as under positive selection is reported as the second column of the table. Last, enrichment Pfam domains from these genes compared with the remaining unselected genes were assessed using two-tailed Fisher’s exact test with q-value FDR, shown in the final column of the table.
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fig2: RAxML phylogeny of 53 nuclear genomes of C. gattii. All sites that were homozygous in all isolates and had an SNP in ≥1 isolate were used (1,432,518 sites, or 8.3% of the total length). Isolate names are colored according to geographic origin (blue, Pacific Northwest [PNW]; red, South America; green, Australia) and labeled. Isolates labeled USA are non-PNW. The asterisk indicates 100% bootstrap support using 1,000 replicates. The branch site model (BSM) of selection in Codeml was employed across 17 subclades highlighted in the table (to the right of the tree) to identify genes under selection across the internal branches within each subclade. Multiple testing correction was performed using both the Storey-Tibshirani and Benjamini-Hochberg methods (requiring q values of <0.05 for each). The number of genes identified as under positive selection is reported as the second column of the table. Last, enrichment Pfam domains from these genes compared with the remaining unselected genes were assessed using two-tailed Fisher’s exact test with q-value FDR, shown in the final column of the table.

Mentions: To identify the phylogenetic relationships of these isolates, variants were identified with reference to the improved C. gattii VGII R265 assembly (see Table S4 in the supplemental material), and a phylogenetic tree was constructed (see Materials and Methods). The tree revealed four highly related groups within VGII (Fig. 2), representing VGIIa, VGIIb, and VGIIc and another, smaller group that we term VGIIx, which falls between VGIIa and VGIIb. Two of these groups (VGIIb and VGIIx) contained isolates from separate continents, suggesting that intercontinental transmission has occurred in recent history. VGIIb includes isolates from the PNW (n = 4), Australia (n = 1), and the Caribbean (n = 1). The VGIIx group includes two isolates from different continents, CBS10090 from Greece and LA55 from Brazil. These transcontinental groups, in conjunction with each of the four lineages spanning 2 or more continents, suggest recent, potentially ongoing dispersal of multiple lineages of C. gattii.


Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii.

Farrer RA, Desjardins CA, Sakthikumar S, Gujja S, Saif S, Zeng Q, Chen Y, Voelz K, Heitman J, May RC, Fisher MC, Cuomo CA - MBio (2015)

RAxML phylogeny of 53 nuclear genomes of C. gattii. All sites that were homozygous in all isolates and had an SNP in ≥1 isolate were used (1,432,518 sites, or 8.3% of the total length). Isolate names are colored according to geographic origin (blue, Pacific Northwest [PNW]; red, South America; green, Australia) and labeled. Isolates labeled USA are non-PNW. The asterisk indicates 100% bootstrap support using 1,000 replicates. The branch site model (BSM) of selection in Codeml was employed across 17 subclades highlighted in the table (to the right of the tree) to identify genes under selection across the internal branches within each subclade. Multiple testing correction was performed using both the Storey-Tibshirani and Benjamini-Hochberg methods (requiring q values of <0.05 for each). The number of genes identified as under positive selection is reported as the second column of the table. Last, enrichment Pfam domains from these genes compared with the remaining unselected genes were assessed using two-tailed Fisher’s exact test with q-value FDR, shown in the final column of the table.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4556806&req=5

fig2: RAxML phylogeny of 53 nuclear genomes of C. gattii. All sites that were homozygous in all isolates and had an SNP in ≥1 isolate were used (1,432,518 sites, or 8.3% of the total length). Isolate names are colored according to geographic origin (blue, Pacific Northwest [PNW]; red, South America; green, Australia) and labeled. Isolates labeled USA are non-PNW. The asterisk indicates 100% bootstrap support using 1,000 replicates. The branch site model (BSM) of selection in Codeml was employed across 17 subclades highlighted in the table (to the right of the tree) to identify genes under selection across the internal branches within each subclade. Multiple testing correction was performed using both the Storey-Tibshirani and Benjamini-Hochberg methods (requiring q values of <0.05 for each). The number of genes identified as under positive selection is reported as the second column of the table. Last, enrichment Pfam domains from these genes compared with the remaining unselected genes were assessed using two-tailed Fisher’s exact test with q-value FDR, shown in the final column of the table.
Mentions: To identify the phylogenetic relationships of these isolates, variants were identified with reference to the improved C. gattii VGII R265 assembly (see Table S4 in the supplemental material), and a phylogenetic tree was constructed (see Materials and Methods). The tree revealed four highly related groups within VGII (Fig. 2), representing VGIIa, VGIIb, and VGIIc and another, smaller group that we term VGIIx, which falls between VGIIa and VGIIb. Two of these groups (VGIIb and VGIIx) contained isolates from separate continents, suggesting that intercontinental transmission has occurred in recent history. VGIIb includes isolates from the PNW (n = 4), Australia (n = 1), and the Caribbean (n = 1). The VGIIx group includes two isolates from different continents, CBS10090 from Greece and LA55 from Brazil. These transcontinental groups, in conjunction with each of the four lineages spanning 2 or more continents, suggest recent, potentially ongoing dispersal of multiple lineages of C. gattii.

Bottom Line: By identifying syntenic regions across assemblies, we found 15 structural rearrangements, which were almost exclusive to the VGI-III-IV lineages.In addition, we found evidence for recent transcontinental spread, mitochondrial genetic exchange, and positive selection in multidrug transporters.Our results suggest that gene expansion/contraction and positive selection are diversifying the mechanisms of pathogenicity across this species complex.

View Article: PubMed Central - PubMed

Affiliation: Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

No MeSH data available.


Related in: MedlinePlus