Using RAPDs to study phylogenetic relationships in Rosa

Nineteen species of rose (Rosa sp.) were analysed using Random Amplified Polymorphic DNA markers (RAPD). Each 10-base-long arbitrary primer produced a specific DNA banding pattern that grouped plants belonging to the same species and botanical sections as predicted from their genetic background. One hundred and seventy-five amplification products were examined by cluster analysis to assess the genetic relationships among species and their genetic distances. All of the accessions belonging to 1 species grouped together before branching to other species. Dendrograms constructed for intra- and inter-specific studies showed a good correlation with previous classifications by different authors based on morphological and cariological studies. Our results show that the RAPD technique is a sensitive and precise tool for genomic analysis in rose, being useful in assigning unclassified accessions to specific taxonomic groups or else allowing accessions classified by traditional criteria to be re-classified.     

Fluorescent banding pattern analysis of eight taxa of Phaseolus and Vigna in relation to their phylogenetic relationships

Phylogenetic relationships among eight taxa of seven species of Phaseolus and Vigna (Phaseolus angularis, P. aureus, P. calcaratus, P. coccineus, P. vulgaris, Vigna sesquipedalis and V. sinensis; 2n = 22 each) were studied by the fluorescent chromosome banding technique. Preparations of somatic metaphase chromosomes of each taxon were sequentially stained with Giemsa, GC-specific fluorochrome chromomycin A₃ (CMA) and AT-specific fluorochrome 4-6-diamidino-2-phenylindole (DAPI). On the basis of the fluorescent banding patterns of the 22 chromosomes of each taxon, P. angularis, P. coccineus (from China and Korea) and P. vulgaris were grouped into one group (Phaseolus group), P. aureus and two Vigna species were grouped into another (Vigna group) and P. calcaratus was grouped in an independent group.     

ADH and phylogenetic relationships ofDrosophila lebanonensis (Scaptodrosophila)

Summary Increasing data onDrosophila alcohol dehydrogenase (ADH) sequences have made it possible to calculate the rate of amino acid replacement per year, which is 1.7×10^–9. This value makes this protein suitable for reconstructing phylogenetic relationships within the genus for those species for which no molecular data are available such asScaptodrosophila. The amino acid sequence ofDrosophila lebanonensis is compared to all of the already knownDrosophila ADHs, stressing the unique characteristic features of this protein such as the conservation of an initiating methionine at the N-terminus, the unique replacement of a glycine by an alanine at a very conserved position in the NAD domain of all dehydrogenases, the lack of a slowmigrating peptide, and the total conservation of the maximally hydrophilic peptide. The functional significance of these features is discussed.Although the percent amino acid identity of the ADH molecule inDrosophila decreases as the number of sequences compared increases, the conservation of residue type in terms of size and hydrophobocity for the ADH molecule is shown to be very high throughout the genusDrosophila. The distance matrix and parsimony methods used to establish the phylogenetic relationships ofD. lebanonensis show that the three subgenera,Scaptodrosophila, Drosophila, andSophophora separated at approximately the same time.     

Assessment of genome relationships in the genus Oryza L. based on seed-protein profile analysis

Summary Cultivated and wild Oryza species belonging to different genomic groups were studied with regard to their soluble seed-protein profiles. There is an essential uniformity in the banding patterns within various genomes and the basic patterns are not species-specific but genome-specific. O. meridionalis contains a subgenome similar to the A genome of O. rufipogon. Certain specific bands present among A genome species have been found to be useful in tracing the phylogenetic affinity between the cultivated species and their presumed wild progenitors.     

Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs

Summary Ninety-three accessions representing 21 species from the genus Oryza were examined for restriction fragment length polymorphism. The majority (78%) of the accessions, for which five individuals were tested, were found to be monomorphic. Most of the polymorphic accessions segregated for only one or two probes and appeared to be mixed pure lines. For most of the Oryza species tested, the majority of the genetic variation (83%) was found between accessions from different species with only 17% between accessions within species. Tetraploid species were found to have, on average, nearly 50% more alleles (unique fragments) per individual than diploid species reflecting the allopolyploid nature of their genomes.Classification of Oryza species based on RFLPs matches remarkably well previous classifications based on morphology, hybridization and isozymes. In the current study, four species complexes could be identified corresponding to those proposed by Vaughan (1989): the O. ridleyi complex, the O. meyeriana complex, the O. officinalis complex and the O. sativa complex. Within the O. sativa complex, accessions of O. rufipogon from Asia (including O. nivara) and perennial forms of O. rufipogon from Australia clustered together with accessions of cultivated rice O. sativa. Surprisingly, indica and japonica (the two major subspecies of cultivated rice) showed closer affinity with different accessions of wild O. Rufipogon than to each other, supporting a hypothesis of independent domestication events for these two types of rice. Australian annual wild rice O. meridionalis (previously classified as O. rufipogon) was clearly distinct from all other O. rufipogon accessions supporting its recent reclassification as O. meridionalis (Ng et al. 1981). Using genetic relatedness as a criterion, it was possible to identify the closest living diploid relatives of the currently known tetraploid rice species. Results from these analyses suggest that BBCC tetraploids (O. malampuzhaensis, O. punctata and O. minuta) are either of independent origins or have experienced introgression from sympatric C-genome diploid rice species. CCDD tetraploid species from America (O. latifolia, O. alta and O. grandiglumis) may be of ancient origin since they show a closer affinity to each other than to any known diploid species. Their closest living diploid relatives belong to C genome (O. eichingeri) and E genome (O. Australiensis) species. Comparisons among African, Australian and Asian rice species suggest that Oryza species in Africa and Australia are of polyphyletic origin and probably migrated to these regions at different times in the past.Finally, on a practical note, the majority of probes used in this study detected polymorphism between cultivated rice and its wild relatives. Hence, RFLP markers and maps based on such markers are likely to be very useful in monitoring and aiding introgression of genes from wild rice into modern cultivars.     

Studies of isozymes in oat species

Summary Starch and polyacrylamide gel electrophoresis of seven isozyme systems was investigated as a means of identifying wild and cultivated species of Avena with different ploidy levels. By examining the characteristic isoenzymatic patterns, it was shown that there was considerable variability within the different species. However, it was nevertheless possible to unequivocally identify the species of wild oats and to distinguish between the different species belonging to the same genomic set, thus providing a definitive reference technique for the identification of Avena species in seed-testing laboratories. The relationships between Avena species were inferred from the electrophoresis data. The divergence of the A. maroccana — A. murphyi complex and its contribution to the AACC genomes are emphasized.     

Biochemical variation to determine phylogenetic relationships betweenHordeum chilense and other American species of the genusHordeum (Poaceae)

Slab gel electrophoresis techniques have been applied to the study of isozyme and kernel protein patterns in 20 accessions ofHordeum chilense and related species in order to elucidate their phylogenetic relationships. On the basis of our results we can conclude that: (1) Conventional classification based on morphological characters does not totally agree with biochemical data. (2) Sectt.Anisolepis andCritesion seem to be clearly differentiated. (3) The accessions classified asH. compressum present biochemical phenotypes quite different from the rest of the species. (4)H. stenostachys, H. muticum andH. chilense constitute a group of variable species with many biochemical similarities and close phylogenetic relationships. (5) The evolutionary pattern of these American species seems to follow a model of reticulate evolution.     

Protoplast-fusion-derived Solanum cybrids: application and phylogenetic limitations

Summary We established interspecific Solanum cybrids in order to study the intrageneric nuclear-organelle compatibility and the introgression of advantageous plasmone-coded breeding traits into potato. Cybridization was performed by the donor-recipient protoplast-fusion procedure. We found that the plastomes of S. chacoense, S. brevidens, and S. etuberosum could be transferred into the cybrids having S. tuberosum nuclear genomes; chondriome components were likewise transferred from the former species into these cybrids. The combination with S. chacoense as organelle donor and potato as recipient resulted in green fertile plants with potato morphology. By using S. etuberosum as an organelle donor and potato as recipient, male-sterile cybrid plants, most of them having pigmentation abnormalities, were obtained. The combination of S. brevidens with potato resulted in palegreen (almost albino) regenerants. The latter albino plantlets had both the chloroplast DNA and the mitochondrial DNA of the donor (S. brevidens) and did not survive the transfer into the greenhouse. An immediately applicative result of this study is the de novo establishment of male-sterile plants in a potato cultivar. Such plants should be useful as seed parents in the production of hybrid, true-potato seeds.     

Phylogenetic relationships in some diploid species of Triticineae: cytogenetic analysis of interspecific hybrids

Summary Ten diploid species from genera Triticum, Aegilops, Haynaldia and Secale were included in a diallel crossing program. Forty-one different interspecific hybrids were obtained. The number of associations between chromosome arms at metaphase I of meiosis in pollen mother cells from the hybrids was taken as an indication of the degree of homology between parental genomes. Genome relationships were defined and indicated a possible pattern of differentiation from a common ancestor. Breeding strategies based on this information are proposed.     

Codon bias in actin multigene families and effects on the reconstruction of phylogenetic relationships

Codon usage patterns and phylogenetic relationships in the actin multigene family have been analyzed for three dipteran species—Drosophila melanogaster, Bactrocera dorsalis, and Ceratitis capitata. In certain phylogenetic tree reconstructions, using synonymous distances, some gene relationships are altered due to a homogenization phenomenon. We present evidence to show that this homogenization phenomenon is due to codon usage bias. A survey of the pattern of synonymous codon preferences for I I actin genes from these three species reveals that five out of the six Drosophila actin genes show high degrees of codon bias as indicated by scaled ² values. In contrast to this, four out of the five actin genes from the other species have low codon bias values. A Monte Carlo contingency test indicates that for those Drosophila actin genes which exhibit codon bias, the patterns of codon usage are different compared to actin genes from the other species. In addition, the genes exhibiting codon bias also appear to have reduced rates of synonymous substitution. The homogenization phenomenon seen in terms of synonymous substitutions is not observed for nonsynonymous changes. Because of this homogenization phenomenon, trees constructed based on synonymous substitutions will be affected. These effects can be overt in the case of multigene families, but similar distortions may underlie reconstructions based on single-copy genes which exhibit codon usage bias.Correspondence to: M. He     

Cytogenetics of F1 hybrids between Cajanus and Atylosia species and its phylogenetic implications

Summary Cytogenetic relationships between two cultivars of Cajanus cajan and six species of Atylosia were investigated. Of the 12 cross combinations obtained, only seven could be studied. Meiotic chromosome pairing, pollen and ovule fertility in parental species and four F1 hybrids were near normal. Some meiotic abnormalities were observed in the Fls: A. lineata x A. scarabaeoides, A. scarabaeoides x A. sericea and C. cajan (UPAS 120) x A. trinervia, indicating varying degrees of chromosomal and genic differences between these species. These observations suggested that A. cajanifolia is the closest wild relative of C. cajan, followed by A. scarabaeoides, A. albicans and A. trinervia. Among the Atylosia species, A. sericea was closer to A. scarabaeoides than to A. lineata.Botanist, Genetic Resources Unit, ICRISAT, Patancheru-502 324, IndiaRegional Plant Production and Protection Officer, FAO, RAPA, Bangkok-2, Thailand     

Fatty acid profiles of nitrite-oxidizing bacteria reflect their phylogenetic heterogeneity

The fatty acid profiles of all described species of the nitrite-oxidizing genera Nitrobacter, Nitrococcus, Nitrospina and Nitrospira were analyzed. The four genera had distinct profiles, which can be used for the differentiation and allocation of new isolates to these genera. The genus Nitrobacter is characterized by vaccenic acid as the main compound with up to 92% of the fatty acids and the absence of hydroxy fatty acids. The genus Nitrococcus showed cis-9-hexadecenoic acid, hexadecanoic acid and vaccenic acid as main parts. Small amounts of 3-hydroxy-dodecanoic acid were detected. The genus Nitrospina possessed tetradecanoic acid and cis-9-hcxadecenoic acid as main compounds, also 3-hydroxy-hexadecanoic acid was detected for this genus. The genus Nitrospira showed a pattern with more variations among the two described species. These organisms are characterized by the cis-7 and cis-11-isomers of hexadecenoic acid. For Nitrospira moscoviensis a specific new fatty acid was found, which represented the major constituent in the fatty acid profiles of autotrophically grown cultures. It was identified as 11-methyl-hexadecanoic acid. Since this compound is not known for other bacterial taxa, it represents a potential lipid marker for the detection of Nitrospira moscoviensis relatives in enrichment cultures and environmental samples. A cluster analysis of the fatty acid profiles is in accordance with 16S rRNA sequence-based phylogeny of the nitrite-oxidizing bacteria.     

A phylogenetic study of the malagasy couas with insights into cuckoo relationships

The avian family Cuculidae (cuckoos) is a diverse group of birds that vary considerably in behaviors of interest to behavioral ecologists, e.g., obligate brood parasitism and cooperative breeding. The taxonomy of this group has historically been relatively stable but has not been extensively evaluated using molecular methods. The goal of this study was to evaluate phylogenetic relationships within the ecologically diverse genus Coua and the placement of Coua among major cuckoo lineages. We sequenced 429 bp of cytochrome b (cyt b) and 522 bp of ND2, both mitochondrial genes, for 26 species of cuckoos spanning 13 genera. We also included the enigmatic hoatzin (Opisthocomus hoazin) and used two Tauraco species as outgroups. ND2 exhibited higher rates of DNA sequence and amino acid substitution than cyt b; however, this did not greatly affect the overall levels of phylogenetic resolution and support provided by these two genes. Combined analyses produced two alternative phylogenies, depending on weighting scheme, both of which were fully resolved and were characterized by high bootstrap support. These phylogenies recovered monophyly for all of the traditional cuckoo subfamilies and indicated, with strong support, that the hoatzin is outside of Cuculidae. Within Coua, an arboreal and a terrestrial clade were identified. In contrast, habitat choice of Coua species did not greatly reflect the phylogeny.     

A preliminary study on the phylogenetic relationships of Copelatus Erichson (Coleoptera: Dytiscidae: Copelatinae) based on larval chaetotaxy and morphology

The phylogenetic relationships of the diving-beetle (Dytiscidae) subfamily Copelatinae are not well known. Some authors postulated a sister-group relationship between Copelatus Erichson and the remaining Dytiscidae, relying mainly on the absence of a mandibular channel in Copelatus. Other authors suggested a more derived position of the genus. Larval characters have been underutilized in phylogenetic studies, mainly because the larvae of many taxa within the family and, in particular, within Copelatinae are unknown. A comprehensive approach aimed to study the phylogenetic placement of a member of this subfamily based on larval characters has not been produced so far. In this study, the phylogenetic relationships of Copelatus are explored based on a cladistic analysis of 24 taxa and 120 chaetotaxic and morphological characters from larvae. For this purpose, larvae of Copelatus longicornis Sharp are described and illustrated in detail for the first time, with particular emphasis on morphometry and chaetotaxy, with the latter being unexplored until now. The results support a derived position of Copelatus within Dytiscidae, with a sister-group relationship between this genus and a clade formed by the subfamilies Lancetinae, Coptotominae, Laccophilinae, Colymbetinae, Matinae, and Dytiscinae, and part of Agabinae. No evidence was found for a sister-group relationship between Copelatus and the remaining Dytiscidae so that the absence of a mandibular channel in this genus is likely a reduction. Copelatus is supported by three apomorphies within Dytiscidae: mandibular channel absent, internal margin of the stipes with three robust spinulae, and seta MX8 inserted subapically on the galea. Handling editor: K. Martens     

Determination of phylogenetic relationships among methicillin-resistant Staphylococcus aureus recovered from infected humans and Companion Animals

Companion animals carry different microorganism of severely public health hazard for human; the kindness relation and contact between humans and companion animals may the route in the transmission of most zoonotic bacteria, including Methicillin-Resistant Staphylococcus aureus (MRSA). Therefore, the current study investigate the companion animals mainly dogs and cat as a reservoir for MRSA and the genetic similarity between the recovered strains of MRSA from such companion animals and their owners. One hundred swabs were collected under aseptic condition from companion animals and seventy swabs were collected from nasal and soft tissue of the infected owners in contact. All samples were examined with standard microbiological techniques, antimicrobial sensitivity, molecular typing and genetic finger printing using RAPD-PCR to determine the genetic finger printing of the recovered strains from humans and companion animals. The prevalence of the MRSA was higher in dog’s swabs than human swabs. Dog swabs showed a rate of (44.4%), cat’s revealed (27.3%), while the owner swabs could detect (42.8%). The antibiotics profiles were 69.2% and all MRSA strains were positive for mecA gene (100%), while only 25 strains (38.5%) were positive for Panton Valentine Leukocidin (PVL gene). Phylogenetic tree revealed 4 clusters with complete genetic relatedness and higher identity between the strains recovered from humans and companion animals. Our results revealed that there is great similarity between the recovered strains, indicating that pets play an important role in colonization and transmitting MRSA to humans, and vice versa.     

Construction of phylogenetic profiles based on the genetic distance of hundreds of genomes

Phylogenetic profiles have been widely applied in functional genomics research, especially in the prediction of protein-protein interactions (PPIs). A key issue in phylogenetic profiling is how to effectively select reference organisms from the available hundreds of genomes. In this study, we performed an assessment of reference organism selection based on the genetic distance between the target organism and 167 reference organisms. We found that inclusion of reference organisms from all distance levels had better performance in the prediction of PPIs than that at each distance level. The PPI prediction reached an optimal level when 70% of the reference organisms at all distance levels were selected; and this performance was similar to that in the optimal condition based on the taxonomy tree in our previous study. Because measurement of genetic distance is direct and simple compared to the topology of the taxonomy tree, we suggest selecting reference organisms based on genetic distance in the construction of phylogenetic profiles.     

A multi-locus plastid phylogenetic analysis of the pantropical genus Diospyros (Ebenaceae), with an emphasis on the radiation and biogeographic origins of the New Caledonian endemic species

We aimed to clarify phylogenetic relationships within the pantropical genus Diospyros (Ebenaceae sensu lato), and ascertain biogeographical patterns in the New Caledonian endemic species. We used DNA sequences from eight plastid regions (rbcL, atpB, matK, ndhF, trnK intron, trnL intron, trnL-trnF spacer, and trnS-trnG spacer) and included 149 accessions representing 119 Diospyros species in our analysis. Results from this study confirmed the monophyly of Diospyros with good support and provided a clearer picture of the relationships within the genus than in previous studies. Evidence from phylogenetic analyses suggests that Diospyros colonized New Caledonia multiple times. The four lineages of Diospyros in New Caledonia also differ in their degree of diversification. The molecular data indicate that one lineage is paleoendemic and derived from an ancient Australian species. The other three lineages are more closely related to several Southeast Asian species; two of them are neoendemics, and one has radiated rapidly and recently.     

Construction of phylogenetic tree forNicotiana species based on RAPD markers

To apply random amplified polymorphic DNA for analysis of phylogenetic relationships, we used 34 synthetic oligonucleotides as primers to examine interspecific and intraspecific variations among 18 genotypes, nine species ofNicotiana. The nine species used in this study belong to sectionsTomentosae andAlatae. In addition, we attempted to clarify the taxonomic position ofN. sylvestris. A total of 354 distinct DNA fragments were obtained by polymerase chain reaction. Pair-wise comparisons of unique and shared amplification products were used to generate Jaccard's similarity coefficients and Nei and Li's similarity coefficients with the computer software of numerical taxonomy and multivariate analysis system. On the basis of the dendrogram constructed with the similarity coefficients, the 18Nicotiana genotypes were divided into two clusters. The classification analyzed by RAPD markers is in accordance with the classification of Goodspeed thatN. sylvestris is a member of sectionAlatae.