Nuclear DNA amounts in Macaronesian angiosperms

Nuclear DNA contents for 104 Macaronesian angiosperms, with particular attention on Canary Islands endemics, were analysed using propidium iodide flow cytometry. Prime estimates for more than one-sixth of the whole Canarian endemic flora (including representatives of 11 endemic genera) were obtained. The resulting 1C DNA values ranged from 0.19 to 7.21 pg for Descurainia bourgeauana and Argyranthemum frutescens, respectively (about 38-fold difference). The majority of species, however, possessed (very) small genomes, with C-values <1.6 pg. The tendency towards small nuclear DNA contents and genome sizes was confirmed by comparing average values for Macaronesian and non-Macaronesian representatives of individual families, genera and major phylogenetic lineages. Our data support the hypothesis that the insular selection pressures in Macaronesia favour small C-values and genome sizes. Both positive and negative correlations between infrageneric nuclear DNA amount variation and environmental conditions on Tenerife were also found in several genera.     

Nuclear DNA amounts in angiosperms: progress, problems and prospects

BACKGROUND: The nuclear DNA amount in an unreplicated haploid chromosome complement (1C-value) is a key diversity character with many uses. Angiosperm C-values have been listed for reference purposes since 1976, and pooled in an electronic database since 1997 (http://www.kew.org/cval/homepage). Such lists are cited frequently and provide data for many comparative studies. The last compilation was published in 2000, so a further supplementary list is timely to monitor progress against targets set at the first plant genome size workshop in 1997 and to facilitate new goal setting. SCOPE: The present work lists DNA C-values for 804 species including first values for 628 species from 88 original sources, not included in any previous compilation, plus additional values for 176 species included in a previous compilation. CONCLUSIONS: 1998-2002 saw striking progress in our knowledge of angiosperm C-values. At least 1700 first values for species were measured (the most in any five-year period) and familial representation rose from 30 % to 50 %. The loss of many densitometers used to measure DNA C-values proved less serious than feared, owing to the development of relatively inexpensive flow cytometers and computer-based image analysis systems. New uses of the term genome (e.g. in 'complete' genome sequencing) can cause confusion. The Arabidopsis Genome Initiative C-value for Arabidopsis thaliana (125 Mb) was a gross underestimate, and an exact C-value based on genome sequencing alone is unlikely to be obtained soon for any angiosperm. Lack of this expected benchmark poses a quandary as to what to use as the basal calibration standard for angiosperms. The next decade offers exciting prospects for angiosperm genome size research. The database (http://www.kew.org/cval/homepage) should become sufficiently representative of the global flora to answer most questions without needing new estimations. DNA amount variation will remain a key interest as an integrated strand of holistic genomics.     

Nuclear dna amounts in angiosperms.

The number of angiosperm species for which nuclear DNA amount estimates have been made has nearly trebled since the last collected lists of such values were published, and therefore, publication of a more comprehensive list is over due. This paper lists absolute nuclear DNA amounts for 753 angiosperm species. The dats were assembled primarily for reference purposes, and so the species are listed in alphabetical order, as this was felt to be more helpful to cyto- and biochemists whom, it is anticipated, will be among its major users. The paper also reviews aspects of the history, nomenclature, methods, accuracy and problems of nuclear DNA estimation in angiosperms. No attempt is made to reconsider those aspects of nuclear DNA estimation which have been fully revised previously, although the bibliography of such aspects is given. Instead, the paper is intended as a source of basic information regarding the terminology, practice and limitations of nuclear DNA estimation, especially by Feulgen microdensitometry, as currently practiced.     

First nuclear DNA amounts in more than 300 angiosperms

BACKGROUND AND AIMS: Genome size (DNA C-value) data are key biodiversity characters of fundamental significance used in a wide variety of biological fields. Since 1976, Bennett and colleagues have made scattered published and unpublished genome size data more widely accessible by assembling them into user-friendly compilations. Initially these were published as hard copy lists, but since 1997 they have also been made available electronically (see the Plant DNA C-values database http://www.kew.org/cval/homepage.html). Nevertheless, at the Second Plant Genome Size Meeting in 2003, Bennett noted that as many as 1000 DNA C-value estimates were still unpublished and hence unavailable. Scientists were strongly encouraged to communicate such unpublished data. The present work combines the databasing experience of the Kew-based authors with the unpublished C-values produced by Zonneveld to make a large body of valuable genome size data available to the scientific community. METHODS: C-values for angiosperm species, selected primarily for their horticultural interest, were estimated by flow cytometry using the fluorochrome propidium iodide. The data were compiled into a table whose form is similar to previously published lists of DNA amounts by Bennett and colleagues. KEY RESULTS AND CONCLUSIONS: The present work contains C-values for 411 taxa including first values for 308 species not listed previously by Bennett and colleagues. Based on a recent estimate of the global published output of angiosperm DNA C-value data (i.e. 200 first C-value estimates per annum) the present work equals 1.5 years of average global published output; and constitutes over 12 % of the latest 5-year global target set by the Second Plant Genome Size Workshop (see http://www.kew.org/cval/workshopreport.html). Hopefully, the present example will encourage others to unveil further valuable data which otherwise may lie forever unpublished and unavailable for comparative analyses.     

Nuclear DNA contents in four primitive angiosperms

The basic (2 C) nuclear DNA content has been determined for the first time in four primitive angiosperms by means of scanning densitometry of Feulgen-stained nuclei. The mean values obtained are the following:Liriodendron tulipifera L. (2n = 38): 1.58 pg;Magnolia soulangiana Soul-bod. (2n = 76): 11.95 pg;Cinnamomum camphora T. Nees (2n = 24): 1.18 pg;Illicium anisatum L. (2n = 28): 6.72 pg. These values do not represent extremes, but rank among low DNA amounts. All species display at least low degress of endopolyploidy.     

Nuclear DNA amounts in pacific Crustacea

Nuclear DNA amounts have been determined for 42 species of crustaceans bringing the total number of species with known nuclear DNA content to over 70. Genome size in Crustacea varies over a 25-fold range with a modal value of 2 to 3 pg haploid being common in many groups. Both average genome size and the amount of variability among species are characteristic for certain groups. A trend towards small genomes is evident in advanced and specialized crustacean groups. Somatic polyploidy is a very pronounced feature of the Crustacea. The data suggest that evolution by polyploidy may be more common in crustaceans than earlier data had indicated. These features and the presence of very characteristic satellite fractions in the nuclear DNA recommend the Crustacea for further studies in evolutionary genetics.     

Nuclear DNA content and nuclear and cell volume are positively correlated in angiosperms

Volumes of flow sorted nuclei were analyzed from two highly endopolyploid (diploids with endopolyploid tissues) species (Arabidopsis thaliana and Barbarea stricta), from a less endopolyploid species (Allium cepa) and from two non-endopolyploid species (Chrysanthemum multicolor and Fritillaria uva-vulpis). Intraspecific as well as interspecific comparisons revealed a highly positive correlation (r > 0.99) between DNA content and nuclear volume. No significant differences between expected and measured nuclear volumes were noted indicating that chromatin packing is not increased with increasing DNA content in the tested plant species. In epidermis cells of A. thaliana, A. cepa and Ch. multicolor, a lower (r between 0.6 and 0.7) but significant positive correlation between nuclear volume and cell volume was found. This correlation is compatible with the hypothesis that endopolyploidization (EP = consecutive replication cycles not separated by nuclear and cell divisions) might speed up the growth of endopolyploid species and compensate for small genome size.     

Nuclear DNA amounts in 112 species of tropical hardwoods -- new estimates

The 4C DNA values of 112 species, belonging to 37 families have a range from 0.83 pg (Bixa orellana) to 15.54 pg (Thryallis angustifolia), showing a 18.72-fold variation. The genome size varies from 0.21 pg (Bixa orellana) to 3.32 (Thespesia populnea), with a 15.8-fold difference. The Bombacaceae has the minimum range (1.08-fold) of variation, while the maximum (5.0-fold) is shown by the Fabaceae. The Boraginaceae, Lauraceae, Malpighiaceae, and Malvaceae generally have higher 4C DNA values of > 10 pg, while the Bixaceae, Caricaceae, Oxalidaceae, and Santalaceae have lower values of < 2.0 pg. These data add further to our knowledge on variation in DNA amount in tropical hardwoods.     

Reproductive development and nuclear DNA content in angiosperms

Correlates of nuclear DNA content in angiosperms have been noted previously for a range of features, cellular to geographic. A new hypothesis, the correlation between nuclear DNA content and reproductive developmental features (after Cavalier-Smith, Journal of Cell Science 34, 247–268, 1978) is posed and tested here. Of three features tested (megasporogenesis, microsporogenesis, and endosperm development), megasporogenesis alone was shown to be correlated with nuclear DNA amount. The hypothesis was examined in 107 families of angiosperms using nonparametric statistics, and in 53 families of monocotyledons and outgroups using a phylogenetic test of association. A correlation was found between large genomes and successive microsporogenesis for all angiosperms, but not for monocots and dicots analyzed separately, thus underlining the importance of taking into account phylogenetic relationships in such studies. A correlation between cellular endosperm and large genomes in dicotyledons needs to be confirmed in a phylogenetic context. A tendency for deviations from monosporic megasporogenesis to occur in taxa that have a nuclear DNA content of over 9.0 pg/C was demonstrated using both phylogenetic and nonphylogenetic tests. It is hypothesized that cytoskeleton dynamics are affected in reproductive cells, enabling decoupling between nuclear and cytoplasmic cell cycles and leading to variation in reproductive development.     

DNA reassociation kinetics and hybridization in different angiosperms

Reassociation kinetics ofDaucus carota andPetroselinum crispum (Apiaceae), andDatura innoxia (Solanaceae) are presented. Hybridization of³H-labelled DNA of two carrot cultivars indicate strong qualitative homologies of DNA sequences; nevertheless, certain quantitative differences in some Cotregions seem to exist. However, homologous sequences ofDaucus DNA with DNA ofDatura, and, suprisingly, even with DNA ofPetroselinum are very restricted: between 8% in the repeated regions and ca. 7–9% in the unique regions.     

Nuclear DNA amounts in the egg and zygote of maize (Zea Mays L.)

The nuclear DNA content of isolated eggs and zygotes of maize was estimated using 4,6-diamidino-2-phenylindole (DAPI) staining and microspectrofluorometry. The data indicate that egg nuclei contain the 1C level of DNA (basic haploid amount) at the time of karyogamy, and that, by inference, the sperm nuclei are also at 1C. Fertilization occurred in most ovules by 24–28 h post-pollination (hpp), and DNA synthesis was well underway by 27–31 hpp. By 30–34 hpp, 80% of the zygotes were at the 3C DNA level or above, and many were undergoing mitosis. This study provides information that is pertinent to experiments on the microinjection of exogenous DNA into isolated zygotes of maize, and it will serve as a comparative base for future determinations of the DNA content of zygotes produced and cultured in vitro.Abbreviations DAPI 4,6-diamidino-2-phenylindole - hpp hours post-pollination We would like to thank R. Blanc, D. Aldon, and C. Digonnet for their expert technical assistance and advice during the course of this study. Partial support for this study by the Organized Research Fund, Northern Arizona University, is gratefully acknowledged. The bulk of this study was carried out while H.L.M. was visiting research professor at the Ecole Normale Supérieure de Lyon.     

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Angiosperms(flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,”hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological,and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics he...     

GC-biased gene conversion impacts ribosomal DNA evolution in vertebrates, angiosperms, and other eukaryotes

Ribosomal DNA (rDNA) is one of the most conserved genes in eukaryotes. The multiples copies of rDNA in the genome evolve in a concerted manner, through unequal crossing over and/or gene conversion, two mechanisms related to homologous recombination. Recombination increases local GC content in several organisms through a process known as GC-biased gene conversion (gBGC). gBGC has been well characterized in mammals, birds, and grasses, but its phylogenetic distribution across the tree of life is poorly understood. Here, we test the hypothesis that recombination affects the evolution of base composition in 18S rDNA and examine the reliability of this thoroughly studied molecule as a marker of gBGC in eukaryotes. Phylogenetic analyses of 18S rDNA in vertebrates and angiosperms reveal significant heterogeneity in the evolution of base composition across both groups. Mammals, birds, and grasses experience increases in the GC content of the 18S rDNA, consistent with previous genome-wide analyses. In addition, we observe increased GC contents in Ostariophysi ray-finned fishes and commelinid monocots (i.e., the clade including grasses), suggesting that the genomes of these two groups have been affected by gBGC. Polymorphism analyses in rDNA confirm that gBGC, not mutation bias, is the most plausible explanation for these patterns. We also find that helix and loop sites of the secondary structure of ribosomal RNA do not evolve at the same pace: loops evolve faster than helices, whereas helices are GC richer than loops. We extend analyses to major lineages of eukaryotes and suggest that gBGC might have also affected base composition in Giardia (Diplomonadina), nudibranch gastropods (Mollusca), and Asterozoa (Echinodermata).     

DNA amounts and chromatin compactness in Vicia

2C DNA amounts and areas of chromatin were determined with a M 86 Vickers microdensitometer in 56 species of Vicia (x=5, 6, 7), exhibiting large differences in chromosome size. There were significant differences between the species both in DNA content and chromatin area. The nuclear DNA amounts range from 3.85 to 27.07 pg. DNA distribution appears discontinuous; species cluster into distinct groups and the average nuclear DNA amount separating each successive pair is approximately the same (2.23 pg). The compaction of DNA in interphase nuclei increases with increasing DNA amount, which is, at least partly, due to a disproportionate increase in the heterochromatin relative to the euchromatin component of DNA. Comparisons of DNA readings at various stages of the cell cycle show that the DNA amounts are underestimated by microdensitometry in nuclei with high DNA density. Estimation of relative DNA content and area of individual chromosomes were made in twelve species. The results show that changes in DNA content within chromosomes affect the degree of metaphase coiling in an orderly fashion.     

Applying DNA C-values to evaluate invasiveness of angiosperms: validity and limitation

DNA C-values might be one of important indices in the evaluation of angiospermous invasiveness. To test this viewpoint, we compared DNA 1C-values and basic genome sizes in 3,676 angiosperms. The results suggest that: (1) the two nuclear values vary greatly among different groups, e.g., significantly higher in herbs than in trees, in monocots than in dicots, in perennials than in non-perennials; (2) the two nuclear values both have significant effects on plant invasiveness, especially in herbs, dicots, monocots, perennials, non-perennials, diploids, polyploids, Compositae, and Poaceae, while not significant in trees and Fabaceae. Similar to weeds, the two values in crops are low, which suggests that crops may commonly hold higher invasive potential; (3) to evaluate the invasiveness of a given species, the information about ploidy level is necessary, and for polyploids, basic genome sizes are more reliable. For the results suggest that the selection favors polyploids in weeds at least partly because of the downsizing of basic genome size along with polyploidization.     

Gynoecium evolution in angiosperms: Monomery,pseudomonomery, and mixomery

The presence of a gynoecium composed of carpels is a key feature of angiosperms. The carpel is often regarded as a homologue of the gymnosperm megasporophyll (that is, an ovule-bearing leaf), but higher complexity of the morphological nature of carpel cannot be ruled out. Angiosperm carpels can fuse to form a syncarpous gynoecium. A syncarpous gynoecium usually includes a well-developed compitum, an area where the pollen tube transmitting tracts of individual carpels unite to enable the transition of pollen tubes from one carpel to another. This phenomenon is a precondition to the emergence of carpel dimorphism manifested as the absence of a functional stigma or fertile ovules in part of the carpels. Pseudomonomery, which is characterized by the presence of a fertile ovule (or ovules) in one carpel only, is a specific case of carpel dimorphism. A pseudomonomerous gynoecium usually has a single plane of symmetry and is likely to share certain features of the regulation of morphogenesis with the monosymmetric perianth and androecium. A genuine monomerous gynoecium consists of a single carpel. Syncarpous gynoecia can be abruptly transformed into monomerous gynoecia in the course of evolution or undergo sterilization and gradual reduction of some carpels. Partial or nearly complete loss of carpel individuality that precludes the assignment of an ovule (or ovules) to an individual carpel is observed in a specific group of gynoecia. We termed this phenomenon mixomery, since it should be distinguished from pseudomonomery.