ArticleGenome biology2013
Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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Who cites it
78 citing papers in PubMed.
- BINge: Multispecies Ortholog Clustering for Differential Gene Expression Analyses.Molecular ecology resources · 2026Article
- Histone fold domain positioning dictates cotranslational heterodimeric assembly of paralogous TAF12/TAF12L in Candida albicans.The Journal of biological chemistry · 2026Article
- Complete diploid genome of the type strain Yarrowia lipolytica YB-423 (ATCC 18942™).Journal of industrial microbiology & biotechnology · 2026Article
- PacBio HiFi reads data sets for the ATCC-authenticated isolate of Candida albicans SC5314 (ATCC MYA-2876).Access microbiology · 2026Article
- Cotranslational assembly confers specificity for in vivo target heterodimerization of paralogous H2B-like TAF12 proteins in the human fungal pathogenbioRxiv : the preprint server for biology · 2025Article
- FunFEA: an R package for fungal functional enrichment analysis.BMC bioinformatics · 2025Article
- Article
- Celastrol boosts fluconazole efficacy against vaginal candidiasis: in vitro and in vivo evidence.AMB Express · 2025Article
- Step-wise evolution of azole resistance through copy number variation followed by KSR1 loss of heterozygosity in Candida albicans.PLoS pathogens · 2024Article
- Candida albicans natural diversity: a resource to dissect fungal commensalism and pathogenesis.Current opinion in microbiology · 2024Review
- A gain-of-function mutation in zinc cluster transcription factor Rob1 drives Candida albicans adaptive growth in the cystic fibrosis lung environment.PLoS pathogens · 2024Article
- The anti-staphylococcal fusidic acid as an efflux pump inhibitor combined with fluconazole against vaginal candidiasis in mouse model.BMC microbiology · 2024Article
- Use of aFrontiers in cellular and infection microbiology · 2024Article
- Article
- Genome-Wide DNA Changes Acquired byMicroorganisms · 2023Article
- Genetic Diversity of Human Fungal Pathogens.Current clinical microbiology reports · 2023Article
- Small Insertions and Deletions Drive Genomic Plasticity during Adaptive Evolution of Yersinia pestis.Microbiology spectrum · 2022Review
- An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function.Science advances · 2022Article
- Proteogenomics analysis of CUG codon translation in the human pathogen Candida albicans.BMC biology · 2021Article
- Allele-specific assembly of a eukaryotic genome corrects apparent frameshifts and reveals a lack of nonsense-mediated mRNA decay.NAR genomics and bioinformatics · 2021Article
18 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
backgroundCandida albicans is a ubiquitous opportunistic fungal pathogen that afflicts immunocompromised human hosts. With rare and transient exceptions the yeast is diploid, yet despite its clinical relevance the respective sequences of its two homologous chromosomes have not been completely resolved.
resultsWe construct a phased diploid genome assembly by deep sequencing a standard laboratory wild-type strain and a panel of strains homozygous for particular chromosomes. The assembly has 700-fold coverage on average,allowing extensive revision and expansion of the number of known SNPs and indels. This phased genome significantly enhances the sensitivity and specificity of allele-specific expression measurements by enabling pooling and cross-validation of signal across multiple polymorphic sites. Additionally, the diploid assembly reveals pervasive and unexpected patterns in allelic differences between homologous chromosomes. Firstly, we see striking clustering of indels, concentrated primarily in the repeat sequences in promoters. Secondly, both indels and their repeat-sequence substrate are enriched near replication origins. Finally, we reveal an intimate link between repeat sequences and indels, which argues that repeat length is under selective pressure for most eukaryotes. This connection is described by a concise one-parameter model that explains repeat-sequence abundance in C. albicans as a function of the indel rate,and provides a general framework to interpret repeat abundance in species ranging from bacteria to humans.
conclusionsThe phased genome assembly and insights into repeat plasticity will be valuable for better understanding allele-specific phenomena and genome evolution.
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