Abstract
Genome rearrangements resulting in copy number variation (CNV) and loss of heterozygosity (LOH) are frequently observed during the somatic evolution of cancer and promote rapid adaptation of fungi to novel environments. In the human fungal pathogen Candida albicans, CNV and LOH confer increased virulence and antifungal drug resistance, yet the mechanisms driving these rearrangements are not completely understood. Here, we unveil an extensive array of long repeat sequences (65-6499 bp) that are associated with CNV, LOH, and chromosomal inversions. Many of these long repeat sequences are uncharacterized and encompass one or more coding sequences that are actively transcribed. Repeats associated with genome rearrangements are predominantly inverted and separated by up to ~1.6 Mb, an extraordinary distance for homology-based DNA repair/recombination in yeast. These repeat sequences are a significant source of genome plasticity across diverse strain backgrounds including clinical, environmental, and experimentally evolved isolates, and represent previously uncharacterized variation in the reference genome.
Highlights
IntroductionDNA insertions and deletions (indels), copy number variations (CNV), and loss of heterozygosity (LOH) are frequently described during the evolution of organisms and of disease states such as cancer
Genome plasticity is surprisingly common in eukaryotes
Given the significant impact of i(5L) on antifungal drug resistance, we focused first on the characterization of a novel segmental aneuploidy detected on Chr4 that arose during in vitro evolution in the presence of FLC
Summary
DNA insertions and deletions (indels), copy number variations (CNV), and loss of heterozygosity (LOH) are frequently described during the evolution of organisms and of disease states such as cancer. The genome plasticity of fungal pathogens was recognized well before whole genome sequencing was available, including genome copy number variation (polyploidy), inter- and intra-chromosomal rearrangements, and aneuploidy (Chibana et al, 2000; Magee and Magee, 2000; Rustchenko-Bulgac, 1991; Suzuki et al, 1982). It undergoes a parasexual process that involves random chromosome loss and rare Spo11-dependent chromosome recombination events (Bennett and Johnson, 2003; Forche et al, 2008; Wang et al, 2018)
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