Delimitation of the species of the Debaryomyces hansenii complex by intron sequence analysis

Abstract

The delineation of species among strains assigned to Debaryomyces hansenii was examined using a gene genealogies-based approach in order to compare spliceosomal intron sequences found in four housekeeping genes (ACT1, TUB2, RPL31 and RPL33). This revealed four distinct groups of strains containing, respectively, D. hansenii var. hansenii CBS 767 T , D. hansenii var. fabryi CBS 789 T , Candida famata var. flareri CBS 1796 T (the anamorph of D. hansenii var. fabryi CBS 789 T ) and Debaryomyces tyrocola CBS 766 T , whose species status was no longer accepted. The sequence divergence between these groups, reaching in some cases over 20 %, unambiguously isolated the groups as separate taxa, leading to a proposal for the reinstatement of the originally described species D. hansenii CBS 767 T and D. tyrocola CBS 766 T . The variety D. hansenii var. fabryi was further subdivided into two taxa, Debaryomyces fabryi CBS 789 T and Candida flareri CBS 1796 T (previously C. famata var. flareri and Blastodendrion flareri). The comparison of intron sequences therefore exposed cryptic species whose phenotypic traits are not distinguishable from known species, but which have significantly diverged from the genetic point of view. Hence, we describe the new taxon Debaryomyces macquariensis sp. nov. CBS 5571 T is related to, but clearly distinct from, the Debaryomyces species mentioned above. The approach used in this work has also revealed the existence of populations within the newly delineated species D. hansenii and genetic exchanges between these populations, indicating an unexpected genetic diversity within this part of the genus Debaryomyces.

Molecular characterization of the closely related Debaryomyces species: Proposition of D. vindobonensis sp. nov. from a municipal wastewater treatment plant

“…In the present study we applied a polyphasic approach to reexamine and taxonomically characterize several yeasts from the ACBR culture collection that demonstrated an affiliation to D. hansenii in our previous studies. Similarly to the already published data (Groenewald et al, 2008;Jacques et al 2009;Nguyen et al 2009), our results showed that the phylogeny based on the sequences of 5.8S-ITSs regions and D1/D2 domain is not sufficient for reliable identification of the Debaryomyces species (Fig. 1A).…”

“…On the basis of the considerable differences of RAPD patterns, Prillinger et al (1999) proposed that the two species D. hansenii and D. fabryi should be reinstated. These results have recently been confirmed by different fingerprinting techniques (PCR and IGS AluI fingerprinting) and phylogenetic analysis of ACT1, TUB2, RPL31 and RPL33 sequences (Groenewald et al, 2008;Jacques et al, 2009;Nguyen et al, 2009 (Groenewald et al, 2008;Jacques et al, 2009;Nguyen et al, 2009). These studies have also indicated that genetic exchanges are not rare among the closely related Debaryomyces species, explaining the high genetic diversity and hybrid nature of several isolates (Jacques et al, 2009;Nguyen et al, 2009).…”

“…Recent comprehensive revisions of strains belonging to the D. hansenii species have revealed an intraspecies genetic complexity and resulted in the reinstatement of D. fabryi, D. hansenii, D. subglobosus and D. tyrocola (Groenewald et al, 2008;Jacques et al, 2009;Nguyen et al, 2009;Prillinger et al, 1999), as well as in a description of the new species D. vietnamensis (Nguyen et al, 2009) and D. macquariensis (Jacques et al, 2009). All these yeasts are phenotypically very similar and they may be delineated at the species level solely by various genotyping techniques and the comparative analysis of different gene sequences.…”

“…Debaryomyces species are haploid and homothallic (conjugation between a mother cell and a bud generally precedes ascus formation), although diploid or partial diploid strains have recently been characterized too (Jacques et al, 2009(Jacques et al, , 2010Suzuki et al, 2011). All Debaryomyces yeasts reproduce asexually by multilateral budding; they cannot assimilate nitrate and CoQ9 is the principal ubiquinone in mitochondrial membranes (Suzuki et al, 2011).…”

Zygosaccharomyces sapae sp. nov., isolated from Italian traditional balsamic vinegar

“…An increasing number of examples have been recently reported on intragenomic polymorphism in ITS sequences within the same strain of fungal and yeast species (Wang & Yao, 2005;Fell et al, 2007;Kageyama et al, 2007;Jacques et al, 2009;Connell et al, 2010;Saksinchai et al, 2012). Z. sapae sp.…”