Quantitative Evaluation by Reassociation Kinetics of Agrobacterium DNA Sequences residing in the Genome of a Crown-gall Tissue 2

The amount of homologous Agrobacterium tumefaciens DNA carriedin the genome of Scorzonera hispanica Crown-gall tissue cultureshas been determined from the reassociation kinetics of ³²P-labelledbacterial DNA in the presence of unlabelled Crown-gall DNA.Unrepeated DNA extracted from Crown-gall tissues was found tocontain sequences homologous to the bacterial DNA; quantitativeestimation shows the equivalent of about one Agrobacterium genomeper copy of unrepeated Crown-gall DNA. It is concluded thatan entire single genome of Agrobacterium is integrated intoeach haploid complement of a Crown-gall cell.     

Replicon Size, Mean Rate of DNA Replication and the Duration of the Cell Cycle and its Component Phases in Eight Monocotyledonous Species of Contrasting DNA C Values

Various aspects of the cell cycle were measured in the apicalmeristem of primary and seminal roots of eight monocotyledonousangiosperms: Oryza sativa (0.6 pg), Zea mays (2.4 pg), Pennisetumamericanum (2.5 pg), Aegilops umbellulata (5.1 pg), Hordeumvulgare (5.5 pg), Triticum monococcum (6.2 pg), Secale cereale(8.6 pg) and Tulipa kaufmanniana (22.6 pg), representing a 38-foldvariation in DNA C values. Using 4-d-old roots of the firstseven species and 21-d-old Tulipa roots, replicon size and ratesof replication were determined by DNA fibre autoradiography,and the duration of the cell cycle and its component phasesby the percentage labelled mitoses method. When tested withDNA C value, no significant relationships existed for repliconsize, rate of DNA replication or duration of G 1. Significantpositive linear relationships were found between DNA C valueand cell cycle duration, duration of mitosis and G2 durationwhen all data were tested, but not when the Tulipa data wereexcluded. The only characters significantly related to DNA C value whenthe Tulipa data were included or excluded were the durationof S-phase, and the ratio of the interval required for a repliconto replicate its allotted DNA (Rs) to the duration of S-phase(Ds). The Rs: Ds ratio is a measure of synchrony of repliconactivation, and the higher the DNA C value the lower this ratiobecame. We concluded that there was a nucleotypic effect ofDNA C value on this ratio and that the interval between activationof replicons became protracted and hence S-phase lengthenedas C value increased. Cell cycle, NA C value, DNA replication, replicon, S-phase     

Identification of the Genomic Constitution ofMusaL. Lines (Bananas, Plantains and Hybrids) Using Molecular Cytogenetics

The genomic constitutions of someMusaL. lines (bananas, plantainsand artificial hybrids) were identified using molecular cytogenetictechniques. Double targetin situDNA:DNA hybridization to chromosomespreads using as probes, total genomic DNA isolated from diploidMusalinesof known AA (labelled with biotin-11-dUTP) and BB (labelledwith digoxigenin-11-dUTP) genome constitution was carried out.The use of 60% acetic acid combined with heating over a flamegave high quality chromosome spreads free of cytoplasm forinsituhybridization. Total genomic A DNA labelled broad centromericregions of all 22 chromosomes of the diploid line, Calcutta4 (M. acuminataColla. ssp.burmanniccoides; A genome) with somechromosomes showing stronger hybridization. Labelled DNA fromthe B genome hybridized strongly to the centromeric regionsof all 22 chromosomes of Butohan 2 (M. balbisianaColla; B genome).The two satellited chromosomes of genome B labelled stronglywith genomic A DNA.In situhybridization of labelled A and Bgenomic DNA to metaphase chromosomes of triploid AAB and ABBcultivars discriminated between A and B genome chromosomes.The plantains Agbagba, Obino l'Ewai and Mbi Egome showed 22genome A and 11 genome B chromosomes while the cooking bananasBluggoe and Fougamou showed 11 genome A and 22 genome B chromosomes.Hybridization of labelled A and B genomic DNA to chromosomesof the hybrids showed that TMP2x 2829-62 has all 22 genome Achromosomes while TMPx 4698-1 has 33 genome A and 11 genomeB chromosomes.In situhybridization of labelled total genomicDNA to chromosomes has immense potential for identificationof chromosome origin and can be used to characterize cultivarsand hybrids produced inMusabreeding.Copyright 1997 Annals ofBotany Company Genomicin situhybridization; banana; plantain; hybrids; plant breeding; genome organization; biodiversity     

Determination of Gardnerella vaginalis Genome Size by Pulsed-Field Gel Electrophoresis

The chromosomal DNA of four strains of Gardnerella vaginaliswere digested with rare cutting restriction enzymes and analyzedby pulsed-field gel electrophoresis (PFGE). The four strainsstudied were two clinical isolates (GVP 004 & GVP 007) andtwo American Type Culture Collection strains (ATCC 14018 &ATCC 14019). The restriction enzyme SfiI generated two DNA fragmentsof about 0.6 Mb and 1.1 Mb in all four strains giving a G. vaginalisgenome size of about 1.7 Mb. A similar genome size was calculatedutilizing two more GC-rich sequence specific restriction endonucleases,NotI and AscI. When digested with AscI, the chromosomal DNAof all four strains gave rise to 11 to 12 DNA fragments rangingbetween 0.01 Mb to 0.43 Mb. DNA from the two clinical isolateswere digested by NotI (yielding 7 to 9 fragments), while theDNA from the two ATCC strains were resistant to NotI digestion.In contrast to the clinical isolates, DNA from the two ATCCstrains gave an identical profile for all restriction endonucleasestested. From double digestion experiments, the two SfiI sitescould be localized on two AscI fragments. From these PFGE studies,it is concluded that the G. vaginalis genome is a circular DNAthat ranges between 1.67 Mb and 1.72 Mb in size.     

Molecular Cytogenetics of the Genus Arabidopsis: In situ Localization of rDNA Sites, Chromosome Numbers and Diversity in Centromeric Heterochromatin

We have used in situ hybridization to determine the number ofsites of rDNA in species in the genus Arabidopsis. A. wallichii(2n = 16) has one major pair of sites and one minor pair ofsites, while A. pumila and A. griffithiana (both 2n = 32) havesix major and two minor rDNA sites. A. thaliana (2n = 10) isknown to have two pairs of rDNA sites. a highly repeated para-centromericsequence from A. thaliana, pAL1, is absent in the other threespecies. Hence the A.thaliana genome is not present (or thecentromeric DNA has evolved substantially) in the polyploidspecies A. pumila and A. griffithiana. Analysis of Arabidopsisspecies is a valuable complement to the large programmes forgenetic analysis of A. thaliana.Copyright 1993, 1999 AcademicPress Arabidopsis, centromeric DNA, maps (genetic), nuclear architecture, repetitive DNA, ribosomal DNA, rDNA, evolution, Brassicaceae, Crucifereae, in situ hybridization     

In Situ Localization of Parental Genomes in a Wide Hybrid

In situ hybridization enabled DNA originating from the two parentalgenomes to be distinguished in plant hybrids. A probe of biotinylatedtotal genomic DNA from Secale africanum labelled the chromosomesof S. africanum origin but not those from Hordeum chilense inroot-tip chromosome spreads of the sexual hybrid between thetwo species. Hybridization of total genomic DNA from S. africanumto DNA on filters (dot blots) confirmed the distinction betweenDNA from Hordeum and Secale. The total genomic probe hybridizedto the whole length of the chromosomes from S. africanum remarkablyuniformly, labelling both euchromatin and heterochromatin, exceptat the centromeric region. The probe binding was visualizedas a yellow colour by the fluorescein-coupled detection systemwhich contrasted with the red fluorescing counterstain of theunlabelled chromatin. The chromosomes originating from bothparents could be seen and distinguished as red and yellow fluorescenceat all stages of the cell cycle. At interphase and prophase,the chromatin originating from the two parental genomes didnot mix. Chromosomes or groups of chromosomes occupied distinctdomains and also tended to be arranged in a Rabl configurationwith the centromeres clustered at one end of the nucleus. Wepropose calling the technique using total genomic DNA as a probe‘genomic in situ hybridization.’ Hordeum chilense, Secale africanum, hybrids, genomic in situ hybridization, DNA, repetitive sequences, chromosomes, chromosome disposition, nuclear order     

Stability of YACs Containing Ribosomal or RCP/GCP Locus DNA in Wild-type S. cerevisiae and RAD Mutant Strains

About 2% of human YAC clones, including tandemly repeated segmentscolor vision pigment DNA, ribosomal DNA and alphoid DNA havebeen reported to be inherently unstable in yeast hosts, producingmore stable deletion products. YACs containing color visionred pigment gene DNA or 1.5 rDNA tandem repeat units were transformedinto hosts bearing lesions at the RAD1, RAD6, RAD51, or RAD52loci. YACs susceptible to deletion during outgrowth of wild-typecells (or in preliminary experiments, in RAD6 transformants)were stable for up to 100 generations or more in the other strains.Thus both the RAD1 and RAD51/RAD52 epistatic pathways are apparentlyinvolved in the instability of YACs containing tandem repeatloci, presumably during recombination-based deletion formation;and a yeast host disarmed in these pathways will likely maintainYACs intact that are otherwise unstable.     

Nuclear DNA Content of 26 Orchid (Orchidaceae) Genera with Emphasis onDendrobium

2C DNA content values for 70 orchid species from 26 genera,including 37Dendrobiumspecies from eight taxonomic sections,were analysed using flow cytometry. The resulting nuclear DNAcontent values for species other thanDendrobiumranged from 1.91pg 2C^-1to 15.19 pg 2C^-1nuclei forCadetia tayloriandVanilla phaeantha,respectively.Dendrobiumnuclear DNA content values ranged from1.53 pg 2C^-1to 4.23 pg 2C^-1nuclei forD. cruentumandD. spectabile,respectively. DNA content measurements varied greatly withinDendrobiumsectionsLatouria and Spatulata. Nuclear DNA content values for the sixspecies analysed within Latouria ranged from 1.88 pg 2C^-1nucleiforD. macrophyllumto 4.23 pg 2C^-1nuclei forD. spectabile. NuclearDNA content values for the 16 species analysed within Spatulataranged from 1.69 pg 2C^-1nuclei forD. discolorto 4.05 pg 2C^-1nucleiforD. samoense. The least variation in DNA content was foundwithin the section Phalaenanthe, with nuclear DNA content valuesof 1.79 pg  2C^-1, 1.86 pg 2C^-1and 1.98 pg 2C^-1forD. bigibbum,D.affineandD. phalaenopsis, respectively.Copyright 1998 Annalsof Botany Company Orchidaceae,Dendrobium, flow cytometry, propidium iodide, nuclear DNA, genome size, 2C values.     

Construction of Libraries for Methylation Sites by In-gel Competitive Reassociation (IGCR)

The in-gel competitive reassociation (IGCR) procedure was successfullyapplied to construct a comprehensive library enriched in DNAfragments containing C^5mCGG sequences from mouse liver and braingenomic DNA. For IGCR, methylation-insensitive restriction enzyme(Msp I) digests were used as target DNA and methylation-sensitiverestriction enzyme (Hpa II) digests as competitor DNA. Southernblot analysis indicated that 60 to 70% of the clones in thelibrary were derived from the methylated sites and overall enrichmentwas 200- to 1000-fold. IGCR was further applied to constructa library for the sites differentially methylated between brainand liver DNA. In the library, approximately 20% of the HpaII sites exhibited different degrees of methylation betweenthese tissues.     

The Role of DNA Synthesis During Hypocotyl Elongation in Light and Dark

Fluorodeoxyuridine, an inhibitor of DNA synthesis, did not affectgermination and post-germinative growth in the aerial part oflettuce and Haplopappus gracilis seedlings when grown in thelight. In the dark, however, elongation of the hypocotyl wasinhibited by fluorodeoxyuridine, strikingly in lettuce and onlyslightly in Haplopappus gracilis. This could imply that thecontrolling mechanism of hypocotyl elongation is in some casesrelated to DNA synthesis, either because mitotic processes (oftenlittle taken into account in considering hypocotyl growth) areinvolved in the elongation of hypocotyls only when they aregrown in the dark, or because DNA synthesis affects cell elongationdirectly, or through the production of a greater number of endopolyploidcells in the dark. Using mainly autoradiographic and cytofluorimetricmethods, these possibilities were tested. Besides lettuce (Lactucasativa L. var. Great Lakes) and H. gracilis (Nutt.) Gray, radish(Raphanus sativus L. var. Tondo rosso quarantino) and soybean(Soya hyspida Sieb. and Zucc. var. Tokyo) seedlings were alsostudied. Fluorodeoxyuridine drastically inhibits cell elongation onlywhen it is preceded or accompanied by mitotic or endomitoticevents. Need for DNA synthesis during hypocotyl elongation,as well as during early post-germinative growth, seems to beof particular importance when endomitotic processes are involved. DNA synthesis, elongation, endoreduplication, fluorodeoxyuridine, Haplopappus gracilis (Nutt.) Gray, Lactuca sativa L., Raphanus sativus L., Soya hyspida Sieb and Zucc     

Physical Characterization of the Chromosomal DNA of the Yeast Saccharomyces exiguus

The number of chromosomes in the yeast Saccharomyces exiguuswas determined to be thirteen by two-dimensional pulsed-fieldgel electrophoresis. The thirteen chromosomes ranged in DNAsize from 520 to 2,600 kbp, with a total length of approximately14 Mbp. Numbers I to XIII were assigned to the chromosomes indecreasing order of DNA length. Southern hybridization analysisusing total DNAs from S. exiguus and S. cerevisiae as probesshowed that there was no significant homology between the chromosomalDNAs of the two species, except in the case of the chromosomalDNA that included rDNA. When rDNA and genes LEU2, TRP1, URA3and HO of S. cerevisiae were used as hybridization probes, itwas apparent that S. exiguus had DNA sequences homologous tothe rDNA and to the LEU2 and HO genes. In S. exiguus, rDNA-likeand LEU2-like DNAs were located on chromosomes I and IX, respectively,and HO-like DNA was located on chromosome VI or VII. (Received May 17, 1993; Accepted July 15, 1993)     

Variation in the DNA Content of Glycine Species

Nuclei were isolated from cotyledons of a range of accessionsfrom 14 species of Glycine. These were stained with ethidiumbromide and the relative fluorescence for each genotype wasmeasured by flow cytometry. The DNA content was estimated bycomparison of relative fluorescence with that from nuclei fromseedling leaves of Allium cepa, whose DNA content has been calculatedpreviously by chemical assay. The 4C amounts for diploid Glycineranged from 3.80 to 6.59 pg. Two groups of diploid species appearedfrom the analysis. The first consisted of species with amountsranging from 3.80 to 5.16 pg and included G. canescens (AA),G. argyrea (A₁ A₁), G. clandestina (A²A²), G. microphylla(BB),G. latifolia (B₁B₁), G. tabacina 2n=40 (B²B²), G. tomentella2n=38 (EE) and 2n=40 (DD), G. max and G. soja (GG), G. arenariaand G. latrobeana. A second group had higher DNA contents rangingfrom 5.27 to 6.59 pg, and consisted of G. curvata, G. cyrtoloba(CC), and G. falcata (FF). The polyploid species, G. tabacina2n=80 (AABB, BBB¹B¹), G. tomentella 2n=78 and 2n=80 (AAEE andDDEE, respectively) contained amounts approximating to the sumsof the respective parental diploid species thought to have givenrise to these allotetraploids. Intraspecific variation was detectedin the DNA content of G. canescens. Within the overall distributionof DNA amounts found in A genome species, each genome containeda range of DNA contents specific to that species. This phenomenonwas also detected amongst B genome species.     

Determining relative abundance of specific DNA sequences in flow cytometrically sorted maize nuclei

A wide breadth of DNA content variation has been reported amongmaize lines. While the extent of this variation has been welldocumented, few studies have focused on its cause. Some of thenuclear DNA content variation has been explained by the presenceof B chromosomes or knobs. However, variation in these two structuresdoes not account for all of the observed variation. In orderto identify other fluctuating DNA sequences, a rapid and reliablemethod of estimating relative abundance of DNA sequences neededto be developed. The potential of flow cytometry in conjunctionwith spot hybridization for determining relative abundance ofspecific DNA sequences in maize was studied. Different numbersof G1 phase nuclei were sorted on nitrocellulose filters andnon-radioactive hybridization and signal detection performed.Results from these experiments revealed a significant, positivelinear correlation between the amount of target sequence andsignal density using both knob (R = 0.98) and ribosomal spacer(R =0.99) DNA sequences. In addition, G1 phase nuclei of eightinbred lines differing in the amount of knob heterochromatin,were sorted on to filters and the non-radioactive hybridizationand signal detection performed. A significant, positive linearcorrelation between C-band number and signal density (R =0.83;P = 0.0051) as well as between per cent heterochromatin andsignal density (R=0.96;P = 0.0002) was observed. These resultsindicate the usefulness of flow cytometry for spot hybridizationin determining the relative abundance of DNA sequences in themaize genome. Key words: Flow cytometry, copy number, non-isotope labelling, spot hybridization, flow sorting, Zea mays L.     

Karyotype, DNA Content and Meiotic Behaviour in Five South American Species ofVicia(Fabaceae)

This paper presents the karyotype, DNA content and meiotic behaviourof five species ofViciafrom Argentina (V. macrogramineaBurk.,V.gramineaSM.,V. epetiolarisBurk.,V. pampicolaBurk. andV. nanaVog.).All the species have the same chromosome number and karyotypeformula (2n=14; 6m+4st+4t). Each species, however, displaysa characteristic number and position of the nucleolar organizerregion (NOR) and different sizes of the respective satellites,confirmed by Ag-NOR banding. Moreover, significant differenceswere found in the total chromosome volume (TCV) and DNA contentof the species. Positive correlations between DNA content andTCV, and between DNA content and type of life cycle were alsofound. TCV and DNA content are lower inV. nana(annual) and higherinV. macrograminea(biennial–perennial). The material displayedmarked karyotypic orthoselection, with similar karyotypes inall studied species, even when the overall chromosome size varied.Evolutionary changes in DNA amount are proportional to the relativelength of each chromosome arm, maintaining karyotypic uniformity.Significant differences were found between the meiotic behaviourofV. gramineaand that of the other species.V. gramineahas alower frequency of ring bivalents and chiasmata per cell, andalso has a lower interstitial chiasma frequency. In general,the results are congruent with the morphological data reportedfor these species.Copyright 1998 Annals of Botany Company. Viciaspecies, karyotype, orthoselection, nuclear DNA content, NOR banding, meiotic behaviour.     

Synthesis of DNA and the Development of Amylase and Phosphatase Activities in Cotyledons of Germinating Seeds of Vaccaria pyramidata

As in cotyledons of Agrostemma githago, synthesis of DNA takesplace after germination in cotyledons of Vaccaria pyramidataand is followed by the formation of hydrolases, in particular,-amylase and acid phosphatase. If DNA synthesis is inhibitedby hydroxyurea, no, or only slight, enzyme activity develops.The possible role of this DNA synthesis is discussed. Key words: DNA synthesis, amylase activity, phosphatase activity, seed germination, cotyledons, Vaccaria pyramidata     

Cloning and Characterization of New Repetitive Sequences in Field Bean (Vicia fabaL.)

Five new repetitive sequences have been isolated from theViciafabagenome, by cloning bands visible on agarose gel electrophoresisafter digestion of genomic DNA with various restriction enzymes.The sequences were 109 to 584 bp long, their abundance rangingfrom 5x10⁴to 5x10⁵copies per haploid genome. Southern blot andinsituhybridization revealed that four of five newly isolatedrepeats were dispersed in theV. fabagenome. One of the repeats(TIII15) showed tandem organization with several major hybridizationspots on mitotic chromosomesin situ.These sites were distributedin euchromatic as well as in heterochromatic chromosomal regions,and in several loci they were simultaneously localized withpreviously describedFokI repeated elements. The sequence ofTIII15 comprises four 26–27 bp subrepeats, but sharesno homology toFokI elements which have similar sequence organization.All newly described sequences were highly specific forV. faba,withlittle or no hybridization to DNA of otherViciaspecies, andno hybridization to DNA of other legumes tested.Copyright 1999Annals of Botany Company Vicia faba, field bean, repeated DNA sequences, FISH, PRINS, genome organization, copy number.     

Nuclear DNA Amounts in Roses

Nuclei isolated from young leaves were stained with propidiumiodide (PI) and their fluorescence intensities were measuredby flow cytometry. The ratio of fluorescence intensities offour calibration standards and 34 roses to an internal standard,parsley (Petroselinum crispum), provided a basis for estimatingthe DNA amounts of P. crispum and rose. The 2C DNA amount ofP. crispum(2 n = 22) was estimated as 4.46 pg (s.d. ±0.08 pg). The 2C DNA amounts of diploid roses (2n = 14) variedbetween subgenera, sections and cultivars, and ranged from 0.78pg (s.d. ± 0.08 pg) in Rosa xanthina and R. sericea(sectionPimpinellifoliae) to 1.29 pg (s.d. ± 0.08 pg) in ‘Félicitéet Perpétue’ (Hybrid Sempervirens). Within eachsection, the DNA amounts of diploid species were similar. Inthe sections Carolinae and Cinnamomeae, DNA amounts were proportionalto ploidy numbers. In the Pimpinellifoliae, DNA amounts of tetraploidswere disproportionately larger than those of diploids whichsuggests that they originated as hybrids with species of sectionswith larger DNA amounts. Ratios of the fluorescence intensitiesof nuclei of roses to P. crispum(internal standard) were alsomeasured using 4',6-diamidino-2-phenylindole (DAPI) which bindspreferentially to AT base pairs. These DAPI ratios were lowerthan, but closely correlated (r² = 0.997) with PI ratios. Fluorescenceintensities of either PI or DAPI-stained nuclei of roses canbe used as rapid indicators of ploidy if variation in the DNAamounts between different taxonomic groups is taken into account.Copyright 2000 Annals of Botany Company Flow cytometry, nuclear DNA amounts, Petroselinum crispum, phenolics, Rosa, roses     

Isolation of Chloroplast DNA from Pinus

Chloroplast DNA isolated from Japanese black pine [Pinus thunbergii)was digested with three restriction endonucleases. The sizeof this DNA was estimated to be 120 kbp. Chloroplast DNA fromJapanese red pine (P. densiflora) could be distinguished fromthat of P. thunbergii by BamHI restriction patterns. ³Present address: Kanto Forest Tree Breeding Institute, Kasahara,Mito, Ibaraki 310, Japan. (Received December 10, 1985; Accepted March 8, 1986)     

Phylogenetic Analysis of Dipterocarps Using Random Amplified Polymorphic DNA Markers

The phylogenetic relationships among 12 species belonging tothree different genera (Shorea, HopeaandAnisoptera) of Dipterocarpaceaewere studied using random amplified polymorphic DNA (RAPD) markers.A modified CTAB DNA extraction protocol was used to obtain tannin-and polysaccharide-free genomic DNA from mature leaves. Clusteranalysis of data from six random primers placed the 12 speciesin three groups corresponding to their respective genera. Fourdistinct nodes ofShoreaspp. and two ofHopeaspp. could be identified.Anisopteramegistocarpaserved as an outgroup, and was unique when comparedto the other genera examined. RAPD profiles of five individualsofH. odoratawith six random primers were identical, suggestingthat there is little intraspecific variation in this species.The RAPD technique can thus be successfully applied for thestudy of phylogenetic relationships of this important groupof tropical timber trees.Copyright 1998 Annals of Botany Company Dipterocarpaceae,Anisopteraspp.,Hopeaspp.,Shoreaspp., RAPD markers, tropical timber trees.     

Stability of rRNA genes during germination of Vicia faba seeds

Germinating Vicia embryos and the roots of 4-day-old seedlingswere assayed for the proportion of DNA that is complementaryto Vicia rRNA. Hybridization experiments which were performedusing DNA purified by ordinary procedures including RNase digestionshowed a higher level of saturation only for the DNA from theembryos. The embryo DNA showed a Tm of 74?C in 0.1?SSC, whereasthe Tm of the root DNA was 70?C. However, our final conclusionis that there is no gross amplification of rRNA genes for Viciafaba, since the saturation level for the embryo DNA did notexceed that for the root DNA when the DNAs were used after additionalpurification on CsCl gradients. ¹ Present address: Department of Botany, Faculty of Education,Utsunomiya University, Utsunomiya 320, Japan. (Received November 25, 1974; )