Nuclear dna amounts in angiosperms

Copy numbers of chloroplast and nuclear genomes are proportional in mature mesophyll cells of Triticum and Aegilops species

The possibility of estimating the proportion of chloroplast DNA (ctDNA) and nuclear DNA (nDNA) in nucleic-acid extracts by selective digestion with the methylation-sensitive restriction enzyme PstI, was tested using leaf extracts from Spinacia oleracea and Triticum aestivum. Values of ctDNA as percentage nDNA were estimated to be 14.58%±0.56 (SE) in S. oleracea leaves and 4.97%±0.36 (SE) in T. aestivum leaves. These estimates agree well with those already reported for the same type of leaf material. Selective digestion and quantitative dot-blot hybridisation were used to determine ctDNA as percentage nDNA in expanded leaf tissue from species of Triticum and Aegilops representing three levels of nuclear ploidy and six types of cytoplasm. No significant differences in leaf ctDNA content were detected: in the diploids the leaf ctDNA percentage ranged between 3.8% and 5.1%, and in the polyploids between 3.5% and 4.9%. Consequently, nuclear ploidy and nDNA amount were proportional to ctDNA amount (r(19)=0.935, P>0.01) and hence to ctDNA copy number in the mature mesophyll cells of these species. There was a slight increase in ctDNA copy numbers per chloroplast at higher ploidy levels. The balance between numbers of nuclear and chloroplast genomes is discussed in relation to polyploidisation and to the nuclear control of ctDNA replication.

Repetitive DNA and chromosome evolution in plants

Most higher plant genomes contain a high proportion of repeated sequences. Thus repetitive DNA is a major contributor to plant chromosome structure. The variation in total DNA content between species is due mostly to variation in repeated DNA content. Some repeats of the same family are arranged in tandem arrays, at the sites of heterochromatin. Examples from the Secale genus are described. Arrays of the same sequence are often present at many chromosomal sites. Heterochromatin often contains arrays of several unrelated sequences. The evolution of such arrays in populations is discussed. Other repeats are dispersed at many locations in the chromosomes. Many are likely to be or have evolved from transposable elements. The structures of some plant transposable elements, in particular the sequences of the terminal inverted repeats, are described. Some elements in soybean, antirrhinum and maize have the same inverted terminal repeat sequences. Other elements of maize and wheat share terminal homology with elements from yeast, Drosophila, man and mouse. The evolution of transposable elements in plant populations is discussed. The amplification, deletion and transposition of different repeated DNA sequences and the spread of the mutations in populations produces a turnover of repetitive DNA during evolution. This turnover process and the molecular mechanisms involved are discussed and shown to be responsible for divergence of chromosome structure between species. Turnover of repeated genes also occurs. The molecular processes affecting repeats imply that the older a repetitive DNA family the more likely it is to exist in different forms and in many locations within a species. Examples to support this hypothesis are provided from the Secale genus.

Variation in cellular ribulose-1,5-bisphosphate-carboxylase content in leaves of Triticum genotypes at three levels of ploidy

Ribulose-1,5-bisphosphate carboxylase/oxygenase (EC 1.1.39) (RuBPCase) was quantified using polyacrylamide-gel electrophoresis in whole 9-d-old first leaves of 14 genotypes of Triticum, and cellular RuBPCase levels calculated. Diploids, tetraploids and hexaploids were analysed and it was confirmed that the RuBPCase level per cell is closely related to ploidy in wheat. Inter-genotypic variation in RuBPCase levels per cell and per leaf were surveyed. It was found that the interactions between leaf size, cell size and RuBPCase levels result in small variations in RuBPCase levels per unit leaf area between genotypes.

Genome size variation among north american minnows (Cyprinidae). I. Distribution of the variation in five species

Genome sizes (nuclear DNA contents) were examined spectrophotometrically from ten individuals of each of five species of North American cyprinid fishes (minnows). The distributions of DNA values both within and between the five species were essentially continuous and normal. Differences between individuals within populations were significant and contributed to approximately 16 per cent of the total variation. Variation between individuals within species ranged from 4.7-13.5 per cent and averaged ca. 7.4 per cent. Variation between species ranged from 0-9.5 per cent and the average difference between any species pair was ca. 4.6 per cent. Statistical analyses showed that the methodology used was sufficient to detect significant differences in genome size as small as 2-3 per cent. Consideration of these data lead to the following tentative conclusions: (i) changes in genome size in cyprinids appear small in amount, frequent in occurrence, to involve both gains and losses of DNA, and to be cumulative and independent in effect; (ii) differences within and between cyprinid taxa are likely the result of accumulations of small changes in DNA quantity; and (iii) the primary focus of quantitative DNA variation in cyprinids is between individuals within populations. The extent of DNA quantity variation which occurs within species would appear to preclude any direct relationship between genome size variation and many of the organismal parameters (including speciation) which differentiate the five species. In short, the data suggest that a significant fraction of the cyprinid genome, perhaps more than 10 per cent, is free to vary quantitatively without phenotypic constraint or biological consequence. This fraction is considerably larger than that theoretically needed for the structural gene component.

Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues

We have developed a DNA extraction procedure for milligram amounts of plant tissue. Yields ranged from 0.3-200 nanograms of DNA per milligram of tissue. The factors affecting yield are discussed. Fresh tissue, as well as herbarium specimens (22-118 years old) and mummified seeds and embryos (500 to greater than 44 600 years old) were used. All tissues attempted (57 types from 29 species) yielded measurable amounts of DNA. In no case tested was inhibition observed for restriction enzymes BamHI or EcoRI.

Condensed chromatin and its underreplication during root differentiation in leguminosae

Interphase nuclear structure was studied in 15 leguminous species. Eleven species showed chromocentric interphase nuclei while the remaining 4 had reticulate nuclei. The number of chromocenters appeared to be dependent on the number of chromosomes (2n). The total proportion of condensed chromatin as determined by planimetry was found to vary from 11-24% in chromocentric nuclei and 29-62% in reticulate nuclei. The condensed chromatin amount showed a direct correlation with the nuclear DNA content (2C). Though the interphase nuclear structure remained same in differentiated cells, the amount of condensed chromatin was considerably less than that in the meristematic cells, indicating underreplication of heterochromatin during differentiation. HCl-Giemsa method seems to be the simplest method for detection of underreplication in plants.

Changes in mitochondrial DNA levels during development of pea (Pisum sativum L.)

The percentage of mitochondrial DNA (mtDNA) present in total DNA isolated from pea tissues was determined using labeled mtDNA in reassociation kinetics reactions. Embryos contained the highest level of mtDNA, equal to 1.5% of total DNA. This value decreased in light- and dark-grown shoots and leaves, and roots. The lowest value found was in dark-grown shoots; their total DNA contained only 0.3% mtDNA. This may be a reflection of increased nuclear ploidy levels without concomitant mtDNA synthesis. It was possible to compare the mtDNA values directly with previous estimates of the amount of chloroplast DNA (ctDNA) per cell because the same preparations of total DNA were used for both analyses. The embryo contained 1.5% of both mtDNA and ctDNA; this equals 410 copies of mtDNA and 1200 copies of ctDNA per diploid cell. Whereas mtDNA levels decreased to 260 copies in leaf cells of pea, the number of copies of ctDNA increased to 10300. In addition, the levels of ctDNA in first leaves of dark-grown and light-transferred pea were determined, and it was found that leaves of plants maintained in the dark had the same percentage of ctDNA as those transferred to the light.

The effects of gibberellic acid and abscisic acid on α-amylase mRNA levels in barley aleurone layers studies using an α-amylase cDNA clone

Two cDNA clones were characterized which correspond to different RNA species whose level is increased by gibberellic acid (GA3) in barley (Hordeum vulgare L.) aleurone layers. On the criteria of amino terminal sequencing, amino acid composition and DNA sequencing it is likely that one of these clones (pHV19) corresponds to the mRNA for α-amylase (1,4-α-D-glucan glucanohydrolase, EC 3.2.1.1.), in particular for the B family of α-amylase isozymes (Jacobsen JV, Higgins TJV: Plant Physiol 70:1647-1653, 1982). Sequence analysis of PHV19 revealed a probable 23 amino acid signal peptide. Southern hybridization of this clone to barley DNA digested with restriction endonucleases indicated approximately eight gene-equivalents per haploid genome.The identity of the other clone (pHV14) is unknown, but from hybridization studies and sequence analysis it is apparently unrelated to the α-amylase clone.Both clones hybridize to RNAs that are similar in size (∼1500b), but which accumulate to different extents following GA3 treatment: α-amylase mRNA increases approximately 50-fold in abundance over control levels, whereas the RNA hybridizing to pHV14 increases approximately 10-fold. In the presence of abscisic acid (ABA) the response to GA3 is largely, but not entirely, abolished. These results suggest that GA3 and ABA regulate synthesis of α-amylase in barley aleurone layers primarily through the accumulation of α-amylase mRNA.

Nuclear DNA content and the control of chloroplast replication in wheat leaves

During development of the first leaf of breadwheat (Triticum aestivum L.) the number of chloroplasts per mesophyll cell increases between three- and four-fold. To establish if chloroplast replication is accompanied by endoreduplication, the nuclear DNA content of the cells was determined by chemical assay of isolated nuclei from mesophyll protoplasts and by microdensitometry of nuclei in mesophyll tissue. The DNA content of the nuclei was constant (27 to 32 pg) at each phase of chloroplast replication. Approximately 93% of the cells had a nuclear DNA content close to the 2C value of 32 pg. It is concluded that chloroplast replication is not dependent on nuclear endoreduplication in seedling leaves of wheat.

Sequence diversity of polysomal mRNAs in roots and shoots of etiolated and greened pea seedlings

The sequence complexity and abundance of polysomal mRNA populations of pea seedlings were measured using RNA excess hybridization to both single-copy DNA and complementary DNA. The estimated sequence complexity of the polysomal mRNA populations was 2.5·10(7) nucleotides or 19,400 different mRNAs of average size. Since the haploid genome size of pea was found to be 4.0·10(9) nucleotide pairs, only 0.62% of the total haploid genome of pea was transcribed into polysomal mRNA. The roots and shoots of 4-d etiolated and light-grown seedlings contained similar numbers of diverse mRNAs. The RNA excess hybridizations, using single-copy DNA enriched for sequences transcribed in either light-grown shoots or etiolated roots and single-copy DNA depleted of such sequences, indicated that at least 92% of the sequence complexity of polysomal mRNAs was identical in roots and shoots irrespective of the presence of a functional photosynthetic system. In contrast, RNA excess hybridization to complementary DNA revealed that 21% of the polysomal polyadenylated mRNA mass found in light-grown shoots was absent in etiolated roots. The kinetics of these hybridizations indicated that this was due to the appearance of a limited number of abundant mRNAs under conditions of illumination.

A high amount of satellite DNA in the genome of Lupinus angustifolius L

Embryo DNA, isolated from ungerminated seeds of Lupinus angustifolius L., contains an exceptionally high amount of guanine-cytosine-rich satellite DNA. The thermal denaturation curve of total embryo DNA is biphasic with an inflexion point at 62% denaturation, indicating the presence of satellite DNA. The satellite fraction could be separated from the mainband DNA by three successive preparative CsCl-gradient centrifugations. The densities of the DNA fractions are 1.7045 g cm(-3) and 1.6925 g cm(-3), respectively. The percentages of guanine-cytosine calculated from these densities are comparable to the percentages of GC calculated from the melting temperatures. Finally, ressociation studies prove that foldback DNA and highly repeated sequences are much more frequent in the satellite DNA fraction than in the mainband DNA.

Repeat sequence interspersion in coding DNA of peas does not reflect that in total pea DNA

The pattern of sequence organization in the regions of the pea genome near sequences coding for mRNA differs significantly from that in total DNA. Interspersion of repeated and single copy sequences is so extensive that 85% of 1300 nucleotide-long fragments contain highly repetitive sequences (about 5000 copies per haploid genome). However, data presented here demonstrate that sequences which code for mRNA are enriched in the small fraction of fragments which do not contain these highly repetitive sequences. Thus, in contrast to the great majority of other sequences in the genome, most mRNA coding sequences are not located within 1300 nucleotides of highly repetitive elements. Moreover, our data indicate that those repeats (if any) which are closely associated with mRNA coding sequences belong to low copy number families characterized by an unusually low degree of sequence divergence.

Genome evolution in pocket gophers (genus Thomomys). II. Variation in cellular DNA content

Cellular DNA content (2 C-value) was measured by fluorescence flow cytometry of chromomycin-A3 stained spleen cells in 2 subgenera, 5 species, and 21 subspecies of pocket gophers (genus Thomomys). The data indicate that, in Thomomys: (1) interspecific variation is extensive but, while some congeneric species differ by as much as 230%, others are identical in C-value: (2) intraspecific differentiation can be extensive with C-values differing by as much as 35%; and (3) populations of the same subspecies with apparently similar karyotypes can differ significantly in C-value. The implications of these results for hypotheses of the "adaptive" significance of C-value variation and genome evolution are discussed.

The karyotype of tuleen 346 barley

Tuleen 346 barley is a triple homozygote for 3 unequal interchanges, T1-5v, T2-6y and T3-7d, which were induced independently in the variety, 'Bonus'. It has great potential value in studying differences in behaviour and position among chromosomes within the same cell in barley and its hybrids since at least 5 and usually all 7 chromosome types can be identified in Feulgen preparations, compared with only 3 types in normal barley. Measurement of chromosome arm and satellite lengths in 10 haploid root-tip metaphases showed that in all comparisons except of the longest with the next longest, the 7 chromosome types were distinct in total length (P<0.001-0.05) and in 8 of the 10 cells, the longest chromosome had a smaller arm ratio than the next longest. In these preparations, each of the 5 shortest chromosomes was easily identifiable by size and morphology. The longest chromosome was about 2.2 times as long as the shortest. C-banding showed that each of the 7 chromosome types had a clearly unique band pattern. The C-band patterns of interchange chromosomes confirmed and increased the precision of previously published breakpoint locations, viz. the short arms of chromosomes 1, 2, 3 and 7 and the long arms of chromosomes 5 and 6.

Evolutionary sequence divergence within repeated DNA families of higher plant genomes. II. Analysis of thermal denaturation

An assay based on derivative analysis of thermal denaturation (melting) behavior of reassociated DNA was developed in an attempt to characterize the sequence relationships in repeated DNA families according to the homogeneous or heterogeneous models of Bendich and Anderson (1977). The validity of the technique was confirmed by the use of deaminated Escherichia coli DNA models for repetitive families. The melting data for DNA reassociated at two different temperatures provided strong evidence that Pisum sativum repeated families are mostly heterogeneous, while homogeneous families predominate in Vigna radiata. These findings, together with other differences between the two genomes, suggest that the rate of sequence amplification has been higher in the evolutionary history of Pisum DNA. A general trend seems to exist for high amplification rates in large, highly repetitive plant genomes such as Pisum and lower rates in smaller plant genomes such as Vigna, as well as in the generally smaller, less repetitive genomes of most animal species.

Restriction map of native and cloned cauliflower mosaic virus DNA

Cloned CaMV DNA replicates faithfully in Escherichia coli, since the restriction map of the cloned DNA can be superimposed over that of the native viral DNA. However, some short fragments were difficult to detect in the restricted native viral DNA, whereas they formed clear bands when derived from cauliflower mosaic virus (CaMV) DNA clones propagated in the E. coli host. Apparently, the small fragments that carry variable-length single-stranded gaps present only in native viral DNA, give rise to diffuse weak bands difficult to recognize in gels. Comparison of maps for several CaMV strains permits evaluation of their possible evolutionary relationship.

The nucleolus organizers of diploid wheats revealed by in situ hybridization

Labelled RNA, transcribed in vitro from wheat ribosomal DNA cloned in a bacterial plasmid, has been hybridised to metaphase chromosomes of five diploid wheats. Autoradiography of the chromosomes has provided unequivocal evidence that these genotypes possess two pairs of nucleolus organizer chromosomes. The diploid wheat accessions used possess widely differing numbers of ribosomal RNA genes.