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Recent studies have suggested that species of the Kazachstania genus may be interesting models of yeast domestication. Among these, Kazachstania barnettii has been isolated from various microbially transformed foodstuffs such as sourdough bread and kefir. In the present work, we sequence, assemble, and annotate the complete genomes of two K. barnettii strains: CLIB 433, being one of the two reference strains for K. barnettii that was isolated as a spoilage organism in soft drink, and CLIB 1767, recently isolated from artisan bread-making sourdough. Both assemblies are of high quality with N50 statistics greater than 1.3 Mb and BUSCO score greater than 99%. An extensive comparison of the two obtained genomes revealed very few differences between the two K. barnettii strains, considering both genome structure and gene content. The proposed genome assemblies will constitute valuable references for future comparative genomic, population genomic, or transcriptomic studies of the K. barnettii species.

International audience; Phoma stem canker, a highly damaging disease of oilseed rape (Brassica napus), is caused by fungi of the Leptosphaeria maculans/Leptosphaeria biglobosa species complex. On B. napus, at least in Europe, L. maculans ‘brassicae’ (LMB) and L. biglobosa ‘brassicae’ (LBB) are often found together, in the same fields. The biology and epidemiology of LMB have been intensively studied, but few studies have investigated the infection and colonization processes of LBB, and unanswered questions remain concerning the relative contributions of these two species to phoma stem canker disease. We addressed this question by developing two species-specific robust quantitative PCR (qPCR) assays, one for each species, for detecting and quantifying these species in field samples of oilseed rape. The assays were highly specific, reproducible, and sensitive. We used them to obtain an overview of stem canker epidemiology in a two-year field study of a B. napus genotype susceptible to LMB, and a near-isogenic line harbouring Rlm11, a gene conferring effective resistance to LMB. Inoculum pressure differed considerably between the two years of the experiment, and we found that LMB leaf spotting intensity at limited observation time points was insufficient for predicting final disease severity. We also found that LBB was more prevalent than previously thought, with epidemiological and colonization biology characteristics very similar to those of LMB, but a necrotrophic lifestyle. The general presence of these two species together on leaves and in the stem tissues of the same individual plant raises questions about their relative incidence and biological interactions within plant tissues.

Two strains (DMKU-GTCP10-8 and CLIB 1740) representing a novel anamorphic yeast species were isolated from a grease sample collected from a grease trap in Thailand and from an unidentified fungus collected in French Guiana, respectively. On the basis of phylogenetic analysis based on the combined D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, Lachancea fermentati CBS 707T was the closely related species with 12.8 % sequence divergence (70 nucleotide substitutions and three gaps in 571 nucleotides) and 28.1 % sequence divergence (93 nucleotide substitutions and 90 gaps in 651 nucleotides) in the D1/D2 domain of the LSU rRNA gene and the ITS region, respectively. Phylogenetic analysis based on the concatenated sequences of the five genes including the small subunit rRNA gene, the D1/D2 domain of the LSU rRNA gene, the ITS region, translation elongation factor-1 alpha (TEF1) and RNA polymerase II subunit 2 (RPB2) genes confirmed that the two strains (DMKU-GTCP10-8 and CLIB 1740) were well-separated from other described yeast genera in Saccharomycetaceae. Hence, Savitreea pentosicarens gen. nov., sp. nov. is proposed to accommodate these two strains as members of the family Saccharomycetaceae. The holotype is S. pentosicarens DMKU-GTCP10-8T (ex-type strain TBRC 12159=PYCC 8490; MycoBank number 835044).

International audience; Analysis of yeasts isolated from various biotopes in French Guiana led to the identification of two strains isolated from flowers and designated CLIB 1634(T) and CLIB 1707(T). Comparison of the D1/D2 domain of the large subunit (LSU D1/D2) rRNA gene sequences of CLIB 1634(T) and CLIB 1707(T) to those in the GenBank database revealed that these strains belong to the Starmerella Glade. Strain CLIB 1634(T) was shown to diverge from the closely related Starmerella apicola type strain CBS 2868 T with a sequence divergence of 1.34 and 1.30 %, in the LSU D1/D2 rRNA gene and internal transcribed spacer (ITS) sequences respectively. Strain CLIB 1634(T) and Candida apicola CBS 2868(T) diverged by 3.81 and 14.96 % at the level of the protein-coding gene partial sequences EF-1 alpha and RPB2, respectively. CLIB 1707(T) was found to have sequence divergence of 3.88 and 9.16 % in the LSU D1/D2 rRNA gene and ITS, respectively, from that of the most closely related species Starmerella ratchasimensis type strain CBS 10611(T). The species Starmerella reginensis f.a., sp. nov. and Starmerella kourouensis f.a., sp. nov. are proposed to accommodate strains CLIB 1634(T) (=CBS 15247(T)) and CLIB 1707(T) (=CBS 15257(T)), respectively.

Geotrichum candidum is an ubiquitous yeast, and an essential component in the production of many soft cheeses. We developed a Multi-Locus Sequence Typing (MLST) scheme with five retained loci (NUP116, URA1, URA3, SAPT4, PLB3) which were sufficiently divergent to distinguish 40 Sequence Types (STs) among the 67 G. candidum strains tested. Phylogenetic analyses defined five main clades; one clade was restricted to environmental isolates, three other clades included distinct environmental isolates and dairy strains, while the fifth clade comprised 34 strains (13 STs), among which all but two were isolated from milk, cheese or dairy environment. These findings suggest an adaptation to the dairy ecosystems by a group of specialized European G. candidum strains. In addition, we developed a PCR inter-LTR scheme, a fast and reproducible RAPD-like method for G. candidum, to type the closely related dairy strains, which could not be distinguished by MLST. Overall, our findings distinguished two types of dairy strains, one forming a homogeneous group with little genetic diversity, and the other more closely related to environmental isolates. Neither regional nor cheese specificity was observed in the dairy G. candidum strains analyzed. This present study sheds light on the genetic diversity of both dairy and environmental strains of G. candidum and thus extends previous characterizations that have focused on the cheese isolates of this species.

Kazachstania saulgeensis is a recently described species isolated from French organic sourdough. Here, we report the high quality genome sequence of a monosporic segregant of the type strain of this species, CLIB 1764(T) (= CBS 14374(T)). The genome has a total length of 12.9 Mb and contains 5326 putative protein-coding genes, excluding pseudogenes and transposons. The nucleotide sequences were deposited into the European Nucleotide Archive under the genome assembly accession numbers FXLY01000001-FXLY01000017.

Using the Genolevures sequencing data, we developed an expression micro-array for the yeast Kluyveromyces lactis consisting of 482 genes, mainly involved in central metabolism, compound transport facilitators and stress response. The array was validated using the LAC/GAL system. By comparing gene expression in the laboratory reference strain CBS2359 and in an industrial strain B1, we demonstrated the influence of two carbon sources, glucose and lactose, on the expression of genes involved in the respiratory and in the fermentative metabolic pathways. We also showed that the two strains, although both originating from dairies, display unexpected differences in gene expression on each type of carbon source.

Ice from Arctic glaciers contains large populations of yeasts. We studied 38 isolates from this environment, which were initially identified as Debaryomyces sp. related to Debaryomyces hansenii by sequence analysis of the D1/D2 domains of 26S rDNA. An analysis of the distribution of mitochondrial DNA insertions in the nuclear genome showed that 25 of these isolates were related to, but distinct from, D. hansenii. Sequence analysis of the ACT1 gene of these 25 isolates revealed that they formed three different types of putative hybrids. In particular, 23 putative hybrids carried an ACT1 sequence identical to that of three Debaryomyces strains, CBS 790, CLIB 660, CLIB 949, previously classified as associated with D. hansenii and an ACT1 sequence of an undescribed taxon. The latter sequence displayed between 22 and 27 bp divergence (2.6-3.2 %) over 841 bp from sequences of closely related Debaryomyces sp., suggesting that this new taxon very likely represents a novel species for which no pure strain is available. Sequence comparisons of CBS 790, CLIB 660, and CLIB 949 with related Debaryomyces type strains also revealed an important sequence divergence. The putative hybrids described in this study could be differentiated from non-hybrid isolates and other Debaryomyces species on the basis of their use of a number of carbon sources.

Background Yeasts belonging to the subphylum Saccharomycotina have been used for centuries in food processing and, more recently, biotechnology. Over the past few decades, these yeasts have also been studied in the interest of their potential to produce oil to replace fossil resources. Developing yeasts for massive oil production requires increasing yield and modifying the profiles of the fatty acids contained in the oil to satisfy specific technical requirements. For example, derivatives of medium-chain fatty acids (MCFAs, containing 6–14 carbons) are used for the production of biodiesels, cleaning products, lubricants and cosmetics. Few studies are available in the literature on the production of MCFAs in yeasts. Results We analyzed the MCFA content in Saccharomyces cerevisiae grown in various conditions. The results revealed that MCFAs preferentially accumulated when cells were grown on synthetic media with a high C/N ratio at low temperature (23 °C). Upon screening deletion mutant strains for genes encoding lipid droplet-associated proteins, we found two genes, LOA1 and TGL3, involved in MCFA homeostasis. A phylogenetic analysis on 16 Saccharomycotina species showed that fatty acid profiles differed drastically among yeasts. Interestingly, MCFAs are only present in post-whole genome duplication yeast species. Conclusions In this study, we produced original data on fatty acid diversity in yeasts. We demonstrated that yeasts are amenable to genetic and metabolic engineering to increase their MCFA production. Furthermore, we revealed that yeast lipid biodiversity has not been fully explored, but that yeasts likely harbor as-yet-undiscovered strains or enzymes that can contribute to the production of high-value fatty acids for green chemistry. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0369-2) contains supplementary material, which is available to authorized users.

We examined aspects of the URE2/[URE3] prion system in Kluyveromyces lactis, which lies on a different evolutionary branch from Saccharomyces. We first analysed the polymorphism of the prion-forming domain in 38 strains. Considerable differences were found between these two genera, with little variation within K. lactis. We then analysed the regulatory function of Ure2p, using a deletion of URE2. We assessed the deregulation of two reporter genes: DAL5 and GDH2. Both were derepressed in the mutant strain, as in Saccharomyces. Finally, we tried to obtain the [URE3] prion from K. lactis. Despite the use of many different experimental conditions, we were unable to obtain a prion from Ure2p. This finding calls into question the extent to which the prion form of Ure2p may be considered an evolutionary adaptation, instead suggesting that an exaptation phenomenon may be more likely than a continuous selection history.

the Consortium National de Recherche en Génomique (CNRG) to Génoscope, CNRS (GDR 2354, Génolevures), The computer framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program "Génotypage et Génomique Comparée," and the ACI IMPBIO "Génolevures En Ligne."; International audience; Polyploidization is an important process in the evolution of eukaryotic genomes, but ensuing molecular mechanisms remain to be clarified. Autopolyploidization or whole-genome duplication events frequently are resolved in resulting lineages by the loss of single genes from most duplicated pairs, causing transient gene dosage imbalance and accelerating speciation through meiotic infertility. Allopolyploidization or formation of interspecies hybrids raises the problem of genetic incompatibility (Bateson-Dobzhansky-Muller effect) and may be resolved by the accumulation of mutational changes in resulting lineages. In this article, we show that an osmotolerant yeast species, Pichia sorbitophila, recently isolated in a concentrated sorbitol solution in industry, illustrates this last situation. Its genome is a mosaic of homologous and homeologous chromosomes, or parts thereof, that corresponds to a recently formed hybrid in the process of evolution. The respective parental contributions to this genome were characterized using existing variations in GC content. The genomic changes that occurred during the short period since hybrid formation were identified (e.g., loss of heterozygosity, unilateral loss of rDNA, reciprocal exchange) and distinguished from those undergone by the two parental genomes after separation from their common ancestor (i.e., NUMT (NUclear sequences of MiTochondrial origin) insertions, gene acquisitions, gene location movements, reciprocal translocation). We found that the physiological characteristics of this new yeast species are determined by specific but unequal contributions of its two parents, one of which could be identified as very closely related to an extant Pichia farinosa strain.

Among ascomycetous yeasts, the CTG clade is so-called because its constituent species translate CTG as serine instead of leucine. Though the biology of certain pathogenic species such as Candida albicans has been much studied, little is known about the life cycles of non-pathogen species of the CTG clade. Taking advantage of the recently obtained sequence of the biotechnological Millerozyma (Pichiasorbitophila) farinosa strain CBS 7064, we used MLST to better define phylogenic relationships between most of the Millerozyma farinosa strains available in public collections. This led to the constitution of four phylogenetic clades diverging from 8% to 15% at the DNA level and possibly constituting a species complex (M. farinosa) and to the proposal of two new species:Millerozyma miso sp. nov. CBS 2004(T) ( = CLIB 1230(T)) and Candida pseudofarinosa sp. nov.NCYC 386(T)( = CLIB 1231(T)). Further analysis showed that M. farinosa isolates exist as haploid and inter-clade hybrids. Despite the sequence divergence between the clades, secondary contacts after reproductive isolation were evidenced, as revealed by both introgression and mitochondria transfer between clades. We also showed that the inter-clade hybrids do sporulate to generate mainly viable vegetative diploid spores that are not the result of meiosis, and very rarely aneuploid spores possibly through the loss of heterozygosity during sporulation. Taken together, these results show that in this part of the CTG clade, non-Mendelian genetic exchanges occur at high rates through hybridization between divergent strains from distinct clades and subsequent massive loss of heterozygosity. This combination of mechanisms could constitute an alternative sexuality leading to an unsuspected biodiversity.

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.