Genome analysis of the yeast Diutina catenulata, a member of the Debaryomycetaceae/Metschnikowiaceae (CTG-Ser) clade

Abstract

Diutina catenulata (Candida catenulata) is an ascomycetous yeast that has been isolated from humans, animals and environmental sources. The species is a contaminant of dairy products, and has been linked to superficial and invasive infections in both humans and animals. Previous phylogenetic analyses have assigned the species to the Saccharomycetales, but failed to identify its specific clade. Here, we report the genome sequence of an environmental isolate of D. catenulata. Examination of the tRNA repertoire and coding potential of this species shows that it translates the CUG codon as serine and not leucine. In addition, two phylogenetic analyses using 204 ubiquitous gene family alignments and 3,826 single-copy genes both confirm the placement of the species in the Debaryomycetaceae/Metschnikowiaceae, or CTG-Ser clade. The sequenced isolate contains an MTLα idiomorph. However, unlike most MTL loci in related species, poly (A) polymerase (PAP) is not adjacent to MTLα1.

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

“…Automated gene prediction resulted in 5,821 protein-coding genes (see Materials and Methods). Despite the fact that the genome size was close to our estimations and similar to the one reported for the closely-related species Diutina catenulata (13.1 Mb), the number of predicted proteins was substantially lower than the 7,128 proteins annotated in the close relative D. catenulata (O’Brien et al 2018). Furthermore, only 64.07% of the reads could be mapped to D. rugosa nuclear genome assembly.…”

“…An earlier study on D. catenulata genome revealed an interesting break in the MAT locus of this species (O’Brien et al 2018). By comparison with the MAT locus of M. guilliermondii (Reedy et al 2009), these authors reported the absence of PAP gene close to MAT alpha1 (Figure 2b), being the PAP gene instead in a different contig of D. catenulata genome assembly (O’Brien et al 2018). Furthermore, they found that this gene was phylogenetically closer to PAP a than to PAP alpha (O’Brien et al 2018).…”

“…By comparison with the MAT locus of M. guilliermondii (Reedy et al 2009), these authors reported the absence of PAP gene close to MAT alpha1 (Figure 2b), being the PAP gene instead in a different contig of D. catenulata genome assembly (O’Brien et al 2018). Furthermore, they found that this gene was phylogenetically closer to PAP a than to PAP alpha (O’Brien et al 2018). To assess whether this characteristic is shared within the Diutina genus, we here inspected the MAT locus of D. rugosa .…”

Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin

“…Within Saccharomycotina, we found two syntenic communities of FIB syntelogs corresponding to the CTG-Ser clade (F-5) and the Saccharomycetaceae family (F-7). The CTG-Ser clade is composed of the Metschnikowiaceae and the Debaryomycetaceae families, which translate the CTG codon to Serine instead of Leucine [42]. The FIB homologue of Babjeviella inositovora, the most basal species from the CTG-Ser clade [43], was the only FIB homolog not included within the F-5 community (S6 Fig).…”

Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes

“…To demonstrate the pipeline’s capabilities we have constructed and analysed a species pan-genome for the oleaginous yeast Yarrowia lipolytica using Pangloss [24]. Y. lipolytica is one of the earliest-diverging yeasts and has seen various applications as a non-conventional yeast model for protein secretion, regulation of dimorphism and lipid accumulation, and is a potential alternative source for biofuels and other oleochemicals [25,26,27,28,29,30,31]. We have also reconstructed the species pan-genome of the opportunistic respiratory pathogen Aspergillus fumigatus from a previous study as a control [11].…”