Constraints upon the composition of supplementary DNA

Determination of genome size variations among different date palm cultivars (Phoenix dactylifera L.) by flow cytometry

Date palm is an important fruit crop and member of palm family, reported with varied ploidy levels, i.e., 14 (2n = 28) to 18 (2n = 36) pairs of chromosomes and genomic size due to the limited work done on its cytological aspect. The amount of nuclear DNA content is extremely important to understand the hereditary constituent of any species. Hence, the present study was conducted with the aim to estimate the ploidy level and especially the genomic size (C value) of date palm by studying fifty date palm cultivars with flow cytometry using propidium iodide (PI) as the fluorescent dye. The maize genome size (5.14 pg) was used as the internal reference. The results obtained regarding genomic size of date palm cultivars significantly varied and ranged from 1.59 to 1.84 pg 2C^-1 or 780.11 to 903.06 Mbp when converted into base pairs of DNA. The average genome size of studied cultivars was observed to be 1.726 2C^-1, while, that of nuclei significantly varied from cultivar to cultivar and appeared independent to the genomic size of the studied cultivars. Intraspecific variations were not detected among five exotic cultivars (Amber, Sugae, Medjool, Safawi and Ajwa) grown in Pakistan in relation to their place of origin. The cluster analysis exhibited two main groups of cultivars, the first group comprised 65.3% (33 cultivars) and the second group contained 35.7% (17 cultivars). In addition, no ploidy was observed among all the studied cultivars. The findings regarding the estimated genomic sizes of studied cultivars may be helpful in understanding date palm genetics, breeding and genome sequencing programs further.

FLOW-CYTOMETRIC ANALYSES OF NUCLEAR DNA CONTENT IN FOUR FAMILIES OF NEOTROPICAL BATS

Flow-cytometric analyses of 29 species of microchiropteran bats representing four families and 20 genera revealed that bats possess only 79% (5.43 pg) of the DNA content of a "typical" mammal (e.g., Mus musculus strain C57BL; 7 pg). Chiroptera, the second largest order of mammals, is thus an exception to the prevailing view that mammals possess a minimum nuclear DNA content of 7 pg. Limitations on cell size resulting from a high metabolic rate may have constrained evolution of DNA content and could explain why the extensive heterochromatic additions that are common in some groups of mammals are absent in bats. Chromosomes of bats have been well studied; detailed chromosomal banding data are available for nearly all the species used in this investigation. However, no significant correlations were found between DNA content and karyotypic characteristics such as 2n, fundamental number, and rate or pattern of chromosomal evolution.

Genome size variation in the North American sunfish genusLepomis(Pisces: Centrarchidae)

Genome sizes (nuclear DNA contents) were documented spectrophotometrically from individuals of each of nine species of the North American centrarchid (sunfish) genusLepomis. The distributions of DNA values within and among the nine species were essentially normal and continuous, suggesting that changes in DNA quantity inLepomisare small in amount, involve both gains and losses of DNA, and are cumulative and independent in effect. Significant differences in mean genome size were found between individuals within populations in all nine species and between species. Nested analysis of variance and comparisons of average genome size difference or distance between individuals drawn from different levels of taxonomic organization revealed that the majority of genome size divergence inLepomisoccurs above the hierarchical level of individuals within populations. TheLepomisdata when compared to similar data from North American cyprinid fishes appear to suggest that: (i) genome size evolution in these fishes at least follows a continuous rather than a discontinuous mode; (ii) the general predictions of hypothetical models relating genome size variation as a function of organismal position along adaptive continua may be oversimplified, or not applicable to complex, higher eukaryotes; and (iii) changes in genome size in these fishes may be concentrated in speciation episodes.

Flow cytometry in plant breeding

Since the first report on the flow cytometric study of plant material 35 years ago, analyzing the nuclear DNA content of field bean, an ever increasing number of applications of FCM has been developed and applied in plant science and industry, but a similar length of time elapsed before the appearance of the first complete volume devoted to FCM of plant cells. Most published information on the uses of FCM addresses various aspects of animal (including human) cell biology, thus failing to provide a pertinent substitute. FCM represents an ideal means for the analysis of both cells and subcellular particles, with a potentially large number of parameters analyzed both rapidly, simultaneously, and quantitatively, thereby furnishing statistically exploitable data and allowing for an accurate and facilitated detection of subpopulations. It is, indeed, the summation of these facts that has established FCM as an important, and sometimes essential, tool for the understanding of fundamental mechanisms and processes underlying plant growth, development, and function. In this review, special attention is paid to FCM as applied to plant cells in the context of plant breeding, and some new and less well-known uses of it for plants will be discussed.

Genome evolution in the mosquitoes and other closely related members of superfamily Culicoidea

Karyotypes and nuclear DNA amounts of 36 species belonging to twelve genera of mosquitoes and other closely related taxa in the superfamily Culicoidea (Dixidae, Chaoboridae, and Culicidae) were studied. The results showed an eight-fold range in haploid DNA amounts and a 4.5-fold range in total chromosomal lengths. It is concluded that the evolutionary trend in this superfamily has been an overall increase in total haploid DNA amounts from the primitive Dixidae to the highly evolved Culcidae, with a concomitant increase in overall chromosome sizes.

Variation of genome size and organization within hexaploid Festuca arundinacea

Cytophotometric, karyological, and biochemical analyses were carried out in the meristems of seedlings obtained from seeds collected from 35 natural populations of hexaploid Festuca amndinacea in Italy. Highly significant differences between populations were observed in the amount of nuclear DNA (up to 32.3%). These changes are linked to variations in the amount of heterochromatin and in the frequency of repeated DNA sequences, and particularly of a fraction of them. Differences between populations in the arm ratios and total length of the chromosomes were also observed. The genome sizes of the populations are correlated positively with the mean temperature during the year and with that of the coldest month at the stations, and correlate negatively with their latitudes. The intraspecific genome changes observed are discussed in relation to other pertinent data to be found in the literature and in relation to their possible role in environmental adaptation.

Intraspecific variation in nuclear DNA content among world populations of a mosquito, Aedes albopictus (Skuse)

Aedes albopictus is commonly distributed in most parts of the Oriental region and on many islands in the Indian and the Pacific Oceans. The species was recently introduced into the United States and Brazil. Feulgen cytophotometric quantitation of haploid nuclear DNA content was carried out for 37 populations of Ae. albopictus to determine the extent of intraspecific variation in nuclear DNA content and whether the range expansion of the species has coincided with an increase in DNA content. The haploid nuclear DNA content varied nearly three-fold. The minimum DNA content was 0.62 pg in Koh Samui from Thailand, and the maximum DNA content was 1.66 pg in Houston-61 from the United States. Statistical comparisons of populations revealed significant differences in DNA contents. No geographic clustering of populations was noted with respect to DNA content. In general, populations from the United States and Brazil had higher DNA contents, but there was no indication that the range expansion had occurred hand in hand with an increase in DNA content. Each population had a specific amount of DNA that is probably imposed by the microenvironment.

Characterization of nuclear DNA in 12 species of Chlorella (Chlorococcales, Chlorophyta) by DNA reassociation

Strains of 12 different species of the genus Chlorella were analyzed for amount, reiteration frequency and kinetic complexity of chromosomal DNA components by C0t analysis. The resulting C0t curves reveal at least two different DNA components consisting of single copy DNA (up to 95%) and of repetitive DNA with complexities of 4.1 x 10(3) base pairs (bp) to approximately 11.7 x 10(3) bp and a reiteration frequency of 100-760. The total amount of repetitive DNA is less than 9% of the nuclear genome and similar in all strains studied. In contrast, the total kinetic complexity varies in a wide range from 1.26 x 10(7) bp to 8.08 x 10(7) bp which is mainly due to differences in the size of single copy DNA. The genome sizes in Chlorella seem not to be correlated with biochemical and physiological characteristics and therefore are unlikely to be useful as a taxonomical marker. A comparison of thermal denaturation profiles showed that the melting points of repetitive and single copy DNA differ by approximately 7 degrees C which may result from base mismatch and/or from a distinct base composition of the repetitive DNA.

DNA hybridization analyses of a Gossypium allotetmploid and two closely related diploid species

The DNAs of two diploid species of Gossypium, G. herbaceum var. africanum (A1 genome) and G. raimondii (D5 genome), and the allotetraploid species, G. hirsutum (Ah and Dh genomes), were characterized by kinetic analyses of single copy and repetitive sequences. Estimated haploid genome sizes of A1 and D5 were 1.04 pg and 0.68 pg, respectively, in approximate agreement with cytological observations that A genome chromosomes are about twice the size of D genome chromosomes. This differences in genome size was accounted for entirely by differences in the major repetitive fraction (0.56 pg versus 0.20 pg), as single copy fractions of the two genomes were essentially identical (0.41 pg for A1 and 0.43 pg for D5). Kinetic analyses and thermal denaturation measurements of single copy duplexes from reciprocal intergenomic hybridizations showed considerable sequence similarity between A1 and D5 genomes (77% duplex formation with an average thermal depression of 6 °C). Moreover, little sequence divergence was detectable between diploid single copy sequences and their corresponding genomes in the allotetraploid, consistent with previous chromosome pairing observations in interspecific F1 hybrids.

Genome size evolution in vertebrates: trends and constraints

1. Studies on the genomic evolution in vertebrates have highlighted the differences existing between anamniotes and amniotes, both in quantitative and compositional terms. 2. These differences do not seem to depend on a different tendency to genic amplification, but rather on the existence of more strict and efficient constraints in amniotes. 3. Some constraints, that may be defined as "intrinsic", would act directly on the genome; among these particularly important is the chiasma frequency during meiosis. 4. Other, "extrinsic", constraints, would act indirectly through genic products or through cell morphometric parameters. 5. The genome size increase seems to depend on various mechanisms. The most wide-spread one seems to be the amplification of interspersed repetitive and non-repetitive sequences.

Nuclear DNA changes within Helianthus annuus L.: cytophotometric, karyological and biochemical analyses

Cytophotometric measurement of the root meristems of seedlings after Feulgen-staining reveals that large differences (up to 58.16%) in nuclear DNA content may occur in the thirty-one cultivated varieties or lines of Helianthus annuus tested. Significant variations (not exceeding 25%) in the amount of DNA, which does not differ between the root and the shoot meristems of a single seedling, are also found to exist within cultivars or lines; even seedlings obtained from seeds collected from different portions of single heads of plants belonging to a selfed line may vary one from the other in this respect. Variations in the number of chromosomes or alterations in the chromosome structure do not account for the differences observed in nuclear DNA content. Karyometric analyses demonstrate that the surface area of squashed interphase nuclei and metaphase chromosomes and the total length of the latter increase with the increase in Feulgen/DNA absorption. DNA thermal denaturation and reassociation kinetics indicate that a frequency variation in repeated DNA sequences goes hand in hand with changes in the size of the genome. These results, supporting the concept that a plant genome is highly flexible, are discussed in relation to other data to be found in the literature on the intraspecific variation in the nuclear DNA content and in relation to the way in which it is produced in H. annuus.

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.

Changes in DNA composition in the evolution of Vicia species

The composition of nuclear DNA in 3 Vicia species are compared. The species V. eriocarpa, V. johannis and V. melanops are from three separate subgeneric sections of Vicia and show a fourfold variation in their amounts of nuclear DNA. DNA melting experiments, buoyant density gradient analysis and Cot reassociation experiments show that the quantitiative change in nuclear DNA between the three species is achieved by changes in the amounts of both repetitive and nonrepetitive DNA sequences. It is suggested that while the increase in the repetitive fraction is achieved by the proliferation of repetitive base sequences the increase in the nonrepetitive fraction is due to the steady accretion of highly diverged base sequences resulting from mutations, deletions, insertions and base sequence rearrangements among families of repetitive sequences.

Eukaryotic genome: model considerations

The paper presents a new model of chromosome structure based on the assumption that multiple circular subunits of DNA exist. The essential difference with previously described models is the circular DNA unit forms a central chromosome axis. Chromosome configurations during various phases of the cell cycle depend on the various conformations of this central integrating unit. The described model can be generalized for all haploid set of eukaryotic nucleus. Some aspects of the chromosome structure and their functions have been discussed.

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.

Nuclear deoxyribonucleic acid characterization of the marine chromophyte Olisthodiscus luteus

Nuclear DNA of the marine chromophytic alga Olisthodiscus luteus was analyzed in this study. Reassociation kinetics analysis has shown that 440-nucleotide DNA fragments from the genome of this alga contain 4% foldback, 58% repetitive, and 34% single-copy sequences. Precise analysis using isolated single-copy DNA revealed that Olisthodiscus has a large haploid DNA content of 1.66 x 10(-12) g/cell. For determination of the organization of single-copy and repetitive sequences within this genome, DNA fragments 3000 nucleotides in length were reassociated to C0t= 100 M . s. At this low C0t value 89% of the DNA bound to hydroxylapatite, suggesting that single-copy and repetitive elements are interspersed. The lengths of the duplexed repetitive DNA on these 3000-nucleotide fragments were measured by electron microscopy after digestion with S1 nuclease which removed the unreassociated single-copy DNA regions. Of these repetitive sequences, 68% were shorter than 1200 nucleotide pairs in length and had a modal length of 350 nucleotide pairs. A minor class of longer (to 4000 nucleotide pairs) repetitive sequences was also observed.