RT Journal
A1 Oggenfuss, Ursula
A1 Todd, Robert T.
A1 Soisangwan, Natthapon
A1 Kemp, Bailey
A1 Guyer, Alison
A1 Beach, Annette
A1 Selmecki, Anna
T1 Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
JF Genome Research 
JO Genome Research 
YR 2025 
FD April 01 
VO 35 
IS 4 
SP 824 
OP 838 
DO 10.1101/gr.279301.124 
UL http://genome.cshlp.org/content/35/4/824.abstract 
AB The human fungal pathogen Candida albicans poses a significant burden on global health, causing high rates of mortality and antifungal drug resistance. C. albicans is a heterozygous diploid organism that reproduces asexually. Structural variants (SVs) are an important source of genomic rearrangement, particularly in species that lack sexual recombination. To comprehensively investigate SVs across clinical isolates of C. albicans, we conducted long-read sequencing and genome-wide SV analysis in three distantly related clinical isolates. Our work includes a new, comprehensive analysis of transposable element (TE) composition, location, and diversity. SVs and TEs are frequently close to coding sequences and many SVs are heterozygous, suggesting that SVs might impact gene and allele-specific expression. Most SVs are uniquely present in only one clinical isolate, indicating that SVs represent a significant source of intraspecies genetic variation. We identify multiple, distinct SVs at the centromeres of Chromosome 4 and Chromosome 5, including inversions and transposon polymorphisms. These two chromosomes are often aneuploid in drug-resistant clinical isolates and can form isochromosome structures with breakpoints near the centromere. Further screening of 100 clinical isolates confirms the widespread presence of centromeric SVs in C. albicans, often appearing in a heterozygous state, indicating that SVs are contributing to centromere evolution in C. albicans. Together, these findings highlight that SVs and TEs are common across diverse clinical isolates of C. albicans and that the centromeres of this organism are important sites of genome rearrangement.