Nucleic acid relationships among the anaerobic mycoplasmas

The genetic relatedness between twelve selected strains among four distinct serovars of anaerobic mycoplasmas was studied using [3H]DNA-DNA hybridization, and the results were compared with data obtained from biochemical and serological tests. Radiolabelled DNA probes were prepared from five strains representing four serovars. Based on the homology results, the anaerobic mycoplasmas can be divided into five distinct groups representing five distinct species and two distinct genera. There are two species in the Anaeroplasma bactoclasticum serovar 1 group represented by strains JR and A-2, one species in serovar 2, one species in A. abactoclasticum serovar 3 and one among the unclassified serovar 4 anaerobic mycoplasmas. The probe to nonsterol-requiring strain 161 of serovar 4 showed no homology with any of the established nonsterol-requiring Acholeplasma species DNAs, or with Mycoplasma hominis DNA, or with avian DNA which served as a negative control. There was good correlation between the phenotypic and genotypic properties of the five distinct anaerobic mycoplasma species but the results indicate that phenotypic properties are not always adequate for speciation of the anaerobic mycoplasmas.     

Serological relationships among some Pichia species.

Antigenic analyses of five species of the genus Pichia were carried out for taxonomic study by the slide agglutination method using monospecific and absorbed antisera and the agglutinin absorption technique. Comparative studies were also performed with a few strains of each of the same species and their classifications are discussed with respect to the antigenic structures and the patterns of proton magnetic resonance (PMR) spectra of their cell wall polysaccharides. ichia delftensis and Pichia zaruensis possessed thermostable antigens 1,2,5 and 11, and the former had also thermoabile antigen m. Both species were closely related to Candida krusei. Pichia toletana possessed thermostable antigens 1,2,5,11,17 and 49. Pichia bovis contained thermostable antigens 1,2,14,15,16,20 and 21, and it was related to most species of the genus Hansenula, although assimilation of potassium nitrate was negative. Finally, Pichia etchellsii possessed thermostable antigens 1,2,3,4,9 and 14, and was closely related to Pichia vini. Patterns of PMR spectra of mannans of these species also supported their serological relationships. Therfore, P. delftensis, P. zaruensis and P. etchellsii are considered to be the synonyms of Pichia fluxuum, Pichia dispora and P. vini respectively, although P. toletanan and P. bovis are independent species.     

Evolutionary relationships among pathogenic Candida species and relatives.

Small subunit rRNA sequences have been determined for 10 of the most clinically important pathogenic species of the yeast genus Candida (including Torulopsis [Candida] glabrata and Yarrowia [Candida] lipolytica) and for Hansenula polymorpha. Phylogenetic analyses of these sequences and those of Saccharomyces cerevisiae, Kluyveromyces marxianus var. lactis, and Aspergillus fumigatus indicate that Candida albicans, C. tropicalis, C. parapsilosis, and C. viswanathii form a subgroup within the genus. The remaining significant pathogen, T. glabrata, falls into a second, distinct subgroup and is specifically related to S. cerevisiae and more distantly related to C. kefyr (psuedotropicalis) and K. marxianus var. lactis. The 18S rRNA sequence of Y. lipolytica has evolved rapidly in relation to the other Candida sequences examined and appears to be only distantly related to them. As anticipated, species of several other genera appear to bear specific relationships to members of the genus Candida.     

Nucleic acid enzymes.

Last year provided new structural data, particularly for the group I intron and the Hepatitis delta ribozymes, that were essential for a better understanding of the RNA structure/function relationship. The role of metal ions in catalysis of ribozyme action still remains elusive, however. In vitro selection has continued to be a rich source for obtaining data on new nucleic acid enzyme activities.     

Endosperm dosage relationships among Lycopersicon species

Summary Accessions of eight Lycopersicon species and five yellow-flowered Solanum species were used as males in crosses with 2x and 4x L. esculentum to observe seed set and progeny ploidy. Species which failed in crosses to L. esculentum were crossed as males to 2x and 4x L. peruvianum. In cases of low seed set, chromosome counts were undertaken to establish the nature of the progeny. Endosperm Balance Number (EBN) relationships were determined for the crossability groups. Results support the basic concept of an L. esculentum crossability complex and an L. peruvianum crossability complex. Within the L. esculentum complex, all EBNs appear identical with a value of 2. Within the L. peruvianum complex, more variability appears to exist. The EBN values of this group are higher, and may be approximately double those of the L. esculentum complex. The EBN of L. peruvianum var humifusum appears to be somewhat lower than other L. peruvianum types. The EBN values of S. lycopersicoides, S. rickii, S. ochranthum and S. juglandtfolium could not be determined experimentally. Differential aspects of Lycopersicon and tuber-bearing Solanum evolution may be interpreted on the basis of endosperm compatibility.Co-operative investigation of the Vegetable Crops Research Unit, U.S. Department of Agriculture, Agricultural Research Service, and the Wisconsin Agricultural Experiment Station     

Differences in incorporation of nucleic acid bases and nucleosides by various Mycoplasma and Acholeplasma species.

Eight species representative of the serological diversity of the Mycoplasmatales were tested for their ability to incorporate radiolabeled nucleic acid precursors into acid-insoluble material. Cultures in complex growth medium were centrifuged and resuspended in minimal essential medium (Eagle). For Acholeplasma laidlawii, labeling occurred mainly during the first 4 h of incubation, with substrate saturation at 20 micron. All organisms tested incorporated uracil, adenine, and guanine; none incorporated cytosine. Thymine was incorporated only by bovine group 7, Mycoplasma putrefaciens, and Mycoplasma pneumoniae (strain 3546), but deoxynucleosides enhanced thymine incorporation in A. laidlawii, Mycoplasma gallisepticum, M. pneumoniae (strain AP-164), and Mycoplasma hyorhinis. Nucleoside incorporation (adenosine, guanosine, uridine, cytidine, and thymidine) was not observed for the arginine-utilizing species, Mycoplasma hominis and Mycoplasma arginini, whereas all other organisms tested incorporated nucleosides. The incorporation pattern provides additional metabolic evidence to support the biochemical and antigenic diversity of these organisms. The recognition of differences in incorporation of nucleic acid precursors is important not only to the specific labeling of these organisms, but also to the study of metabolism and transport.     

Genetic relationships among the annual species of Cicer L.

Summary Genetic relationships between 7 annual species of the genus Cicer, including the cultivated chickpea, have been studied. These species were assigned to 3 crossability groups. In each group interspecific hybrids could be obtained but their fertility differed considerably in the various cross combinations. Crosses between members of different groups yielded no viable seeds. The possibility of gene transfer from the wild species to the cultivated chickpea C. arietinum was also assessed. Only two species could be considered for this purpose, C. reticulatum, which is the wild progenitor of the cultivated species, and C. echinospermum, which is in the secondary gene pool of C. arietinum. A unique postzygotic reproductive barrier mechanism was found between the members of Group II, C. judaicum, C. pinnatifidum and C. bijugum. It is based on a disharmony in the growth rate of the stigma and the anthers at the time of anthesis of the F₁ interspecific hybrid so that selfpollination is avoided. It is proposed that this kind of mechanism has been involved only when an effective spatial isolation between the three species had been obtained.     

Deoxyribonucleic acid relationships among members of the genus Aeromonas.

Polynucleotide sequences among 24 motile and 11 non-motile aeromonads were studied by analysis of deoxyribonucleic acid - deoxyribonucleic acid (DNA-DNA) duplexes with endonuclease S1. In addition, DNA base composition (mole % guanine and cytosine (G + C)) and relative genome sizes were determined for selected strains. Large variations in genome size were found and % GC ranged from 57.1 to 62.9%. On the basis of the strains examined, the Genus Aeromonas consists of two genotypically legitimate groups: a diverse group of motile aeromonads, and the genetically more homogeneous non-motile aeromonads, comprising the species Aeromonas salmonicida. Internal homology groups could not be demonstrated within the motile aeromonads, and significant divergence in related sequences was indicated. This diverse motile group forms the single species Aeromonas hydrophila.     

Nucleic acid sequence-based amplification (NASBA) detection of medically important Candida species.

Nucleic Acid Sequence Based Amplification (iNASBA), an isothermal amplification technique for nucleic acids, was evaluated for the identification of medically important Candida species using primers selected from 18S rRNA sequences conserved in fungi. An RNA fragment of 257 nucleotides was amplified for Candida albicans. Nineteen different fungi were tested for rRNA amplification with the NASBA. All were positive when analyzed on agarose gel, whereas human RNA was negative. For the identification of Candida species, NASBA amplification products were analyzed in an enzyme bead-based detection format, using species-specific biotinylated probes and a generic Candida HRPO probe or a membrane-based system using biotinylated probes and avidin-HPRO. Discrimination of the major human pathogenic Candida spp. was based on a panel of biotinylated probes for C. krusei, C. tropicalis, C. albicans, C. glabrata, and C. lusitaniae. Using rRNA dilutions obtained from pure cultures of C. albicans, the combination of NASBA and the enzymatic bead-based detection yielded a sensitivity equivalent to 0.01 CFU. In a model system using 1 ml of artificially contaminated blood as few as 1-10 CFU of C. albicans could be detected. Testing of 68 clinical blood samples from patients suspected of candidemia showed that eight samples were positive for C. albicans and one for C. glabrata. Testing of 13 clinical plasma samples from patients suspected of fungemia identified the presence of C. albicans in two specimens. The whole procedure of sample preparation, amplification and identification by hybridization can be performed in 1 day. This speed and the observed sensitivity of the assay make the NASBA a good alternative to PCR for the detection of candidemia.     

Phylogenetic relationships among Chilean Sophora species

Phylogenetic affinities among Chilean Sophora species are not clear. We suggest a new hypothesis for the origin of the section Edwardsia on the basis of parsimony analysis, which allows a South American origin to be established for the species of this section. The seed alkaloid composition did not provide useful information for the filiation of Edwardsia species, and the shortest tree was obtained using morphological characters only. Two branches are clearly distinguishable by the pubescence of the leaflets and the flag/wings length ratio: one of them includes S. chrysophylla, S. tetraptera, S. toromiro, S. howinsula and S. denudata; the other one includes S. macnabiana, S. microphylla, S. masafuerana, S. prostrata and S. fernandeziana. In contrast, S. macrocarpa, an ancient element of the South American flora, is closely related to species belonging to the section Sophora represented in the region by S. tomentosa, S. linearifolia and S. rhynchocarpa. Sections Calia and Styphnolobium are clearly related to each other, both morphologically and chemically.     

Genetic relationships among Pistacia species using AFLP markers

This study addresses the phylogenetic relationship between Pistacia species by amplified fragment length polymorphism (AFLP). The plant materials of this study consisted of a total of 44 accessions belonging to P. vera, P. eurycarpa, P. khinjuk, all subspecies of P. atlantica (atlantica, mutica, kurdica and cabulica), three unknown genotypes and three accessions, proposed to be hybrid from P. eurycarpa × P. atlantica. The accessions were from Iran, Turkey, USA and Syria. Six AFLP primer combinations produced a total of 475 fragments, with average of 79.16 fragments per primer pair, of which, 336 bands were polymorphic. Unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on jaccard’s similarity coefficient matrix and also average similarity of each species. According to the results, two main clusters were developed and P. vera, P. eurycarpa, P. atlantica (subsp. atlantica, kurdica, mutica, cabulica) and the hybrid genotypes located in the first main cluster. P. khinjuk accessions from Iran and USA localized in second main cluster. The hybrid accessions located between eurycarpa and atlantica species and their hybrid nature between these two species were confirmed. One of the unknown accessions clustered with the hybrid ones and the two other were grouped closely with P. Khinjuk. According to this study, the closest species to P. vera was Eurycarpa group, followed by P. atlantica. UPGMA analysis separated P. atlantica subsp. mutica and cabulica from P. atlantica and P. eurycarpa. Subspecies mutica and cabulica were two closest genotypes; hence, P. atlantica subsp. mutica could be classified as a distinct species as P. mutica and the cabulica as a subspecies of P. mutica. This study revealed that P. eurycarpa is synonym for P. atlantica subsp. kurdica and should be considered distinct from P. atlantica; however, P. atlantica showed a closer genetic similarity to P. eurycarpa than the other species.     

Nucleic acid and protein clocks.

The use of pairwise comparisons of correctly aligned DNA and protein sequences for the measurement of time in historical biology remains a contentious matter. However, the limited success of some molecular evolutionary clocks provides a stimulus to attempt to improve their resolution by the judicious selection of sequences for ease of alignment, commonality of function, taxonomic breadth and appropriate rates of evolution. Existing algorithms for correcting observed distances for superimposed nucleotide substitutions or amino acid replacements appear adequate for the task, given the noise that results from the inherent variability of the process. Some possible approaches are illustrated through the use of gene and protein sequences of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase: an enzyme that is demonstrably homologous from purple bacteria to flowering plants.     

Phylogenetic relationships among Phialocephala species and other ascomycetes

Phialocephala was established for species in the Leptographium complex that produce conidia from phialides at the apices of dark mononematous conidiophores. Some species previously included in Phialocephala were re-allocated to Sporendocladia because they resembled Thielaviopsis in having ring-wall-building conidial development and conidia with two attachment points that emerge in false chains. Despite this significant realignment of the genus, a great deal of morphological heterogeneity remains in Phialocephala. The objective of this study was to consider the heterogeneity among Phialocephala spp. based on comparisons of sequence data derived from the large and small subunits (LSU and SSU) of the rRNA operon of species in Phialocephala. Phialocephala dimorphospora, the type species of the genus, and P. fortinii grouped with genera of the Helotiales in phylogenetic trees generated based on the LSU and SSU datasets. Phialocephala xalapensis and P. fusca clearly are unrelated to Phialocephala sensu stricto and should represent a new genus in the Ophiostomatales. Phialocephala compacta resides with representatives of the Hypocreales, and we believe that it represents a distinct genus. Phialocephala scopiformis and P. repens are not closely related to the other Phialocephala species and group within the Dothideales. The morphological heterogeneity among species of Phialocephala clearly is reflected by phylogenetic analysis of sequence data from two conserved rRNA gene regions. Appropriate genera now need to be found to accommodate these fungi.     

Antigenic relationships among Cladosporium species of medical importance

We analyzed the exoantigens of 54 isolates belonging to the pathogenic Cladosporium species. Cladophialophora ajelloi was found to be antigenically identical to Cladosporium carrionii. All human and cat isolates of C. bantianum and C. trichoides were found to share the same antigens. Although cross-reactions were observed among the four species of Cladosporium: C. carrionii, C. bantianum, c. herbarum, and C. cladosporioides they were identified and differentiated specifically with four monospecific factor sera obtained through absorption procedures. The exoantigen serologic procedure also permitted us to identify cultures of these four Cladosporium spp. within 8 days.     

Phylogenetic relationships among Secale species revealed by amplified fragment length polymorphisms.

Amplified fragment length polymorphism (AFLP) data were utilized to analyze the phylogenetic relationships among 29 accessions representing 14 of the most commonly recognized ranked species or subspecies in the genus Secale. We observed 789 AFLP markers of 1130 fragments utilizing 18 P-/M- and E-/M- primer combinations. All polymorphic fragments were used to construct phenetic and phylogenetic trees. The resulting phenogram and cladogram had similar tree topologies. Cluster analysis showed that Secale sylvestre was the most distantly related to all other ryes. Annual forms were grouped together, and the perennial forms appeared more closely related to each other. This suggested that life cycle could have played an important role in determining the relationships among Secale species. Secale sylvestre was considered to be the most ancient species, whereas Secale cereale was the most recently evolved species. Amplified fragment length polymorphism analysis clearly separated all Secale species into only 3 major species groups, within the genus Secale: S. sylvestre, Secale montanum (syn. Secale strictum) for perennial forms, and S. cereale for annual forms. This study demonstrated that the AFLP approach is a useful tool for discriminating species differences, and also gave a much better resolution in discerning genetic relationships among Secale species as compared with previous studies using other approaches.     

Taxonomic relationships among Arachis sect. Arachis species as revealed by AFLP markers.

Cultivated peanut, Arachis hypogaea L., is a tetraploid (2n = 4x = 40) species thought to be of allopolyploid origin. Its closest relatives are the diploid (2n = 2x = 20) annual and perennial species included with it in Arachis sect. Arachis. Species in section Arachis represent an important source of novel alleles for improvement of cultivated peanut. A better understanding of the level of speciation and taxonomic relationships between taxa within section Arachis is a prerequisite to the effective use of this secondary gene pool in peanut breeding programs. The AFLP technique was used to determine intra- and interspecific relationships among and within 108 accessions of 26 species of this section. A total of 1328 fragments were generated with 8 primer combinations. From those, 239 bands ranging in size from 65 to 760 bp were scored as binary data. Genetic distances among accessions ranged from 0 to 0.50. Average distances among diploid species (0.30) were much higher than that detected between tetraploid species (0.05). Cluster analysis using different methods and principal component analysis were performed. The resulting grouping of accessions and species supports previous taxonomic classifications and genome designations. Based on genetic distances and cluster analysis, A-genome accessions KG 30029 (Arachis helodes) and KSSc 36009 (Arachis simpsonii) and B-genome accession KGBSPSc 30076 (A. ipaensis) were the most closely related to both Arachis hypogaea and Arachis monticola. This finding suggests their involvement in the evolution of the tetraploid peanut species.