Nuclear DNA Base Composition Research Articles

Tetrapisispora namnaonensis sp. nov., a novel ascomycetous yeast species isolated from forest soil of Nam Nao National Park, Thailand

Twenty-one strains of a novel ascomycetous yeast species were isolated from soil collected in three kinds of natural forest, namely a dry dipterocarp forest, a mixed deciduous forest and a pine forest, in Nam Nao National Park, Phetchabun province, Thailand. The strains formed asci containing one to four ovoid to reniform ascospores, assimilated glucose, galactose and glycerol, fermented glucose and galactose vigorously and contained ubiquinone Q-6, indicating that they belonged to the genus Tetrapisispora. A comparative analysis of the small subunit rDNA (SSU rDNA) and the D1/D2 domain of the large subunit rDNA (LSU rDNA) of all available sequences for ascomycetous yeasts confirmed that the strains were phylogenetically related to the genus Tetrapisispora. All strains had identical nucleotide sequences in the D1/D2 domain of the LSU rDNA and differed from the nearest species, Tetrapisispora arboricola IFO 10925(T), by 6.4% nucleotide substitutions. The strains differed from Tetrapisispora arboricola by the ability to assimilate D-gluconic acid, the inability to grow on 50% glucose medium, the nuclear DNA base composition and deliquescent asci. The strains were differentiated from the other four species of Tetrapisispora on the basis of trehalose assimilation, the ability to grow on 50% glucose or 10% NaCl plus 5% glucose, vitamin requirement, the nuclear DNA base composition and the type of ascus. Based on the characteristics mentioned above, the strains are recognized as a single novel species of the genus Tetrapisispora and the name Tetrapisispora namnaonensis sp. nov. is proposed. The type strain is TN1-01(T) (=TISTR 5828(T)=JCM 12664(T)=CBS 10093(T)).

A new yeast genus, Tetrapisispora gen. nov.: Tetrapisispora iriomotensis sp. nov., Tetrapisispora nanseiensis sp. nov. and Tetrapisispora arboricola sp. nov., from the Nansei Islands, and reclassification of Kluyveromyces phaffii (van der Walt) van der Walt as Tetrapisispora phaffii comb. nov.

Seven strains of three new yeast species were isolated from soil, flowers and leaves in the Nansei Islands, Japan. These isolates most closely resembled Kluyveromyces phaffii in physiological characteristics and nuclear DNA base composition (30-32 mol% G + C), but on the basis of DNA-DNA hybridization and electrophoretic karyotyping they were categorized into three new species different from K. phaffii. Phylogenetic analysis using 18S rRNA gene sequences showed that the three new species and K. phaffii were highly related to one another and phylogenetically separate from the members of other species. On the basis of phylogeny and physiological characters, it is proposed that the three new species represent novel taxa and should be designated Tetrapisispora iriomotensis gen. nov., sp. nov. (type strain IFO 10929T), Tetrapisispora nanseiensis gen. nov., sp. nov. (type strain IFO 10899T) and Tetrapisispora arboricola gen. nov., sp. nov. (type strain IFO 10925T), while Kluyveromyces phaffii becomes Tetrapisispora phaffii comb. nov.

Debaryomyces prosopidis sp. nov., a yeast from exudates of mesquite trees

Nine strains were studied of a new haploid species of the genus Debaryomyces Lodder & Kreger-van Rij that had been isolated from exudates of mesquite (Prosopis juliflora) trees in southern Arizona and from Drosophila carboneria that breeds in these exudates. Their physiological characteristics, life cycle, and nuclear DNA base composition (approx. 37·5 mol% G+C) led to their original classification as Debaryomyces hansenii (Zopf) Kreger-van Rij. However, the two taxa are, at most, distantly related based on DNA reassociation values that indicated low base sequence complementarity. The two taxa also have distinctly different electrophoretic karyotypes. Debaryomyces hansenii has two varieties, D. hansenii var. hansenii and D. hansenii var. fabryi. Debaryomyces prosopidis can be differentiated phenotypically from both varieties by lack of growth on cellobiose after 2 weeks incubation and from the variety hansenii by a higher maximum temperature for growth. The type strain of Debaryomyces prosopidis sp. nov. is strain UCD-FST 84-100T (= DBVPG 7010T = CBS 8450T = ATCC 201611T).

Molecular taxonomy and epidemiology of Blastomyces and Histoplasma species.

Cladistic analysis of partial 26S rRNA sequences was used to estimate evolutionary distances among species and varieties of the dimorphic onygenalean genera Blastomyces, Coccidioides, Emmonsia, Histoplasma and Paracoccidioides. With the exception of Coccidioides, all genera were closely related, with about 5% base differences and even less (1-2%) between Blastomyces and Emmonsia. These data were supported by a teleomorph in the same genus Ajellomyces. In a phylogenic study of a wide range of ascomycete orders and families, Coccidioides immitis was found to be closest to Aphanoascus fulvescens and Chrysosporium keratinophilum, and to have relative distances to the remaining dimorphic genera (family Onygenaceae) similar to those of the dermatophytes (family Arthrodermataceae). The sequencing data were confirmed by genomic comparisons. All dimorphic genera had a nuclear DNA base composition in the same range of 46.6-47.3% G + C. The DNA melting curves of Blastomyces and Histoplasma strains showed irregularities that were ascribed to the presence of AT-rich stretches in satellite DNA rather than in mitochondrial DNA. Derivative profiles proved to be highly reproducible within regional populations and coincided with differences in clinical behaviour of each species. Blastomyces dermatitidis generated two kinds of curves, corresponding to the geographically distinct serotypes 1 and 2. The African type (serotype 2) was characterized by a classical sigmoidal melting curve similar to that for all strains of Coccidioides, Emmonsia and Paracoccidioides. In contrast, the American type (serotype 1) contained satellite DNA (27% G + C). A rRNA base difference of 1.5% was observed between geographical types, a value slightly higher than that noted between Histoplasma capsulatum and its variety farciminosum (0.9%). All three H. capsulatum varieties presented irregularities in their DNA melting curves. The molecular data support the recognition of two of them as agents of blastomycosis and the assignment of more than one species and two varieties to the genus Emmonsia.

DNA base composition heterogeneity in some agarophytes (Gracilariales, Rhodophyta) from Mexico and the Philippines

Estimates of nuclear DNA base composition by determination of thermal denaturation temperatures (Tm) indicate guanine + cytosine (G + C) levels of 35.4–46.8% for ten species of the Gracilariaceae, representing the generaGracilaria andHydropuntia. Tm values were found to be reproducible with variation among most samples and replicates of less than 1 °C and 2 mol%. Interspecific variation in G + C values was less than 11.4% amongGracilaria species. Calculation of intragenomic base pair composition distribution based on mid-resolution thermal denaturation (ΔA 1 °C/min with 4s interval ΔH and dT logging) indicated an inverse relationship between maximum similarity values and taxonomic rank. Intraspecific (population level) maximum similarity (homology) values were estimated to range from 79–90% inGracilaria tikvahiae (4 isolates). Interspecific values of 46–69% were found in 13 species ofGracilaria. Nucleotide distribution similarity values for the Gracilariaceae are compared with previous information for genome organization and complexity, genome size and karyotype patterns.

DNA base modification inChlorella

The nuclear DNA base composition of 26 strains of green algae belonging to the Chlorococcales was analysed by reversed-phase high-performance liquid chromatography (HPLC). 5-Methyldeoxycytidine was the only modified nucleoside detected in addition to the standard nucleosides deoxyadenosine, deoxycytidine, deoxyguanosine and deoxythymidine. The amount of 5-methyldeoxycytidine varied from 1·5 mol% to 12·0 mol% and was correlated with the deoxyguanosine + deoxycytidine (G + C) content of the DNA. No significant influence of deoxycytidine methylation on the thermal stability of the DNA double strand was found. The variation of DNA base composition previously observed within the genus Chlorella and, in particular, within C. sorokiniana, could not be explained by the influence of variable amounts of modified bases on the DNA melting temperature from which the G + C contents were derived.

Kluyveromyces bacillisporus sp. nov., a Yeast from Emory Oak Exudate

Three strains of a new diploid species of the genus Kluyveromyces van der Walt emend. van der Walt were isolated from exudates of Emory oak (Quercus emoryi) trees in Arizona. In physiological characteristics and nuclear DNA base composition (38 mol% G+C) these isolates most closely resemble Kluyveromyces africanus and Kluyveromyces delphensis, but the three taxa are genetically unrelated, as shown by DNA reassociation and ribosomal DNA restriction mapping. The morphology of these organisms is typical of the genus Kluyveromyces, except that the mature ascospores (four and occasionally more spores per ascus) are characteristically bacilliform rather than spheroidal, ellipsoidal, or reniform. Mitochondrial DNA (21 mol% G+C) is present in unusually large proportions (ca. one-half of the total DNA). The type strain of Kluyveromyces bacillisporus sp. nov. is strain UWO(PS) 85-349.2 (= ATCC 90019 = CBS 7720).

Chemotaxonomy of Aspergillus and Associated Teleomorphs

The complexity of Aspergillus has been emphasized by the diversity of teleomorph and the heterogeneity of ubiquinone systems. The resolution by traditional morphological approaches has been limited, and a need for newer approaches has become apparent. Current trends in Aspergillus chemotaxonomy are presented based mainly on our previously published and unpublished data on electrophoretic comparisons of enzymes and their numerical analyses, ubiquinone systems, and partial sequences of 18S ribosomal RNA. Combinations of such chemotaxonomic indicators including nuclear DNA base composition and DNA-DNA homology support or bring into question taxonomic decisions in recent years based primarily on the morphological species concepts in Aspergillus and associated teleomorph, while further comparisons of 18S ribosomal RNA partial sequences can shed light on the phylogenetic and evolutionary background of both.

Variation in nuclear DNA base composition (mol % G + C) in three orders of marine green algae

Variation in nuclear DNA base composition (mol % G + C) in three orders of marine green algae

Validation of the yeastSporidiobolus ruinenii based on its deoxyribonucleic acid relatedness to other species of the genusSporidiobolus

The yeastSporidiobolus ruinenii was described in 1970 but without a Latin diagnosis and is therefore not validly published. It differed from the only other species in the genus,Sporidiobolus johnsonii, by not assimilating melezitose and α-methyl-d-glucoside and by assimilating raffinose and galactitol. We have now shown thatSporidiobolus johnsonii andSporidiobolus ruinenii differ by 1.2 mol% G+C in nuclear DNA base composition and share only about 8.5% of their nuclear DNA base sequences. The new species also differs fromSporidiobolus salmonicolor. Sporidiobolus ruinenii thus represents a separate species and a Latin description is provided. The type strain is UCD (FS&T) 67-67 (CBS 5001).

Fractionation of Saprolegnia diclina (oomycetes) satellite DNAs by AgNO 3/Cs 2SO 4 density gradient centrifugation

Saprolegnia diclina DNA has been fractionated using preparative AgNO 3/Cs 2SO 4 and CsCl density gradients. In addition to the previously identified major satellite DNA, there are two minor DNA components banding at 1.682 and 1.701 g · cm −3 in CsCl. Purified major satellite DNA bands at 1.707 g · cm −3 giving a base composition of 48% G + C in good agreement with 47% G + C calculated from its T m value. The nuclear DNA base composition is 58% G + C by both methods. The base composition of the major satellite DNA suggests that it may represent ribosomal DNA cistrons.