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1 National Veterinary Institute, Ullevålsveien 68, PO Box 8156 Dep., 0033 Oslo, Norway
2 Centraalbureau voor Schimmelcultures, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
Correspondence
V. Robert
robert{at}cbs.knaw.nl
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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The GenBank/EMBL/DDBJ accession numbers for the D1/D2 and ITS sequences obtained in this study are AM268436–AM268482 (D1/D2), AM279219–AM279270 (ITS) and EF405984 (D1/D2), as detailed in Fig. 2.
Results of DNA–DNA reassociation experiments and details of ITS sequence differences are available as supplementary material with the online version of this paper.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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; Yarrow, 1998), the strains are able to grow on various types of hydrocarbons (Wickerham et al., 1970) and, therefore, are used to produce single-cell proteins from these compounds. Additionally, it has been observed that Y. lipolytica can secrete several kinds of metabolites in large quantities, such as organic acids (Franke-Rinker et al., 1983; Furukawa et al., 1982; Kapoor et al., 1982; Mattey, 1992; Oogaki et al., 1983; Tsugawa et al., 1969) and extracellular proteins (Abdelal et al., 1977; Ogrydziak, 1988; Ogrydziak & Scharf, 1982; Yamada & Ogrydziak, 1983). Among the latter, the lipases are very significant (Fickers et al., 2003; Hadeball, 1991; Kalle et al., 1972; Novotn
et al., 1994). The reviews of Barth & Gaillardin (1996, 1997) contain additional references on these topics.
Y. lipolytica is the only known taxon in the teleomorph genus Yarrowia and has its anamorph in the genus Candida as Candida lipolytica (F. C. Harrison) Diddens & Lodder (van der Walt & von Arx, 1980; Kurtzman & Fell, 1998). Analyses of the 18S rRNA gene (Barns et al., 1991) and the 26S rRNA gene (Kurtzman & Robnett, 1995, 1998) have shown that Y. lipolytica is taxonomically assigned to the Hemiascomycetes, a class that contains very divergent groups of yeasts, from which the species differs by several properties such as the relatively high G+C content of the nuclear DNA (nDNA) (Kurtzman & Fell, 1998) and the unique genomic organization of the rRNA genes (Fournier et al., 1986). Reports on intraspecific differences in the genetic make-up of Y. lipolytica have also been published. Naumova et al. (1993) mentioned the presence of chromosomal polymorphism and, studying the triacylglycerol lipase gene family, Bigey et al. (2003) found sequence differences in the coding region of the lipase genes in Y. lipolytica and Candida deformans, the latter, by phenotypic comparison, considered as one of the synonyms of Y. lipolytica (Kurtzman & Fell, 1998; Barnett et al., 2000). Therefore, Bigey et al. (2003) considered C. deformans to be a taxon separate from Y. lipolytica, and this view is supported by their finding of 14 nucleotide differences in domains 1 and 2 of the 26S rRNA gene (D1/D2). In view of the taxonomic conclusion of Bigey et al. (2003) and the biotechnological importance of Y. lipolytica strains, it seemed useful to re-examine the type strains of all 11 basionym species placed in synonymy with Y. lipolytica (Kurtzman & Fell, 1998; Barnett et al., 2000) and to re-evaluate the classification of the genus. The methods and criteria applied here were PCR-mediated fingerprint determinations, whole-genome comparisons and sequence analyses of D1/D2 and the ITS (internal transcribed spacer) domains. The ability to produce ascospores was re-examined. Along with strains previously classified as Y. lipolytica or C. deformans, six strains isolated from spoiled food from different sources in Norway were included that showed similar physiological properties to Y. lipolytica but differed in molecular markers. In some parts of this study, strains were added of the species Candida galli Péter, Dlauchy, Vasdinyei, Tornai-Lehoczki & Deák (Péter et al., 2004) and Candida yakushimensis, the latter being introduced by Benno (2004) without a Latin diagnosis and therefore a nomen invalidum. These strains were isolated from poultry and termites, respectively, and showed similar physiological properties to Y. lipolytica and C. deformans.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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) from cells grown in 2 l YM broth (Yarrow, 1998) for 2 days.
PCR-fingerprinting analysis.
For PCR-fingerprinting analyses, the core sequence of the bacteriophage M13, 5'-GAGGGTGGCGGTTCT-3' (Vassart et al., 1987; Meyer et al., 1997), and primer (GAC)5 (Baleiras Couto et al., 1996) were used as single primers in PCR amplifications. The final reaction mixtures (50 µl) contained 200 µM each dNTP (Bioline), 1.5 mM MgCl2 and 1x NH4 buffer supplied with 2 U BIOTAQ DNA polymerase (Bioline), 0.5 µM primer and 1 µl genomic DNA. The reactions were processed in a GeneAmp PCR System 9700 (Applied Biosystems) with the following program for the M13 primer: 94 °C for 120 s at the start, followed by 40 cycles of 94 °C for 30 s, 50 °C for 60 s and 72 °C for 120 s and a final extension of 72 °C for 7 min. For the (GAC)5 primer, the annealing temperature was raised to 54 °C. The PCR products were separated on 1.5 % agarose gels in 1x TAE buffer at 30 V for 20 min followed by 80 V for 2 h. Gels were stained with ethidium bromide and photographed in UV light. Group designations were made by visual inspection of the gels.
DNA G+C content and DNA–DNA reassociations.
DNA G+C content was determined by the thermal denaturation (Tm) method of Marmur & Doty (1962) and levels of DNA–DNA reassociation were determined spectrophotometrically using the method of Seidler & Mandel (1971) as modified by Kurtzman et al. (1980). Reassociation experiments were performed twice. Strains used in reassociation experiments are indicated in Table 1
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rRNA gene sequencing and sequence analysis.
To amplify the rDNA for sequencing, primers V9G (de Hoog & Gerrits van den Ende, 1998) and LR5 (Vilgalys & Hester, 1990) were used in the following reaction mixture (50 µl): 200 µM each dNTP (Bioline), 10 mM Tris/HCl (pH 9.5), 50 mM KCl, 1.5 mM MgCl2, 0.01 % gelatin, 0.5 U BIOTAQ DNA polymerase (Bioline), 0.5 µM each primer and 1 µl genomic DNA. The PCR was processed in a GeneAmp PCR System 9700 (Applied Biosystems). The following program was used: 94 °C for 5 min at the start followed by 35 cycles of 94 °C for 35 s, 55 °C for 50 s and 72 °C for 2 min and a final extension of 72 °C for 5 min. The specificity of the PCR product was checked on an agarose gel before it was purified by GFX columns (Amersham Pharmacia). To sequence both strands of the D1/D2 domain of the 26S rRNA gene, primers NL-1 and NL-4 (O'Donnell, 1993) were used, whereas primers ITS1 and ITS4 (White et al., 1990) were used for the ITS domain (ITS 1, ITS 2 and the intervening 5.8S rRNA gene). Sequencing was performed using the BigDye terminator chemistry (Applied Biosystems) following the manufacturer's instructions. The final sequence reaction mixture (10 µl) contained 1 µl BigDye terminator ready reaction mix v. 3.1 (Applied Biosystems), 1 µl (5 µM) primer, 3 µl BigDye dilution buffer (Applied Biosystems), 4 µl MQ water (Millipore; product no. Biocel A 10) and 1 µl PCR product. The sequencing reactions were purified using G50 Superfine Sephadex columns (Amersham Pharmacia) and loaded on an ABI 3730 XL Genetic Analyzer (Applied Biosystems). Sequences of D1/D2 and the ITS domains were edited and trimmed using the BioEdit sequence alignment editor, version 7.0.2 (Hall, 1999). Some strains had double peaks at several positions for the ITS sequence, and these haplotype polymorphisms were determined by cloning. The D1/D2 and ITS sequences were aligned using the CLUSTAL X software (Thompson et al., 1997) and adjusted manually by visual inspection. Phylogenetic analyses were performed using a maximum-likelihood phylogenetic approach based on PHYML software (Guindon & Gascuel, 2003; Guindon et al., 2005) and also using the Bayesian Markov chain Monte Carlo method based on MrBayes software (Ronquist & Huelsenbeck, 2003) and were based on a concatenated alignment of the ITS and D1/D2 datasets. Candida hispaniensis CBS 9994 (Kurtzman, 2005) was used as the outgroup in all the analyses.
Cloning.
Primers V9 and LR5 were used in a PCR to amplify the yeast DNA using conditions described previously. PCR products were purified using GFX columns (Amersham Biosciences) and ligation was carried out using the pGEM-T kit (Promega). Electroporation of electrocompetent Escherichia coli DH10B cells (Invitrogen) was done according to manufacturer's instructions.
Blue/white screening of transformants was performed by plating on selective Luria–Bertani (LB) agar plates containing 100 µg ampicillin ml–1 (Sigma), 40 µg X-Gal ml–1 (Promega) and 20 µg IPTG ml–1 (Sigma).
Single-colony transformants were transferred individually to vials of 15 µl LB broth containing 100 µg ampicillin ml–1. A direct colony PCR was performed by transferring 1 µl bacterial suspension from the previous transformant dilution into a PCR containing flanking primers T7 and SP6 (Promega).
The size of the insert was determined by electrophoresis on a 1 % agarose gel.
Transformants carrying the pGEM plasmid containing the V9–LR5 insert were cultured in LB broth containing 100 µg ampicillin ml–1. Preparation of plasmid DNA for sequencing purposes was carried out using a plasmid mini prep kit (Marligen) to obtain high-purity plasmid DNA. Of each strain, three transformants containing the V9–LR5 PCR product were sequenced using the procedure described above.
Ascospore formation.
Ascospore production was tested by inoculating cultures, grown in 5 ml broth containing glucose (4 %), tryptone (1 %) and yeast extract (5 %) for 1–2 days, on YM agar medium (Yarrow, 1998) alone or mixed with either the tester mating types A and B, CBS 6124.1 and CBS 6124.2, respectively, of Y. lipolytica (mating type designation adopted from Wickerham et al., 1970) or with strains of known mating type. Ascospore formation was followed at regular intervals from 3 days up to 4 weeks.
Physiology.
Physiological characteristics were determined in microplates (Kurtzman et al., 2003) and processed using the BioloMICS system (Robert, 2003). All tests were replicated. Growth at different temperatures was determined by incubation on GPYA for 48 h.
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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) were determined using the primers M13 and (GAC)5. Six different fingerprint types were obtained with each primer. Results obtained with each of the primers showed identical grouping of the strains. In Fig. 1, the fingerprints and groups obtained with M13 are shown. The majority of strains, including the type and the mating types of Y. lipolytica and 10 synonyms of the species, generated similar fingerprints. A group of four strains produced similar patterns that were different from the patterns of the majority of strains. This group is represented by CBS 2071 (the type of C. deformans), CBS 2076, labelled Y. lipolytica, strain G04-83, received from F. Bigey as a subculture of the type strain CBS 2071, and M59. The latter strain represented a subculture cultivated from the type of C. deformans lyophilized in 1979 at the CBS. Identical patterns were observed in the two strains of C. galli. Strain CBS 4855, identified physiologically as Y. lipolytica, stood apart. The six unidentified strains showed two different patterns by which they were separated from the other groups of strains. The first group included CBS 10145, CBS 10146, CBS 10147 and CBS 10148; the second group included CBS 10149 and CBS 10151.
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), were selected for whole-genome comparisons.
DNA base composition and DNA–DNA reassociation.
The DNA base compositions of the selected strains expressed as mol% G+C contents are presented in Table 1. The G+C content of strains labelled Y. lipolytica ranged from 46.7 to 48.8 mol% and that of strains of C. deformans ranged from 46.1 to 49.2 mol%. The G+C content of the five selected unidentified strains ranged from 43.5 to 45.9 mol%.
Intra- and interspecific reassociation values among the selected strains are shown in Supplementary Fig. S1 (available in IJSEM Online). The strains were separated into six groups, which coincided with the grouping based on fingerprints. The major group of 12 strains, including the type of Y. lipolytica and seven synonyms, showed DNA reassociation ranging from 92 to 100 %, which indicates that the strains of this group are conspecific. High reassociation values ranging from 84 to 100 % were observed among the two C. deformans strains and CBS 2076, labelled Y. lipolytica, which implies that the latter is indeed conspecific with C. deformans as observed from their fingerprints. The five selected unidentified strains could be subdivided into two reassociation groups; one group of three strains, CBS 10146, CBS 10147 and CBS 10148, and a second group of two strains, CBS 10149 and CBS 10151, showing reassociation values of 93–100 and 100 %, respectively. The two strains of C. galli showed a mutual reassociation value of 87 %. Strain CBS 4855 remained alone, showing reassociation values of 15–37 % with members of the other five groups.
The mean interspecific reassociation values among the six different reassociation clusters ranged from 15 to 50 %. By these values, the separate status of C. deformans from Y. lipolytica, as suggested by Bigey et al. (2003), is supported. Additionally, three distinct groups separate from Y. lipolytica, C. deformans and C. galli could be recognized.
Sequences and phylogeny.
Among the strains of Y. lipolytica, sequences of the ITS revealed differences between individual clones generated from the same strain. This confirms that non-orthologous ITS sequences can be present within the same strain of some fungal species (O'Donnell & Cigelnik, 1997; Ko & Jung, 2002). The differences between haplotypes of CBS 6659, CBS 6660, CBS 7133 and CBS 10150 are presented in Supplementary Fig. S2. Additionally, strains CBS 2787, CBS 6114, CBS 6124.1, CBS 6303, CBS 6317 and CBS 6659 had either six or seven T repeats at nucleotide positions 255–261. Preliminary phylogenetic analysis containing all the haplotypes resulted in the same topology as it did when only one haplotype per strain was included. The trimmed alignment of the D1/D2 sequences resulted in 505 characters, whereas the ITS alignment yielded 329 characters. Table 1 presents the accession numbers of the strains included. The Bayesian phylogenetic analysis allowed the separation of the strains into six well-supported clades with 99 or 100 % probability (Fig. 2): I, Y. lipolytica; II, C. yakushimensis nom. inval.; III, CBS 10145, CBS 10146, CBS 10147 and CBS 10148 (Candida oslonensis sp. nov.); IV, C. galli; V, C. deformans; and VI, CBS 10149 and CBS 10151 (Candida alimentaria sp. nov.). Strain CBS 4855 was separated from all the clades. CBS 10149 and CBS 10151 diverged by nine characters in the D1/D2 sequences but only by one character in the ITS sequences. Most yeast species are more conserved in D1/D2 than in the ITS domain, and it has been suggested that strains showing more than 1 % difference or 3 nucleotide differences in this domain are likely to represent different species (Kurtzman & Robnett, 1998; Fell et al., 2000). Others, however, have seen greater differences in D1/D2 between strains of the same species (Lachance et al., 2003). Low sequence divergence in the ITS domain, fingerprinting results and DNA–DNA reassociation data support the hypothesis that the two strains CBS 10149 and CBS 10151 belong to the same species. The Bayesian and maximum-likelihood analyses (data not shown) of both domains support the distinction between the three recognized species and three additional evolutionary groups that may represent novel species.
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). Intraspecific mating of strains of the C. deformans reassociation group with inclusion of CBS 2076 (labelled Y. lipolytica) did not result in the development of the teleomorph state in culture, neither did the mating within the species C. galli or within the other reassociation groups. However, asci with hat-shaped ascospores were observed in some interspecific crossings. Positive results, although low (+), were observed after mixing the two strains of C. galli with Y. lipolytica mating type A strains CBS 6124.1 and CBS 6303. Consequently, both isolates of the former species must belong to mating type B. Moderate (++) to low (+) ascospore formation was also observed by mixing the two strains of C. galli with strain CBS 2076 of the C. deformans reassociation group (Fig. 3). Consequently, strain CBS 2076 could be designated mating type A. Ascospores were not produced by the individual cultures.
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), Zygoascus (Smith et al., 2005) and Arthroascus (Naumov et al., 2006). The latter study in particular showed by genetic analysis that recombinants were not produced, despite the occurrence of mating between taxa showing low DNA–DNA relatedness. Consequently, the presence of mating indicates close relatedness and not conspecificity per se. Molecular data reveal the extent of relatedness.
Physiology
The physiological characters of the novel species proposed are presented in Table 2. Reliable identification on the basis of physiological characters seems unlikely because of the few available isolates of each taxon. Therefore, molecular determinations using ITS and D1/D2 rDNA sequences are recommended.
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Latin diagnosis of Candida oslonensis Knutsen, V. Robert & M. Th. Smith sp. nov.
In YM liquido post dies 3 ad 25 °C, cellulae vegetativae ovoidae aut globosae (3.0–6.0x3.0–9.0 µm), singulae, binae vel racemis parvis connexae, hyphae absunt. In YM agaro post dies 3 ad 25 °C pseudohyphae et hyphae verae formantur. Charactera physiologica in Table 2.
Typus: Holotypus CBS 10146 (NRRL Y-48252) lyophilus in collectione zymotica Centraalbureau voor Schimmelcultures, Trajectum ad Rhenum.
Description of Candida oslonensis Knutsen, V. Robert & M. Th. Smith sp. nov.
Candida oslonensis (os.lo.nen'sis. N.L. fem. adj. oslonensis referring to the origin of the isolates, the city of Oslo in Norway).
Mycobank number MB 510769.
After 3 days at 25 °C in YM broth, cells are ovoid to globose, 3.0–6.0x3.0–9.0 µm in size. Vegetative reproduction is by multilateral budding and cells occur singly, in pairs and in small clusters. No hyphal elements are produced. On Dalmau plate with YM agar, pseudohyphae and true hyphae are produced after 3 days at 25 °C. Physiological characters are presented in Table 2.
Type strain: the holotype CBS 10146T (=NRRL Y-48252T), isolated by A. K. K. from yoghurt, Norway, is deposited as a lyophilized preparation in the collection of the Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands.
Latin diagnosis of Candida alimentaria Knutsen, V. Robert & M. Th. Smith sp. nov.
In YM liquido post dies 3 ad 25 °C, cellulae vegetativae ovoidae aut globosae (3.0–6.0x4.0–7.0 µm), singulae, binae vel racemis parvis connexae, hyphae absunt. In YM agaro post dies 3 ad 25 °C pseudohyphae et hyphae verae formantur. Charactera physiologica in Table 2.
Typus: Holotypus CBS 10151 (NRRL Y-48253) lyophilus depositus in collectione zymotica Centraalbureau voor Schimmelcultures, Trajectum ad Rhenum.
Description of Candida alimentaria Knutsen, V. Robert & M. Th. Smith sp. nov.
Candida alimentaria (a.li.men.ta'ri.a. L. fem. adj. alimentaria relating to food, because the specimens were isolated from different food products).
Mycobank number MB 510770.
After 3 days at 25 °C in YM broth, cells are ovoid to globose, 3.0–6.0x4.0–7.0 µm in size. Vegetative reproduction is by multilateral budding and cells occur singly, in pairs and in small clusters. No hyphal elements are produced. On Dalmau plate with YM agar, pseudohyphae and true hyphae are produced after 3 days at 25 °C. Physiological characters are presented in Table 2.
Type strain: the holotype CBS 10151T (=NRRL Y-48253T), isolated by A. K. K. from ham, Norway, is deposited as a lyophilized preparation in the collection of the Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands.
Latin diagnosis of Candida hollandica Knutsen, V. Robert & M. Th. Smith sp. nov.
In YM liquido post dies 3 ad 25 °C, cellulae vegetativae ovoidae aut globosae (3.0–5.0x5.0–9.0 µm), singulae, binae vel racemis parvis connexae, hyphae absunt. In YM agaro post dies 3 ad 25 °C pseudohyphae et hyphae verae formantur. Charactera physiologica in Table 2.
Typus: CBS 4855 (NRRL Y-48254) lyophilus depositus in collectione zymotica Centraalbureau voor Schimmelcultures, Trajectum ad Rhenum.
Description of Candida hollandica Knutsen, V. Robert & M. Th. Smith sp. nov.
Candida hollandica [hol.lan'di.ca. N.L. fem. adj. hollandica from Holland, referring to the country of origin of the isolate, The Netherlands (commonly referred to in English as Holland)].
Mycobank number MB 510771.
After 3 days at 25 °C in YM broth, cells are ovoid to globose, 3.0–5.0x5.0–9.0 µm in size. Vegetative reproduction is by multilateral budding and cells occur singly, in pairs and in small clusters. No hyphal elements are produced. On Dalmau plate with YM agar, pseudohyphae and true hyphae are produced after 3 days at 25 °C. Other physiological characters are presented in Table 2.
Type strain: CBS 4855T (=NRRL Y-48254T), isolated from the back of a cow in The Netherlands, is deposited as a lyophilized preparation in the collection of the Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands.
The formal description of Candida yakushimensis is left to Y. Benno and co-workers, who introduced this taxon as a provisional name without Latin diagnosis (Benno, 2004).
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ACKNOWLEDGEMENTS |
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REFERENCES |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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Baleiras Couto, M. M., Hartog, B. J., Huis in't Veld, J. H. J., Hofstra, H. & van der Vossen, J. M. B. M. (1996). Identification of spoilage yeasts in a food-production chain by microsatellite polymerase chain reaction fingerprinting. Food Microbiol 13, 59–67.[Medline]
Barnett, J. A., Payne, R. W. & Yarrow, D. (2000). Yeasts: Characteristics and Identification, 3rd edn. Cambridge: Cambridge University Press.
Barns, S. M., Lane, D. J., Sogin, M. L., Bibeau, C. & Weisburg, W. G. (1991). Evolutionary relationships among pathogenic Candida species and relatives. J Bacteriol 173, 2250–2255.
Barth, G. & Gaillardin, C. (1996). Yarrowia lipolytica. In Nonconventional Yeasts in Biotechnology: a Handbook, pp. 313–388. Edited by K. Wolf. Berlin & London: Springer.
Barth, G. & Gaillardin, C. (1997). Physiology and genetics of the dimorphic fungus Yarrowia lipolytica. FEMS Microbiol Rev 19, 219–237.[CrossRef][Medline]
Benno, Y. (2004). Microbe division (RIKEN BRC JCM). In Annual Report of the Riken Biological Research Center, pp. 905–914. Wako, Japan: RIKEN (in Japanese with English translation).
Bigey, F., Tuery, K., Bougard, D., Nicaud, J. & Moulin, G. (2003). Identification of a triacylglycerol lipase gene family in Candida deformans: molecular cloning and functional expression. Yeast 20, 233–248.[CrossRef][Medline]
de Hoog, G. S. & Gerrits van den Ende, A. H. (1998). Molecular diagnostics of clinical strains of filamentous Basidiomycetes. Mycoses 41, 183–189.[Medline]
Fell, J. W., Boekhout, T., Fonseca, A., Scorzetti, G. & Statzell-Tallman, A. (2000). Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis. Int J Syst Evol Microbiol 50, 1351–1371.[Abstract]
Fickers, P., Nicaud, J. M., Destain, J. & Thonart, P. (2003). Overproduction of lipase by Yarrowia lipolytica mutants. Appl Microbiol Biotechnol 63, 136–142.[CrossRef][Medline]
Fournier, P., Gaillardin, C., Persuy, M.-C., Klootwijk, J. & van Heerikhuizen, H. (1986). Heterogeneity in the ribosomal family of the yeast Yarrowia lipolytica: genomic organization and segregation. Gene 42, 273–282.[CrossRef][Medline]
Franke-Rinker, D., Behrens, U., Nockel, E., Forner, C. & Portnowa, A. (1983). Joint utilization of glucose and n-alkanes in citric acid synthesis by Saccharomycopsis lipolytica. Z Allg Mikrobiol 23, 9–16.[CrossRef][Medline]
Furukawa, T., Ogina, T. & Matsuyoshi, T. (1982). Fermentative production of citric acid from n-paraffins by Saccharomycopsis lipolytica. J Ferment Technol 60, 281–286.
Guindon, S. & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696–704.
Guindon, S., Lethiec, F., Duroux, P. & Gascuel, O. (2005). PHYML Online – a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33, W557–W559.
Hadeball, W. (1991). Production of lipase by Yarrowia lipolytica. Acta Biotechnol 11, 159–167.[CrossRef]
Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95–98.
Kalle, G. P., Gadkari, S. V. & Deshpande, S. Y. (1972). Inducibility of lipase in Candida lipolytica. Indian J Biochem Biophys 9, 171–175.[Medline]
Kapoor, K. K., Chaudhary, K. & Tauro, P. (1982). Citric acid. In Prescott & Dunn's Industrial Microbiology, 4th edn, pp. 709–747. Edited by G. Reed. Westport, CT: AVI Publishing.
Ko, K. S. & Jung, H. S. (2002). Three nonorthologous ITS1 types are present in a polypore fungus Trichaptum abietinum. Mol Phylogenet Evol 23, 112–122.[CrossRef][Medline]
Kurtzman, C. P. (2005). New species and a new combination in the Hyphopichia and Yarrowia yeast clades. Antonie van Leeuwenhoek 88, 121–130.[CrossRef][Medline]
Kurtzman, C. P. & Fell, J. W. (editors) (1998). The Yeasts: a Taxonomic Study, 4th edn. Amsterdam: Elsevier.
Kurtzman, C. P. & Robnett, C. J. (1995). Molecular relationships among hyphal ascomycetous yeasts and yeastlike taxa. Can J Bot 73, S824–S830.[CrossRef]
Kurtzman, C. P. & Robnett, C. J. (1998). Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek 73, 331–371.[CrossRef][Medline]
Kurtzman, C. P., Smiley, M. J., Johnson, C. J. & Wickerham, L. J. (1980). Two closely related heterothallic species, Pichia amylophila and Pichia mississipiensis: characterization by hybridization and deoxyribonucleic acid reassociation. Int J Syst Bacteriol 30, 206–216.
Kurtzman, C. P., Boekhout, T., Robert, V., Fell, J. W., Yarrow, D. & Deak, T. (2003). Methods to identify yeasts. In Yeasts in Food, pp. 69–122. Edited by T. Boekhout & V. Robert. Hamburg: Behr's Verlag.
Lachance, M.-A., Daniel, H. M., Meyer, W., Prasad, G. S., Gautam, S. P. & Boundy-Mills, K. (2003). The D1/D2 domain of the large-subunit rDNA of the yeast species Clavispora lustianiae is unusually polymorphic. FEMS Yeast Res 4, 253–258.[CrossRef][Medline]
Marmur, J. & Doty, P. (1962). Determination of the base composition of DNA from its thermal denaturation temperature. J Mol Biol 5, 109–118.[Medline]
Mattey, M. (1992). The production of organic acids. Crit Rev Biotechnol 12, 87–132.[Medline]
Meyer, W., Latouche, G. N., Thanos, M., Mitchell, T. G., Yarrow, D., Schönian, G. & Sorrell, T. C. (1997). Identification of pathogenic yeasts of the imperfect genus Candida by polymerase chain reaction fingerprinting. Electrophoresis 18, 1548–1559.[CrossRef][Medline]
Naumov, G. I., Naumova, E. S., Smith, M. Th & de Hoog, G. S. (2006). Molecular-genetic diversity of the ascomycetous yeast genus Arthroascus: Arthroascus babjevae sp. nov., Arthroascus fermentans var. arxii var. nov. and geographical populations of Arthroascus schoenii. Int J Syst Evol Microbiol 56, 1997–2007.
Naumova, E., Naumov, G., Fournier, P., Nguyen, H.-V. & Gaillardin, C. (1993). Chromosomal polymorphism of the yeast Yarrowia lipolytica and related species: electrophoretic karyotyping and hybridization with cloned genes. Curr Genet 23, 450–454.[CrossRef][Medline]
Novotn, C., Dole
alová, L. & Lieblová, J. (1994). Dimorphic growth and lipase production in lipolytic yeasts. Folia Microbiol (Praha) 39, 71–73.[Medline]
O'Donnell, K. (1993). Fusarium and its near relatives. In The Fungal Holomorph: Mitotic, Meiotic and Pleomorphic Speciation in Fungal Systematics, pp. 225–233. Wallingford, UK: CAB International.
O'Donnell, K. & Cigelnik, E. (1997). Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Mol Phylogenet Evol 7, 103–116.[CrossRef][Medline]
Ogrydziak, D. M. (1988). Production of alkaline extracellular protease by Yarrowia lipolytica. Crit Rev Biotechnol 8, 177–187.
Ogrydziak, D. M. & Scharf, S. J. (1982). Alkaline extracellular protease produced by Saccharomycopsis lipolytica CX161-1B. J Gen Microbiol 128, 1225–1234.
Oogaki, M., Nakahara, T., Uchiyama, H. & Tabuchi, T. (1983). Extracellular production of D-(+)-2-hydroxyglutaric acid by Yarrowia lipolytica from glucose under aerobic, thiamine-deficient conditions. Agric Biol Chem 47, 2619–2624.
Péter, G., Dlauchy, D., Vasdinyei, R., Tornoi-Lehockzi, J. & Deak, T. (2004). Candida galli sp. nov., a new yeast from poultry. Antonie van Leeuwenhoek 86, 105–110.[CrossRef][Medline]
Robert, V. (2003). Data processing. In Yeasts in Food, pp. 139–170. Edited by T. Boekhout & V. Robert. Hamburg: Behr's Verlag.
Ronquist, F. & Huelsenbeck, J. P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574.
Seidler, R. J. & Mandel, M. (1971). Quantitative aspects of deoxy-ribonucleic acid renaturation: base composition, site of chromosome replication, and polynucleotide homologies. J Bacteriol 106, 608–614.
Smith, M. T., de Cock, A. W. A. M., Poot, G. A. & Steensma, H. Y. (1995). Genome comparisons in the yeastlike fungal genus Galactomyces Redhead et Malloch. Int J Syst Bacteriol 45, 826–831.
Smith, M. Th., Robert, V., Poot, G. A., Epping, W. & de Cock, A. W. A. M. (2005). Taxonomy and phylogeny of the ascomycetous yeast genus Zygoascus, with proposal of Zygoascus meyerae sp. nov. and related anamorphic varieties. Int J Syst Evol Microbiol 55, 1353–1363.
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.
Tsugawa, R., Nakase, T., Koyabashi, T., Yamashita, K. & Okumura, S. (1969). Fermentation of n-paraffins by yeast. Part III. 
-Ketoglutarate productivity of various yeasts. Agric Biol Chem 33, 929–938.
Ueda-Nishimura, K. & Mikata, K. (2002). Species distinction of the ascomycetous heterothallic yeast-like fungus Stephanoascus ciferrii complex: description of Candida allociferrii sp. nov. and reinstatement of Candida mucifera Kocková-Kratochvílová et Sláviková. Int J Syst Evol Microbiol 52, 463–471.[Abstract]
van der Walt, J. P. & von Arx, J. A. (1980). The yeast genus Yarrowia gen. nov. Antonie van Leeuwenhoek 46, 517–521.[CrossRef][Medline]
Vassart, G., Georges, M., Monsieur, R., Brocas, H., Lequarré, A. S. & Christophe, D. (1987). A sequence in M13 phage detects hypervariable minisatellites in human and animal DNA. Science 235, 683–684.
Vilgalys, R. & Hester, M. (1990). Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 172, 4238–4246.
White, T. J., Bruns, T., Lee, S. & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: a Guide to Methods and Applications, pp. 315–322. Edited by N. Innis, D. Gelfand, J. Sninsky & T. White. New York: Academic Press.
Wickerham, L. J., Kurtzman, C. P. & Herman, A. I. (1970). Sexuality in Candida lipolytica. In Recent Trends in Yeast Research (Spectrum, vol. 1), pp. 31–92. Edited by D. G. Ahearn. Atlanta: Georgia State University.
Yamada, T. & Ogrydziak, D. M. (1983). Extracellular acid proteases produced by Saccharomycopsis lipolytica. J Bacteriol 154, 23–31.
Yarrow, D. (1998). Methods for the isolation, maintenance and identification of yeasts. In The Yeasts: a Taxonomic Study, 4th edn, pp. 77–100. Edited by C. P. Kurtzman & J. W. Fell. Amsterdam: Elsevier.
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