Genome Comparison of Candida orthopsilosis Clinical Strains Reveals the Existence of Hybrids between Two Distinct Subspecies

Abstract

The Candida parapsilosis species complex comprises a group of emerging human pathogens of varying virulence. This complex was recently subdivided into three different species: C. parapsilosis sensu stricto, C. metapsilosis, and C. orthopsilosis. Within the latter, at least two clearly distinct subspecies seem to be present among clinical isolates (Type 1 and Type 2). To gain insight into the genomic differences between these subspecies, we undertook the sequencing of a clinical isolate classified as Type 1 and compared it with the available sequence of a Type 2 clinical strain. Unexpectedly, the analysis of the newly sequenced strain revealed a highly heterozygous genome, which we show to be the consequence of a hybridization event between both identified subspecies. This implicitly suggests that C. orthopsilosis is able to mate, a so-far unanswered question. The resulting hybrid shows a chimeric genome that maintains a similar gene dosage from both parental lineages and displays ongoing loss of heterozygosity. Several of the differences found between the gene content in both strains relate to virulent-related families, with the hybrid strain presenting a higher copy number of genes coding for efflux pumps or secreted lipases. Remarkably, two clinical strains isolated from distant geographical locations (Texas and Singapore) are descendants of the same hybrid line, raising the intriguing possibility of a relationship between the hybridization event and the global spread of a virulent clone.

Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species

“…One isolate (Sample 427) was also sequenced using PacBio technology, which was used to characterize genome structure. Previously sequenced isolates 90–125 and MCO456 [39, 40] were included in the subsequent analysis. We identified an assembly error in the 90–125 reference genome, an artefactual translocation between chromosomes 2 and chromosome 6 (S1 Fig).…”

“…^The genome sequences of MCO456 and 90–125 were described previously [39, 40]. Tav = Tavanti et al (2007) [32].…”

“…parapsilosis [29, 39]. However, further studies identified two highly heterozygous isolates, which were suggested to result from the same hybridization event, possibly between Type 1 and Type 2 parents [40]. Here, we carried out a population genomics analysis of 27 worldwide C .…”

Genomics and the making of yeast biodiversity

“…Similarly, genome sequencing of a wine spoilage strain purported to be B. bruxellensis revealed it to be allotriploid [48]. Several clinical isolates from the C. parapsilosis species complex are also interspecies hybrids [49]. …”

Evolutionary Perspectives on Human Fungal Pathogens

“…Other Candida species, including C. parapsilosis and its close relatives, C. metapsilosis and C. orthopsilosis, have also been investigated, with the finding that C. parapsilosis and C. metapsilosis isolates have just one mating idiomorph, whereas C. orthopsilosis has a balance of both (Sai et al 2011). By inference, one might expect that only C. orthopsilosis would be recombining in nature, as demonstrated by the discovery of natural hybridization among strains from two of its populations (Pryszcz et al 2014). However, comparison of genomes of just a few C. parapsilosis strains also showed genetic variation consistent with recombination and independent adaptation to an environmental stress, arsenite (Pryszcz et al 2013).…”