Distribution and evolution of two satellite DNAs in the genus Beta

Summary EcoRI monomers of a highly repetitive DNA family of Beta vulgaris have been cloned. Sequence analysis revealed that the repeat length varies between 157–160 bp. The percentage of AT-residues is 62% on average. The basic repeat does not show significant homology to the BamHI sequence family of B. vulgaris that was analyzed by us earlier. Both the EcoRI and BamHI sequences are investigated and compared to each other with respect to their genomic organization in the genus Beta. Both repeats were found to be tandemly arranged in the genome of B. vulgaris in a satellite-like manner. The EcoRI satellite DNA is present in three sections (Beta, Corollinae and Nanae) of the genus, whereas the BamHI satellite DNA exists only in the section Beta. The distribution of the EcoRI and BamHI satellite families in the genus is discussed with respect to their evolution.     

Variations of chloroplast DNAs in the genus Pelargonium and their biparental inheritance

Summary The comparison of EcoRI patterns of chloroplast DNAs (ctDNAs) from five species of the genus Pelargonium and from 16 cultivars and varieties of Pelargonium zonale hort. demonstrates a remarkable inter- and intraspecific ctDNA (plastome) variation. The plastome of the P. zonale varieties could be differentiated into groups I, II and III. Reasons for this variation seem to be: occurrence of numerous spontaneous plastome mutations, intense hybridisation by gardeners and breeders, and biparental plastid inheritance.Crosses of P. zonale varieties with different ctDNA types lead to the direct evidence on the molecular level of biparental plastid inheritance and plastid sorting-out in F₁-hybrids.     

Physical mapping of plastid DNA variation among eleven Nicotiana species

Summary Plastid DNA of seven American and four Australian species of the genus Nicotiana was examined by restriction endonuclease analysis using the enzymes Sal I, Bgl I, Pst I, Kpn I, Xho I, Pvu II and Eco RI. These endonucleases collectively distinguish more than 120 sites on N. tabacum plastid DNA. The DNAs of all ten species exhibited restriction patterns distinguishable from those of N. tabacum for at least one of the enzymes used. All distinctive sites were physically mapped taking advantage of the restriction cleavage site map available for plastid DNA from Nicotiana tabacum (Seyer et al. 1981). This map was extended for the restriction endonucleases Pst I and Kpn I. In spite of variation in detail, the overall fragment order was found to be the same for plastid DNA from the eleven Nicotiana species. Most of the DNA changes resulted from small insertions/deletions and, possibly, inversions. They are located within seven regions scattered along the plastid chromosome. The divergence pattern of the Nicotiana plastid chromosomes was strikingly similar to that found in the genus Oenothera subsection Euoenothera (Gordon et al. 1982). The possible role of replication as a factor in the evolution of divergence patterns is discussed. The restriction patterns of plastid DNA from species within a continent resembled each other with one exception in each instance. The American species N. repanda showed patterns similar to those of most Australian species, and those of the Australian species N. debneyi resembled those of most American species.Abbreviations ims isonuclear male sterile - ptDNA plastid chloroplast DNA - Rubisco ribulosebisphosphate carboxylase/oxygenase - kbp kilobase pairs - LSU large subunit of Rubisco     

Restriction fragment length polymorphisms of the phytohemagglutinin genes inPhaseolus andVigna (Leguminosae)

Restriction fragment length polymorphisms at the phytohemagglutinin (PHA) locus were determined among 21 genotypes ofPhaseolus vulgaris, P. coccineus, P. acutifolius, P. lunatus, and threeVigna species, using five restriction enzymes and one double digestion, in order to provide molecular evidence for their genetic relatedness. The dissimilarity between genotypes was estimated from binary RFLP data. The dissimilarity was high among species (from 0.75 to 0.95), and of variable extent among genotypes of the same species (0.33–0.89). InP. vulgaris, two different DNA hybridization patterns were found, giving further evidence for two major gene pools in that species. The restriction patterns ofP. vulgaris var.aborigineus, the putative ancestral form ofP. vulgaris, exhibit clear homology toP. vulgaris genotypes. An undefined landrace from Taiwan could be identified as aP. vulgaris genotype. RFLP-based trees for the phytohemagglutinin genes of the species studied were computed with several distance matrix and parsimony methods.     

Variation in culture,isoenzyme patterns and plastid DNA in the genusDaucus

Summary To identify markers for fusion and transformation studies, cell suspension cultures of four members of theDaucus genus were examined to determine differences in culture conditions, isoenzyme patterns, and plastid DNA. The four were:D. carota subsp.sativus cv. Danvers,D. carota subsp.gummifer, D. capillifolius, andD. pusillus. Under appropriate conditions, all four grew well as liquid cell suspension cultures and regenerated from protoplasts into plants. Enzyme activities of homoserine dehydrogenase (HSDH) and alcohol dehydrogenase from cell culture extracts were analyzed on electrophoretic gels. Although only one form of HSDH was present in eachDaucus line, the rate of migration of HSDH from cv. Danvers was different from that of the other cell lines. Multiple isoenzymic forms of ADH were present in eachDaucus cultivar. Camparison of endonuclease restriction fragment patterns from plastid DNAs digested by BamHI revealed only small differences between plastid DNAs of cv. Danvers and subsp.Gummifer, whereas large differences were observed between cv. Danvers andD. pusillus plastid DNA patterns. No differences were found between cv. Danvers andD. capillifolius plastid DNA patterns when examined using eight different restriction enzymes. The data indicate that specific isoenzyme and organelle DNA restriction fragment patterns will be useful markers for precise identification of genomes of differentDaucus species in somatic hybridization experiments. This research was supported by the U.S. Department of Agriculture under Agreement 59-2246-1-1-737-0.     

A unique cytoplasmic male sterility (CMS) determinant is present in three Phaseolus species characterized by different mitochondrial genomes

Previous results have shown that cytoplasmic male sterility (CMS) in lines from Phaseolus coccineus and Phaseolus vulgaris contain the same CMS-specific sequence, raising the question of whether this sequence rearrangement arose before divergence of the two species or afterward with subsequent transfer by introgression. Hybridization patterns of total DNA from eight P. vulgaris lines with cytoplasm from P. coccineus and three P. vulgaris lines were examined in order to analyze the mitochondrial DNA (mtDNA) diversity within each species and to determine differences between CMS lines derived from the two species. Three restriction enzymes and 17 heterologous mtDNA sequences were used. The analysis of the different hybridization patterns revealed a considerable diversity in mtDNA organization particularly within P. coccineus. We obtained distinctive hybridization patterns for the five CMS lines tested. The resulting classification showed that mitochondrial genomes from P. coccineus CMS lines group with those of fertile P. coccineus but not with CMS lines from P. vulgaris. The groupings concur with the taxonomic classification of these lines. The results support the hypothesis of a single ancient origin of the CMS determinant and exclude the transfer of cytoplasm by introgression from P. vulgaris to P. coccineus and P. coccineus ssp polyanthus.     

Mitochondrial genome size variation and restriction fragment length polymorphisms in threePhaseolus species

Summary Restriction patterns of mitochondrial DNA (mtDNA) from threePhaseolus species were examined to estimate their relative genome sizes and to determine the level of interspecific variability and relatedness. Three restriction endonucleases that produced relatively simple profiles were identified and used to determine the genome size of the three species. Taking into account fragment stoichiometries, the average estimates across enzymes were 456, 324, and 400 kb, respectively, forP. vulgaris, P. coccineus, andP. acutifolius. Restriction fragment length polymorphisms (RFLPs) differentiated the species when the mtDNAs were digested with seven endonucleases and hybridized with five cosmid clones covering ca. 200 kb of mtDNA sequences. Proportions of shared restriction fragments between every two species were computed as F-values and demonstrated thatP. vulgaris andP. coccineus are more related to each other than either is toP. acutifolius, and that the latter has a similar degree of relationship to the other two species.     

Variation of plastid and mitochondrial DNAs in the genus Hedysarum

Summary Plastid and mitochondrial DNAs from Hedysarum species of the western Mediterranean basin, H. spinosissimum ssp eu-spinosissimum, H. spinosissimum ssp capitatum, H. carnosum, H. coronarium and H. flexuosum, were compared by restriction endonuclease fragment analysis. ctDNA fragment patterns for ssp eu-spinosissimum and ssp capitatum were indistinguishable in different enzyme digests. An identical ctDNA variation was found in Hpa II digests with two Sardinian populations of ssp capitatum. Each of the two subspecies was characterized by specific mt DNA patterns with Pst I, Bam HI, Sma I and EcoRI. No variation was detected in populations of different geographical origins for a given subspecies. H. carnosum, H. coronarium and H. flexuosum generated specific ct and mt DNA patterns. Comparison of mitochondrial fragments indicated: — a strong homology between the two subspecies, — a closer homology among the three other diploids, each being closer to the other two than to H. spinosissimum subspecies — as was also the case for the plastid genomes.     

Structure and variability of nuclear ribosomal genes in the genus Helianthus

Summary The restriction map of the rDNA unit of Helianthus annuus was constructed using EcoRI, BamHI, HindIII, KpnI and SacI restriction enzymes. Variations in this map among 61 ecotypes representing 39 species of the genus Helianthus were analyzed. The sizes of the rDNA unit ranged from 9.8 to 11.0 kbp, due to a length-repeat heterogeneity of the external non-transcribed spacer by increments of 200 base pair segments. Lengthrepeat heterogeneity and restriction polymorphism were found to be characteristic of populations or species of Helianthus. Restriction patterns and thermal melting with probes of a cloned H. annuus ENTS segment allowed us to differentiate species from each other. However, most lines of the cultivated sunflower were found to be identical on the basis of the physical properties of their ribosomal DNA.     

Polymorphism and gene arrangement among plastomes of ten Epilobium species

Summary Plastid DNAs of ten different Epilobium species from four continents have been analysed using the restriction endonucleases BamHI, BglI, BglII, EcoRI, PstI, PvuII and SalI. With respect to the position of cleavage sites of those enzymes, each species has a specific plastome. Fragment patterns of different species from the same continent show a higher degree of similarity than those from different continents. Physical maps of the circular plastid DNA molecule have been constructed for each of the ten species by localising the cleavage sites of the enzymes BglI, PvuII and SalI. As in most other higher plants, the plastid DNA of Epilobium is segmentally organized into two inverted repeats separated by a large and a small single copy region. In heterologous hybridization experiments using radioactively labelled gene probes, the positions of structural genes coding for the rRNAs and for seven polypeptides have been determined. In contrast to its closest relative, Oenothera, the gene arrangement of Epilobium plastomes has the same order as in spinach. This indicates that changes in gene arrangement may be genus-specific and not the result of one or several events affecting all members of a plant family.Abbreviations kbp kilobase pairs - ptDNA plastid DNA - rDNA ribosomal DNA - rRNA ribosomal RNA - SDS sodium dodecyl sulfate     

Cytoplasmic male sterility inBeta is associated with structural rearrangements of the mitochondrial DNA and is not due to interspecific organelle transfer

Summary Chloroplast (ct) and mitochondrial (mt) DNAs from four cytoplasmic male sterile (cms) and 22 normal fertile sugar beet lines and accessions of wild beets from the genusBeta have been compared with restriction analyses and Southern hybridizations. We have used restriction analyses of ctDNA as a phylogenetic marker to confirm the taxonomic relationships between the different cytoplasms. According to the ctDNA data, all four cms cytoplasms belong to the same taxonomic section,Beta. Restriction patterns of ct and mtDNA from fertile accessions produced analogous trees of similarity and showed a close correlation between the organellar DNA diversity and the accepted taxonomic classification of the species studied. However, the mtDNA restriction profiles of the four cms types differed dramatically from each other and from those of all fertile accessions from the genus. No indication of cytoplasmic introgression was found in any of the four investigated cms types. Southern hybridization to mtDNA revealed variant genomic arrangements in the different fertile and cms cytoplasms, indicating that rearrangement of the mitochondrial genome is a common denominator to the different cms systems inBeta. It may, indeed, be a common property to spontaneously occurring cms in all or most species.     

Paternal inheritance of plastids in the genus Daucus

Summary The plastid DNAs of the species Daucus carota (ssp. sativus, libanotifolia, gingidium), D. maximus and D. muricatus were compared by restriction enzyme analysis. A number of restriction fragment length polymorphisms (RFLPs) were observed. As expected from taxonomic data the degree of plastid DNA homology between D. carota and D. maximus is significantly higher (97%) than between D. carota and D. muricatus (70%). On the basis of RFLPs of plastid DNA the mode of plastid inheritance in interspecific crosses between D. muricatus and D. c. sativus was analysed. The results clearly indicate paternal plastid inheritance. Thus Daucus is the second genus among angiosperms transmitting predominantly male plastids.     

A Family of Differentially Amplified Repetitive DNA Sequences in the Genus Beta Reveals Genetic Variation in Beta vulgaris Subspecies and Cultivars

Members of a highly abundant restriction satellite family have been isolated from the wild beet species Beta nana. The satellite DNA sequence is characterized by a conserved RsaI restriction site and is present in three of four sections of the genus Beta, namely Nanae, Corollinae, and Beta. It was not detected in species of the evolutionary old section Procumbentes, suggesting its amplification after separation of this section. Sequences of eight monomers were aligned revealing a size variation from 209 to 233 bp and an AT content ranging from 56.5% to 60.5%. The similarity between monomers in B. nana varied from 77.7% to 92.2%. Diverged subfamilies were identified by sequence analysis and Southern hybridization. A comparative study of this repetitive DNA element by fluorescent in situ hybridization and Southern analyses in three representative species was performed showing a variable genomic organization and heterogeneous localizations along metaphase chromosomes both within and between species. In B. nana the copy number of this satellite, with some 30,000 per haploid genome, is more than tenfold higher than in Beta lomatogona and up to 200 times higher than in Beta vulgaris, indicating different levels of sequence amplification during evolution in the genus Beta. In sugar beet (B. vulgaris), the large-scale organization of this tandem repeat was examined by pulsed-field gel electrophoresis. Southern hybridization to genomic DNA digested with DraI demonstrated that satellite arrays are located in AT-rich regions and the tandem repeat is a useful probe for the detection of genetic variation in closely related B. vulgaris cultivars, accessions, and subspecies. Received: 24 May 1996 / Accepted: 13 September 1996     

Chloroplast DNA differences between two species of Oenothera subsection Munzia: location in the chloroplast genome and relevance to possible interactions between nuclear and plastid genomes

Summary The chloroplast DNAs (cpDNAs) of Oenothera berteriana and Oe. odorata (subsection Munzia) were examined by restriction endonuclease analysis with Sal I, Pvu II, Kpn I, Pst I, Hind III, and Bam HI. The fragment patterns show that these cpDNAs have all 133 restriction sites in common as well as a lot of individual bands. Nevertheless the cpDNAs of the two species can be distinguished by distinct differences in size between a small number of fragments. The 42 cleavage sites produced by Sal I, Pvu II and Kpn I were mapped on the circular cpDNAs. This was achieved by an approach which combined experimental and mathematical procedures. The overall serial order of the fragments was found to be the same for both cpDNAs. The size differences of individual fragments in the Sal I, Pvu II and Kpn I patterns between Oe. berteriana and Oe. odorata cpDNA are located within five regions scattered along the plastid chromosome. Two of these regions have been localized in the larger and one in the smaller of the two single-copy parts of the cpDNA molecule. The remaining two overlap the borders between the large single-copy and each of the duplicated parts of the molecule. The positions of distinct restriction sites are altered among the two Oenothera plastome DNAs by 0.02–0.4 MDa (30–600 base pairs). These alterations probably result from insertions/deletions.Abbreviations cpDNA chloroplast, plastid DNA - Oe. Oenothera - MDa Megadalton - rRNA, rDNA ribosomal RNA, DNA Dedicated to Professor Berthold Schwemmle, Tübingen, on the occasion of his 60th birthday     

DNA analysis methods for recognizing species invasion: the example of Codium,and generally applicable methods for algae

Analysis of DNA can help to distinguish those morphological characters indicative of species difference from those representing retained traits or parallel evolution. This can be of great value in detecting recent invaders. The choice of which DNA characters to examine not only dictates the methodology to be used but must also be appropriate for the detection level sought. Restriction endonuclease fragment comparisons of plastid DNA have been used to assess Codium species; the results show C. fragile subsp. tomentosoides from east and west coast North America to be identical while sympatric endemic Codium species each display their own unique set of fragments. For species of other algae, plastid DNA fragment patterns are not necessarily identical across a morphological species, e.g. Pandorina morum. Such repetitive element probes as M13 and the use of RAPDs are more appropriate for analysis of populations within species. DNA base sequence comparisons of nuclear rDNA genes often yield too few variant bases between closely related species for reliable identifications. Analysis of the more variable Internal Transcribed Spacer (ITS) region, lying between the small and large ribosomal subunit genes in nuclear DNA, yields more extensive base pair variation between species and relatively little within species; it may be an alternative choice for endonuclease restriction fragment analysis or for sequencing.     

Recent approaches to the taxonomy of the Gracilariaceae (Gracilariales,Rhodophyta) and the Gracilaria verrucosa problem

Recognition of species in the Gracilariaceae, often notoriously difficult, is being aided by a combination of classical and modern techniques. We review some recent findings and present new results that may lead to redefinition of Gracilaria verrucosa, the type species of its genus. Plastid DNA restriction profiles (patterns of banding obtained by electrophoresis of DNA after restriction endonuclease digestion) from eleven strains ascribed to G. verrucosa indicated that the concept of this species in northern Europe includes possibly three taxa, one of which is known now to be a species of Gracilariopsis. In contrast, restriction profiles from Argentinian and Japanese strains were closely similar to the predominant pattern for European G. verrucosa. Profiles of several other strains, from the western Atlantic and eastern Pacific, were dissimilar to the European group and to each other. A chromosome number of n = 24 was determined for a representative of the predominant European group, and preliminary results of hybridization trials suggest that these strains, and others with approximately the same plastid DNA restriction pattern, are interfertile.NRCC 30559     

Phylogenetic and genetic studies in Papaver section Oxytona: cytogenetics,isozyme analysis and chloroplast DNA variation

Summary Chromosome behaviour at meiosis, isozyme studies and analysis of the chloroplast DNA restriction fragments were used to assess the phylogenetic relations among the three Papaver species of the section Oxytona. The multivalents observed in diplotene — diakinesis stages of meiosis of the hexaploid P. pseudo-orientale and its tetraploid hybrid with P. bracteatum indicate the autopolyploid nature of this section. Further evidence supporting this conclusion was obtained from isozyme analysis. The same number of isozymes was expressed in all the species regardless of their ploidy level. Inheritance studies conducted with Pgi, Dia and Acp allozymes demonstrated, for the first time, the transfer and expression of genetic material among these species. The differences found in the chloroplast DNA restriction fragments of the Oxytona species and of P. somniferum indicate intensive evolution of the chloroplast DNA in the genus Papaver. The similarity of the chloroplast DNA restriction patterns and of the isozymes in P. orientale and P. pseudo-orientale suggested that P. orientale was the female parent in the cross generating P. pseudo-orientale and that the latter species is of recent origin.Contribution no. 2199 —E, 1987 series from the Agricultural Research Organization, The Volcani center, Bet Dagan 50 250, Israel     

Chloroplast DNA diversity in wild and cultivated species of rice (Genus Oryza,section Oryza). Cladistic-mutation and genetic-distance analysis

Summary Using a novel nonaqueous procedure, chloroplast DNA was isolated from 318 individual adult rice plants, representing 247 accessions and the breadth of the diversity in section Oryza of genus Oryza. Among them, 32 different cpDNA restriction patterns were distinguished using the restriction endonucleases EcoRI and AvaI, and they were further characterized by restriction with BamHI, HindIII, SmaI, PstI, and BstEII enzymes. The differences in the electrophoretic band patterns were parsimoniously interpreted as being the result of 110 mutations, including 47 restriction site mutations. The relationships between band patterns were studied by a cladistic analysis based on shared mutations and by the computation of genetic distances based on shared bands. The deduced relationships were compared with earlier taxonomical studies. The maternal parents for BC genome allotetraploids were deduced. Within species, cpDNA diversity was found larger in those species with an evolutionary history of recent introgression and/or allotetraploidization. Occasional paternal inheritance and recombination of cpDNA in rice was suggested.     

The plastome of a brown alga,Dictyota dichotoma

Summary Plastids of the brown algaDictyota dichotoma contain a single homogeneous DNA species which bands at a buoyant density of 1.693 g/cm³ in neutral CsCl equilibrium density gradients. The corresponding nuclear DNA has a density of 1.715 g/cm³. The molecular size of the plastid DNA is 123 kbp as calculated by both electron microscopy of spread intact circular molecules and gel electrophoresis following single and double digestions with various restriction enzymes. A restriction map has been constructed using the endonucleases Sal I, Bam HI, and Bgl II which cleave theDictyota plastome into 6, 12, and 17 fragments, respectively. No large repeated regions, as found in chlorophycean andEuglena plastid DNAs, were detected.Dictyota dichotoma is the first member from the chlorophyll c-line of the algal pedigree for which a physical map of plastid DNA has been established. Dedicated to Professor Dr. W. Stubbe on the occasion of his 65th birthday.     

Chloroplast DNA and isozyme evidence on the evolution ofSenecio vulgaris (Asteraceae)

Chloroplast DNA (cpDNA) and isozyme variation were analyzed over a range of populations of two infraspecific taxa of the tetraploidSenecio vulgaris. The isozyme data were supportive of the hypothesis that the weedy and cosmopolitanS. vulgaris var.vulgaris is an evolutionary derivative ofS. vulgaris subsp.denticulatus from the coasts of W Europe and montane altitudes in S Spain and Sicily. The two taxa exhibited a very high genetic identity with subsp.denticulatus containing slightly more isozyme diversity than was found in var.vulgaris. — Three cpDNA haplotypes (A, B, C) already known from other Mediterranean diploid species ofSenecio were resolved in var.vulgaris, and an additional fourth haplotype (E) was found in subsp.denticulatus. Two alternative hypotheses were chosen to account for the origin and maintenance of the observed cpDNA composition ofS. vulgaris. It either reflects (1) the retention of an ancestral polymorphism which stems from the recurrent and polytopic formation of ancestral tetraploid lineages; or (2)S. vulgaris originally was characterized by haplotype E, and haplotypes A, B and C were acquired through repeated introgressive hybridization with related diploid species. The finding that very low levels of nuclear (isozyme) diversity were present in both taxa ofS. vulgaris examined supports the second of these two hypotheses; however, more detailed analysis of nuclear genetic diversity is required before a firm conclusion can be reached on this matter.Dedicated to emer. Univ.-Prof. DrFriedrich Ehrendorfer on the occasion of his 70th birthday