Genome Assemblies of Two Rare Opportunistic Yeast Pathogens:Diutina rugosa(syn.Candida rugosa) andTrichomonascus ciferrii(syn.Candida ciferrii)

Abstract

Infections caused by opportunistic yeast pathogens have increased over the last years. These infections can be originated by a large number of diverse yeast species of varying incidence, and with distinct clinically relevant phenotypic traits, such as different susceptibility profiles to antifungal drugs, which challenge diagnosis and treatment. Diutina rugosa (syn. Candida rugosa) and Trichomonascus ciferrii (syn. Candida ciferrii) are two opportunistic rare yeast pathogens, which low incidence (< 1%) limits available clinical experience. Furthermore, these yeasts have elevated Minimum Inhibitory Concentration (MIC) levels to at least one class of antifungal agents. This makes it more difficult to manage their infections, and thus they are associated with high rates of mortality and clinical failure. With the aim of improving our knowledge on these opportunistic pathogens, we assembled and annotated their genomes. A phylogenomics approach revealed that genes specifically duplicated in each of the two species are often involved in transmembrane transport activities. These genomes and the reconstructed complete catalog of gene phylogenies and homology relationships constitute useful resources for future studies on these pathogens.

Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations

“…Our results revealed that C. subhashii has 501 orphan genes, and that genes specifically duplicated in this species are enriched in transmembrane transport activity ( Supplementary File S2 ). This result is similar to what was previously obtained for other Candida pathogens, such as C. inconspicua , Diutina (Candida) rugosa and Trichomonascus (Candida) ciferrii , 7 , 28 and reinforces the previously proposed hypothesis that cell wall composition may play a role in the adoption of an opportunistic pathogenic behaviour by Candida species. 38 As previous reports suggest that the human body is not the main habitat of C. subhashii , 12 we hypothesize that the duplication of cell wall proteins must have been advantageous in non-human environments while perhaps secondarily facilitating opportunistic colonization of humans.…”

“…Mitochondria-related genes were identified with TargetP v1. 27 Phylome reconstruction was performed as previously described 28 and deposited in the PhylomeDB database ( http://beta.phylomedb.org, 31 May 2021, date last accessed ). 29 Phylome results were used to infer orthology and paralogy relations and determine the associated GO terms.…”

Identification and Antifungal Susceptibility Analysis of Stephanoascus ciferrii Complex Species Isolated From Patients With Chronic Suppurative Otitis Media

“…Stephanoascus ciferrii , which is first discovered in 1965, is an opportunistic rare yeast pathogen with low prevalence (<1% of clinical Candida infections) ( Kreger-Van Rij, 1965 ; Mixao et al, 2019 ). The literature about S. ciferrii is limited, and it is usually reported in some sporadic cases of infections ( Villanueva-Lozano et al, 2016 ).…”

Genome analysis of five recently described species of the CUG-Ser clade uncoversCandida theaeas a new hybrid lineage with pathogenic potential in theCandida parapsilosisspecies complex

“…PhylomeDB pipeline 43 was used for phylome reconstruction as described in Mixão et al, 44 considering the 28 species specified in Supplementary File S1 , and using each of the five target species of this study as seed. Gene gain and loss analysis in the seed branch was performed based on the phylome results.…”