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. 2018 Jun 26;13(6):e0198957.
doi: 10.1371/journal.pone.0198957. eCollection 2018.

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

Caoimhe E O'Brien  1 , Charley G P McCarthy  2 , Annie E Walshe  1 , Dennis R Shaw  1 , Deirdre A Sumski  1 , Tadeusz Krassowski  3 , David A Fitzpatrick  2 , Geraldine Butler  1
Affiliations

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

Caoimhe E O'Brien et al. PLoS One. .

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.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Diutina catenulata is a member of the Debaryomycetaceae/Metschnikowiaceae clade.
The phylogenetic tree was inferred from a superalignment of 204 ubiquitous gene families from 42 species. A consensus Bayesian supermatrix phylogeny was generated using PhyloBayes [38]. Clades within the Saccharomycotina (Debaryomycetaceae/Metschnikowiaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae and Saccharomycetaceae) are highlighted in color. Species within the Lodderomyces clade in the Debaryomycetaceae/Metschnikowiaceae are surrounded with a gray box. The exact definition of the Lodderomyces clade is not clear, and it may include Spathaspora species [48]. The branch supports show Bayesian Posterior Probabilities.
Fig 2
Fig 2. D. catenulata translates CUG codons as serine.
A. Bar plot showing frequencies of amino acid matches to CUG codons in the D. catenulata genome. The values on the Y-axis represent the number of CUG codon sites that align with the amino acid residues shown on the X-axis in the YGOB protein database [41]. Analysis of all codons is shown in S1 File. B. Comparison of tRNASer(CAG) from D. catenulata with the same tRNA encoded by other species in the Debaryomycetaceae/Metschnikowiaceae. The discriminator base at the 3’ end (highlighted in red) is G in tRNASer(CAG), and A in most tRNALeu(CAG) molecules. The G base just 5’ to the anticodon (highlighted in blue) also reduces leucylation [54].
Fig 3
Fig 3. The Mating Type-like Locus in D. catenulata.
A. Gene order around MTLα in M. guilliermondii and D. catenulata. Orthologous genes are connected with gray lines. Mating-type genes are filled in pink, and other genes associated with the MTL are edged in pink. The assembly of the D. catenulata contig stops at OBP. B. Phylogenetic relationship of PAPα and PAPa from the indicated species from the Debaryomycetaceae/Metschnikowiaceae clade. The PAP protein from D. catenulata (which is not found at the MTL locus) is more closely related to PAPa than to PAPα alleles. Alignments and phylogenetic trees were constructed using PhyML in SeaView [39].
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