Diversity and affinities among species and strains of Lipomyces

Phylogenetic relationships of the yeast genus Lipomyces were studied using sequences from fragments of 5.8S rRNA gene and from internal transcribed spacer region ITS2 of 13 strains (7 type strains included) representing five species and subtaxa, and originating from different geographical locations (Japan, Trinidad, Nigeria, North America, Western Europe, Russia, South Africa, Mauritius). Parsimony and distance analyses were performed. Tree topology from the parsimony and distance analyses of the sequences confirmed the results of nDNA reassociation. Results segregate the 13 isolates of Lipomyces into five major clades.     

Babjevia gen. nov. — a new genus of the Lipomycetaceae

The species described asLipomyces anomalus Babjeva & Gorin shows significant genetic and phenotypic divergence from the type speciesLipomyces starkeyi Lodder & Kreger-van Rij in terms of rRNA base sequence substitution and ascosporal and septal ultrastructure. The species is consequently reclassified in the new, unispecific genusBabjevia, asBabjevia anomala.     

The nucleotide sequence of the S RNA of Impatiens necrotic spot virus, a novel tospovirus.

Impatiens necrotic spot virus (INSV) shares a number of properties with tomato spotted wilt virus (TSWV), the type species of the genus tospovirus within the family Bunyaviridae. INSV, however, differs from TSWV in plant host range and serology. In order to define the genomic structure and the taxonomic status of this TSWV-like virus, the nucleotide sequence of its genomic S RNA segment has been determined. The molecular data obtained demonstrate that, like TSWV, INSV has an ambisense S RNA molecule, encoding a non-structural protein in viral sense and the nucleocapsid protein in viral complementary sense. The level of nucleotide sequence homology between their S RNAs, as well as the divergence in amino acid sequence homology of their gene products, confirm previous conclusions from serological studies that INSV and TSWV represent distinct virus species within the newly created genus, tospovirus.     

<Emphasis Type="Italic">Streptomyces gulbargensis</Emphasis> sp. nov., isolated from soil in Karnataka,India

During the course of screening for industrially important microorganisms, an alkali-tolerant and thermotolerant actinomycete, strain DAS 131T, was isolated from a soil sample collected from the Gulbarga region, Karnataka province, India. The strain was characterized by a polyphasic approach that showed that it belonged to the genus Streptomyces. Growth was observed over a wide pH range (pH 6-12) and at 45 degrees C. The 16S rRNA gene sequence of strain DAS 131T was deposited in the GenBank database under the accession number DQ317411. 16S rRNA gene sequence analysis revealed that strain DAS 131T was most closely related to Streptomyces venezuelae ISP 5230T (AY999739) with a sequence similarity of 99.5% (8 nucleotide differences out of 1,477). Despite this very high sequence similarity, strain DAS 131T was phenetically distinct from S. venezuelae. The DNA relatedness between these strains was 54%, indicating that strain DAS 131T is a distinct genomic species. On the basis of phenetic and genetic analyses, strain DAS 131T is classified as a new species in the genus Streptomyces, for which we propose the name Streptomyces gulbargensis sp. nov.     

Molecular characterization of DNA encoding 16S-23S rRNA intergenic spacer regions and 16S rRNA of pectolytic Erwinia species

Sequences of 16S rDNAs and the intergenic spacer (IGS) regions between the 16S and 23S rDNA of bacterial strains from genus Erwinia were determined. Comparison of 16S rDNA sequences from different species and subspecies clearly revealed intraspecies-subspecies homology and interspecies heterogeneity. Phylogenetic analyses of 16S rDNA sequence data revealed that Erwinia spp. formed a discrete monophyletic clade with moderate to high bootstrap values. PCR amplification of the 16S-23S rDNA regions using primers complementary to the 3' end of 16S and 5' end of 23S rRNA genes generated two DNA fragments. The small 16S-23S rDNA IGS regions of Erwinia spp. examined in this study varied considerably in size and nucleotide sequence. Multiple sequence alignment and phylogenetic analysis of small IGS sequence data showed a consistent relationship among the test strains that was roughly in agreement with the 16S rDNA data that reflected the accepted species and subspecies structure of the taxon. Sequence data derived from the large IGS resolved the strains into coherent groups; however, the sequence information would not allow any phylogenetic conclusion, because it failed to reflect the accepted species structure of the test strains.     

Multigene phylogenetic analysis of the Lipomycetaceae and the proposed transfer of Zygozyma species to Lipomyces and Babjevia anomala to Dipodascopsis

Phylogenetic relationships among species assigned to genera of the family Lipomycetaceae were determined from analysis of the nearly entire large, subunit rRNA gene, the small subunit rRNA gene, mitochondrial small subunit rRNA gene and the translation elongation factor-1alpha gene. Monophyly of the Lipomycetaceae was strongly supported, and currently described species appear genetically unique. The multigene analysis provided no support for maintaining the genera Kawasakia, Smithiozyma, Waltomyces or Zygozyma, and it is proposed that species in these genera be assigned to the genus Lipomyces. The monotypic genus Babjevia is a member of the Dipodascopsis clade and it is proposed to reassign Babjevia anomala to Dipodascopsis. The proposed changes will result in the Lipomycetaceae having two ascosporic genera, Lipomyces and Dipodascopsis, and the anamorphic genus Myxozyma.     

Molecular characterization of major and minor rDNA repeats and genetic variability assessment in different species of mahseer found in North India

Relationship among the mahseer species (Family: Cyprinidae) has long been debated in fish systematics. Present study concentrates on the nature of the phylogenetic relationship among the five mahseer species using the sequence of major ribosomal DNA (45S rDNA). We have covered rDNA sequence of approximately 5.2 kb per individual, 26.0 kb per species and 130.0 kb as a whole. We also characterized the 45S and 5S rDNA regions with respect to their nucleotide composition. For phylogenetic analyses, nucleotide sequences were divided into four datasets. First and second datasets contained 18S rDNA and ITS1 sequence, whereas third and fourth datasets consisted of ITS2 and complete 18S-ITS1-5.8S-ITS2-28S, respectively. The NJ tree was constructed for all the datasets. The mahseer species under study formed a monophyletic group well separated from the outgroup species. Similarly, the individuals of Neolissochilus hexagonolepis form monophyletic group with Tor species, indicating Neolissochilus as a sister genus of Tor. The findings from the present study provide greater insights into taxonomic status of mahseer, and set the stage for future investigations dealing with phylo-geography, taxonomy, conservation and co-evolution within this interesting and important group of fish.     

Phylogenetic relationships among species of Sterigmatomyces and Fellomyces as determined from partial rRNA sequences

Sequence comparisons of selected regions from small (18S) and large (25S) subunit rRNAs were used to examine species relationships in the anamorphic yeast genera Sterigmatomyces, Fellomyces, Tsuchiyaea, and Kurtzmanomyces. On the basis of sequence similarity, the genus Sterigmatomyces is comprised of Sterigmatomyces halophilus and Sterigmatomyces elviae, while the genus Fellomyces contains three recognized species, Fellomyces fuzhouensis, Fellomyces penicillatus, and Fellomyces polyborus. Tsuchiyaea wingfieldii and Kurtzmanomyces nectairii are well separated from the other species which we examined. Comparison with selected teleomorphs indicated that the genus Fellomyces is closely related to the genus Sterigmatosporidium, whereas the genus Sterigmatomyces exhibited somewhat closer relatedness with the genus Leucosporidium. Impacting on our estimates of relatedness was the finding that nucleotide substitution in the rRNA regions which we examined seems relatively constant only among closely related species.     

Lecithinase activity of various yeast strains]

The activity of lecithinase was studied among 50 yeast strains belonging to the genera Rhodotorula Harrison, Cryptococcus Kütz, and Lipomyces Lodder et Kreger van Rij. The maximum activity of lecithinase is typical of epiphyte yeast strains belonging to the genus Rhodotorula and is not manifested by species of the henus Lipomyces which inhabit soil. Strains of the genus Cryptococcus cannot be distinctly differentiated into soil and epiphyte cultures, and occupy an intermediate position by the activity of lecithinase.     

Torulaspora maleeae sp. nov., a novel ascomycetous yeast species from Japan and Thailand

Nine strains of a new Torulaspora species were isolated from natural samples collected in Japan and Thailand including one strain obtained from a leaf of Rhizophora stylosa (NBRC 11061T), one strain from soil (NBRC 11062), six strains from mosses (ST-14, ST-266, ST-510, ST-511, ST-513 and ST-581) and one strain from sediment in mangrove forest (RV-51). On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and the sequence analyses of the D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) (ITS1-5.8S rRNA gene-ITS2) region, the nine strains were found to represent a single novel species of the genus Torulaspora, which were named Torulaspora maleeae sp. nov. The type strain is NBRC 11061T (BCC 25515T=CBS 10694T). In the phylogenetic trees based on the sequences of the D1/D2 domain of the LSU rRNA gene, T. maleeae showed a close relationship with the five recognized species of the genus Torulaspora, Torulaspora delbrueckii, Torulaspora franciscae, Torulaspora globosa, Torulaspora microellipsoides and Torulaspora pretoriensis. Torulaspora maleeae differed from the five recognized species of the genus Torulaspora by six to 12 nucleotide substitutions (1.1-2.1%) in the D1/D2 domain of the LSU rRNA gene and by 6.4-11.7% nucleotide substitutions in the ITS (ITS1-5.8S rRNA gene-ITS2) region.     

Re-evaluation of the phylogenetic relationship among species of the genus Tricholoma

The internal transcribed spacer sequences spanning the regions between the 17S and 25S rRNAs (ITS1 and ITS2) and including the complete sequence of the 5.8S rRNA were used for phylogenetic analyses. This approach to define phylogenetic relationships within the genus Tricholoma was tested using different isolates of T. terreum. Fruitbodies identified in nature were analysed in order to allow use of morphology for taxonomy. The isolates from different locations were closely related as could be expected for one species. Thus, the method could be applied to different Tricholoma species. Three clusters within the genus Tricholoma can be distinguished with four additional species not included in any of these clusters. Molecular analyses of two Cortinarius species confirm a phylogenetically distinct genus.     

从12S rRNA和Cyt b基因部分序列研究13种猫科动物的分子系统关系

为探讨中国猫科动物(Felidae)的系统发生关系,本文对中国产13种猫科动物的12SrRNA基因(约371bp)和细胞色素b基因(Cytb)部分序列(约355bp)进行了分析,并采用“最大简约法”和“最大似然法”构建了分子系统树。结果表明:在Cytb基因序列中,有113个位点存在变异(约为总位点数的31.8%),高于12SrRNA基因序列的44个变异位点(约为总位点数的11.9%);构建的分子系统树显示,猞猁(Lynxlynx)可能是中国最早起源的猫科动物,与其它猫科动物之间的亲缘关系较远,支持将其立为猞猁属(Lynx)的观点;草原斑猫(Felislibyca)、丛林猫(Felischaus)、兔狲(Otocolobusmanul)和荒漠猫(Felisbieti)具有较近的亲缘关系,支持将兔狲划归于猫属(Felis)的观点;金猫(Caopumatemminckii)、云猫(Pardofelismarmorata)具有较近的亲缘关系,但它们与猫属物种之间的亲缘关系可能较远,不支持将它们划归于猫属;豹猫(Ponailurusribengalensis)、渔猫(Prionailurusviverrinus)具有较近的亲缘关系,支持将它们同归于豹猫属(Ponailurus);云豹(Neofelisnebulosa)、豹(Pantherapardus)、雪豹(Unciauncia)、虎(Pantheratigris)具有较近的亲缘关系,支持将它们同归于豹属(Panthera)的观点     

Intraspecific variation of Spirometra erinaceieuropaei and phylogenetic relationship between Spirometra and Diphyllobothrium inferred from mitochondrial CO1 gene sequences

Spirometra erinaceieuropaei is a diphyllobothriid cestode whose adult stage occurs mainly in cat-like carnivores, but occasionally in canids and humans. Although it is generally accepted that the distribution of S. erinaceieuropaei is cosmopolitan, it is controversial as to whether all of S. erinaceieuropaei reported are the same species. This study determined partial sequences of the CO1 gene from several isolates in Asian countries and compared them to sequence data from the GenBank/EMBL/DDBJ nucleotide sequence database. Then intraspecific variation of S. erinaceieuropaei and its phylogenetic relationship with Diphyllobothrium were evaluated. The level of nucleotide variation in the CO1 gene sequences within S. erinaceieuropaei was less than 2.6%. Although it was a little larger than that within each species of Diphyllobothrium (0.1-1.0%), it was much smaller than the interspecific variation within the genus Diphyllobothrium (6.2-14%). These facts indicate that all isolates of S. erinaceieuropaei used in this study, which were collected from Asia, Australia and New Zealand, belong to the same species. Based on CO1 gene sequences, genus Spirometra is clearly separate from the genus Diphyllobothrium. It seems that the genus Spirometra is not a synonym of the genus Diphyllobothrium. The phylogenetic relationship between S. erinaceieuropaei and Sparganum proliferum inferred from the CO1 gene clearly confirm the previous opinion that S. proliferum is a distinct species from S. erinaceieuropaei.     

Molecular phylogeny of Sinocyclocheilus (Cypriniformes: Cyprinidae) inferred from mitochondrial DNA sequences

More than 10 species within the freshwater fish genus Sinoncyclocheilus adapt to caves and show different degrees of degeneration of eyes and pigmentation. Therefore, this genus can be useful for studying evolutionary developmental mechanisms, role of natural selection and adaptation in cave animals. To better understand these processes, it is indispensable to have background knowledge about phylogenetic relationships of surface and cave species within this genus. To investigate phylogenetic relationships among species within this genus, we determined nucleotide sequences of complete mitochondrial cytochrome b gene (1140 bp) and partial ND4 gene (1032 bp) of 31 recognized ingroup species and one outgroup species Barbodes laticeps. Phylogenetic trees were reconstructed using maximum parsimony, Bayesian, and maximum likelihood analyses. Our phylogenetic results showed that all species except for two surface species S. jii and S. macrolepis clustered as five major monophyletic clades (I, II, III, IV, and V) with strong supports. S. jii was the most basal species in all analyses, but the position of S. macrolepis was not resolved. The cave species were polyphyletic and occurred in these five major clades. Our results indicate that adaptation to cave environments has occurred multiple times during the evolutionary history of Sinocyclocheilus. The branching orders among the clades I, II, III, and IV were not resolved, and this might be due to early rapid radiation in Sinocyclocheilus. All species distributed in Yunnan except for S. rhinocerous and S. hyalinus formed a strongly supported monophyletic group (clade V), probably reflecting their common origins. This result suggested that the diversification of Sinocyclocheilus in Yunnan may correlate with the uplifting of Yunnan Plateau.     

Molecular organization of 5S rDNA in fishes of the genus Brycon.

There are few reports on the genomic organization of 5S rDNA in fish species. To characterize the 5S rDNA nucleotide sequence and chromosomal localization in the Neotropical fishes of the genus Brycon, 5S rDNA copies from seven species were generated by PCR. The nucleotide sequences of the coding region (5S rRNA gene) and the nontranscribed spacer (NTS) were determined, revealing that the 5S rRNA genes were highly conserved, while the NTSs were widely variable among the species analyzed. Moreover, two classes of NTS were detected in each species, characterized by base substitutions and insertions-deletions. Using fluorescence in situ hybridization (FISH), two 5S rDNA chromosome loci that could be related to the two 5S rDNA NTS classes were observed in at least one of the species studied. 5S rDNA sequencing and chromosomal localization permitted the characterization of Brycon spp. and suggest a higher similarity among some of them. The data obtained indicate that the 5S rDNA can be an useful genetic marker for species identification and evolutionary studies.     

Development of a new chemically defined sporulation medium for the yeasts in the genus Lipomyces

A chemically defined sporulation medium (AF medium) for the yeasts belonging to the genus Lipomyces was developed. The chemical composition was derived from chemical analyses of soybean extract. Some chemical modification of the AF medium indicated that the nitrogen sources (aspartic and glutamic acids) and zinc ion were essential for sporulation. The significance of medium pH was discussed.     

Phylogenetic analyses reveal deeply divergent species lineages in the genus Sphaerobolus (Phallales: Basidiomycota)

Phylogenetic analyses of 27 artillery fungus (Sphaerobolus sp.) isolates were conducted to identify species boundaries in the genus Sphaerobolus. Multiple gene genealogies inferred from maximum likelihood, Bayesian, and maximum-parsimony analyses of sequence data from individual loci (mtSSU, ITS, EF 1-alpha, and LSU) and a combined dataset (mtSSU, ITS, and EF 1-alpha) concordantly indicate the existence of three deeply divergent lineages in the genus Sphaerobolus, each representing a phylogenetic species. These three phylogenetic species correspond to two known species: Sphaerobolus iowensis and Sphaerobolus stellatus, and a newly discovered species. Suprageneric phylogenetic analyses of the mtSSU and LSU datasets containing representatives of related genera of the gomphoid-phalloid clade of Homobasidiomycetes suggested that the undescribed taxon likely is more closely related to S. stellatus than to S. iowensis.     

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation.