ArticleBMC genomics2016
Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Population Genomics of Aspergillus sojae is Shaped by the Food Environment.Genome biology and evolution · 2025Article
- Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen.Nature communications · 2024Article
- The promise and pitfalls of synteny in phylogenomics.PLoS biology · 2024Article
- Drug Target Elucidation Through Isolation and Analysis of Drug-Resistant Mutants in Cryptococcus neoformans.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Genome Organization and Copy-Number Variation Reveal Clues to Virulence Evolution inJournal of fungi (Basel, Switzerland) · 2022Article
- Article
- Intra-Species Genomic Variation in the Pine PathogenJournal of fungi (Basel, Switzerland) · 2022Article
- Gene, virulence and related regulatory mechanisms inActa biochimica et biophysica Sinica · 2022Review
- Evolution of the human pathogenic lifestyle in fungi.Nature microbiology · 2022Review
- Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures.Molecular biology and evolution · 2022Article
- Bioinformatic Analyzes of the Association Between Upregulated Expression ofFrontiers in medicine · 2022Article
- Microevolution in the pansecondary metabolome ofProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Emergence and diversification of a highly invasive chestnut pathogen lineage across southeastern Europe.eLife · 2021Article
- Gene diversity explains variation in biological features of insect killing fungus, Beauveria bassiana.Scientific reports · 2021Article
- Gene Copy Number Variation Does Not Reflect Structure or Environmental Selection in Two Recently Diverged California Populations ofG3 (Bethesda, Md.) · 2020Article
- Article
- A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands.mBio · 2019Article
- Review
- Gene Presence-Absence Polymorphism in Castrating Anther-Smut Fungi: Recent Gene Gains and Phylogeographic Structure.Genome biology and evolution · 2018Article
- Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation.Frontiers in microbiology · 2018Review
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Authors and funding
4 authors.
Funding
Abstract
backgroundCopy number variants (CNVs) are a class of structural variants (SVs) and are defined as fragments of DNA that are present at variable copy number in comparison with a reference genome. Recent advances in bioinformatics methodologies and sequencing technologies have enabled the high-resolution quantification of genome-wide CNVs. In pathogenic fungi SVs have been shown to alter gene expression, influence host specificity, and drive fungicide resistance, but little attention has focused specifically on CNVs. Using publicly available sequencing data, we identified 90 isolates across 212 Cryptococcus gattii genomes that belong to the VGII subgroups responsible for the recent deadly outbreaks in the North American Pacific Northwest. We generated CNV profiles for each sample to investigate the prevalence and function of CNV in C. gattii.
resultsWe identified eight genetic clusters among publicly available Illumina whole genome sequence data from 212 C. gattii isolates through population structure analysis. Three clusters represent the VGIIa, VGIIb, and VGIIc subgroups from the North American Pacific Northwest. CNV was bioinformatically predicted and affected ~300-400 Kilobases (Kb) of the C. gattii VGII subgroup genomes. Sixty-seven loci, encompassing 58 genes, showed highly divergent patterns of copy number variation between VGII subgroups. Analysis of PFam domains within divergent CN variable genes revealed enrichment of protein domains associated with transport, cell wall organization and external encapsulating structure.
conclusionsCNVs may contribute to pathological and phenotypic differences observed between the C. gattii VGIIa, VGIIb, and VGIIc subpopulations. Genes overlapping with population differentiated CNVs were enriched for several virulence related functional terms. These results uncover novel candidate genes to examine the genetic and functional underpinnings of C. gattii pathogenicity.
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