YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens

Expanding echinocandin use to prevent or treat invasive fungal infections has led to an increase in the number of breakthrough infections due to resistant Candida species. Although it is uncommon, echinocandin resistance is well documented for Candida albicans, which is among the most prevalent bloodstream organisms. A better understanding is needed to assess the cellular factors that promote tolerance and predispose infecting cells to clinical breakthrough. We previously showed that some mutants that were adapted to growth in the presence of toxic sorbose due to loss of one chromosome 5 (Ch5) also became more tolerant to caspofungin. We found here, following direct selection of mutants on caspofungin, that tolerance can be conferred by at least three mechanisms: (i) monosomy of Ch5, (ii) combined monosomy of the left arm and trisomy of the right arm of Ch5, and (iii) an aneuploidyindependent mechanism. Tolerant mutants possessed cell walls with elevated chitin and showed downregulation of genes involved in cell wall biosynthesis, namely, FKS, located outside Ch5, and CHT2, located on Ch5, irrespective of Ch5 ploidy. Also irrespective of Ch5 ploidy, the CNB1 and MID1 genes on Ch5, which are involved in the calcineurin signaling pathway, were expressed at the diploid level. Thus, multiple mechanisms can affect the relative expression of the aforementioned genes, controlling them in similar ways. Although breakthrough mutations in two specific regions of FKS1 have previously been associated with caspofungin resistance, we found mechanisms of caspofungin tolerance that are independent of FKS1 and thus represent an earlier event in resistance development.

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“…DNA-seq data were analyzed with the YMAP pipeline (41). Copy number analysis was based upon read depth across the genome.…”

Section: Methodsmentioning

confidence: 99%

Tolerance to Caspofungin in Candida albicans Is Associated with at Least Three Distinctive Mechanisms That Govern Expression of FKS Genes and Cell Wall Remodeling

Yang

Zhang

Wakabayashi

et al. 2017

Antimicrob Agents Chemother

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“…Ploidy diversity among isolates has previously been observed in both environmental and clinical populations of S. cerevisiae (Ezov et al 2006;Zhu et al 2016). This type of ploidy variation is also observed in the opportunistic human pathogen C. albicans (Suzuki et al 1982;Marr et al 1997;Hickman et al 2013;Abbey et al 2014), a budding yeast that diverged from S. cerevisiae prior to the whole-genome duplication (Diezmann et al 2004;Kellis et al 2004). The isolation of natural ploidy variants suggests these atypical ploidy individuals may play an important evolutionary role.…”

mentioning

confidence: 69%

“…2 and S1), while many evolved lines from the other polyploid clinical strain (4N2) and laboratory strains (4N3, 4N4) retained subpopulations of cells with their initial genome size (Fig. 4N1 has a unique karyotype that contains both tetrasomies and trisomies as well as two copies of isochromosome 5L (Table 1, Abbey et al 2014). 4N1 has a unique karyotype that contains both tetrasomies and trisomies as well as two copies of isochromosome 5L (Table 1, Abbey et al 2014).…”

Section: Discussionmentioning

confidence: 99%

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Ploidy tug-of-war: Evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen

et al. 2017

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Variation in baseline ploidy is seen throughout the tree of life, yet the factors that determine why one ploidy level is maintained over another remain poorly understood. Experimental evolution studies using asexual fungal microbes with manipulated ploidy levels intriguingly reveals a propensity to return to the historical baseline ploidy, a phenomenon that we term "ploidy drive." We evolved haploid, diploid, and polyploid strains of the human fungal pathogen Candida albicans under three different nutrient limitation environments to test whether these conditions, hypothesized to select for low ploidy levels, could counteract ploidy drive. Strains generally maintained or acquired smaller genome sizes (measured as total nuclear DNA through flow cytometry) in minimal medium and under phosphorus depletion compared to in a complete medium, while mostly maintained or acquired increased genome sizes under nitrogen depletion. Improvements in fitness often ran counter to changes in genome size; in a number of scenarios lines that maintained their original genome size often increased in fitness more than lines that converged toward diploidy (the baseline ploidy of C. albicans). Combined, this work demonstrates a role for both the environment and genotype in determination of the rate of ploidy drive, and highlights questions that remain about the force(s) that cause genome size variation.

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“…Sequencing methods allow SNP frequencies to define allelic ratios and LOH events [11,39,40], and can be performed independently of a reference genome sequence [61]. Y MAP , a recently developed informatics pipeline, facilitates this analysis for several C. albicans strain backgrounds by processing sequence reads directly and constructing a visualization of copy number variation and allelic ratios from SNP-CGH or NGS data [62].…”

Section: Genomic Architecturementioning

confidence: 99%

Budding off: bringing functional genomics toCandida albicans

Anderson¹,

Bennett²

2015

Briefings in Functional Genomics

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Candida species are the most prevalent human fungal pathogens, with Candida albicans being the most clinically relevant species. Candida albicans resides as a commensal of the human gastrointestinal tract but is a frequent cause of opportunistic mucosal and systemic infections. Investigation of C. albicans virulence has traditionally relied on candidate gene approaches, but recent advances in functional genomics have now facilitated global, unbiased studies of gene function. Such studies include comparative genomics (both between and within Candida species), analysis of total RNA expression, and regulation and delineation of protein-DNA interactions. Additionally, large collections of mutant strains have begun to aid systematic screening of clinically relevant phenotypes. Here, we will highlight the development of functional genomics in C. albicans and discuss the use of these approaches to addressing both commensalism and pathogenesis in this species.

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YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens

Cited by 128 publications

References 43 publications

Tolerance to Caspofungin in Candida albicans Is Associated with at Least Three Distinctive Mechanisms That Govern Expression of FKS Genes and Cell Wall Remodeling

Tolerance to Caspofungin in Candida albicans Is Associated with at Least Three Distinctive Mechanisms That Govern Expression of FKS Genes and Cell Wall Remodeling

Ploidy tug-of-war: Evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen

Budding off: bringing functional genomics toCandida albicans

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