Evolution of pathogenicity and sexual reproduction in eight Candida genomes

By G. Butler, Matthew D. Rasmussen, Michael F. Lin, Manuel A. S. Santos, Sharadha Sakthikumar, C. Munro, Esther Rheinbay, Manfred G. Grabherr, A. Forche, J. Reedy and 41 more. Nature, 2009

1,036 citations recorded by the source corpus.

Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/α2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes.

Subfields: Cell Biology, Epidemiology, Infectious Diseases

View Paper: https://www.semanticscholar.org/paper/771d36de346decb86f3c78935bcbde73d419dffb

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In Epidemiology

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Citations in the corpus

• PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions (2010, methodology): “In addition to analyzing novel transcript models, such methods also have applications in evaluating and revising existing gene annotations [2, 3, 4, 5, 6], and as input features for de novo gene structure predictors [7, 8].”
• A Recently Evolved Transcriptional Network Controls Biofilm Development in Candida albicans (2012, background): “Genes found only in pathogenic species are potentially interesting because they may identify a pathogenesis module (Butler et al., 2009).”
• Candida glabrata, Candida parapsilosis and Candida tropicalis: biology, epidemiology, pathogenicity and antifungal resistance. (2012, background): “Genetically, C. tropicalis has the highest similarity to C. albicans, and C. glabrata the least (Butler et al., 2009).”
• Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses (2017, background): “5 Mb, similar to that of other Candida species [25].”
• The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data (2016, methodology): “Optional tracks highlight the sequence variation between the two Assembly 22 haplotypes, as well as the variation between the common strains SC5314 and WO-1 (32).”
• Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement (2014, neutral): “somes display loss of heterozygosity [21,22].”