Quantum patterns of genome size variation in angiosperms

Aims: The discontinuous pattern of genome size variation in angiosperms is an unsolved problem related to genome evolution. We introduce a genome evolution operator and solve the related eigen-value equation to deduce the discontinuous pattern. Background: Genome is a well-defined system for studying evolution of species. One of the basic problems is the genome size evolution. The DNA amounts for angiosperm species are highly variable differing over 1000-fold. One big surprise is the discovery of the discontinuous distribution of nuclear DNA amounts in many angiosperm genera. Objective: The discontinuous distribution of nuclear DNA amounts have certain regularity much like a group of quantum states in atomic physics. The quantum pattern has not been explained by all the evolutionary theories so far and we shall interpret it through the quantum simulation of genome evolution. Methods: We have introduced a genome evolution operator H to deduce the distribution of DNA amount. The nuclear DNA amount in angiosperms is studied from the eigen-value equation of the genome evolution operator H. The operator H is introduced by physical simulation and it is defined as a function of the genome size N and the derivative with respective to the size. Results: The discontinuity of DNA size distribution and its synergetic occurrence in related angiosperms species are successfully deduced from the solution of the equation. The results agree well with the existing experimental data of Aloe, Clarkia, Nicotiana, Lathyrus, Allium and other genera. Conclusion: The success of our approach may infer the existence of a set of genomic evolutionary equations satisfying classical – quantum duality. The classical phase of evolution means it obeying classical deterministic law, while the quantum phase means it obeying quantum stochastic law. The discontinuity of DNA size distribution provides fresh evidence on the quantum evolution of angiosperms. People realize that the discontinuous pattern is due to the existence of some unknown evolutionary constrains. However, our study indicates that these constrains on angiosperm genome are essentially of quantum origin.

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Chromosome and nuclear DNA study on Luzula - a genus with holokinetic chromosomes

Genome ◽

10.1139/g03-121 ◽

2004 ◽

Vol 47 (2) ◽

pp. 246-256 ◽

Cited By ~ 18

Author(s):

Elzbieta Kuta ◽

Borut Bohanec ◽

Ewa Dubas ◽

Liliana Vizintin ◽

Leslaw Przywara

Keyword(s):

Genome Size ◽

Nuclear Dna ◽

Size Variation ◽

Nuclear Genome ◽

Dna Amount ◽

Genome Size Variation ◽

Chromosome Fusion ◽

Holokinetic Chromosomes ◽

Nuclear Dna Amount ◽

Leaf Tissues

Chromosomes and nuclear DNA amount were analyzed in leaf tissues of Luzula nivea, Luzula luzuloides, and Luzula multiflora. Intra- and interspecific karyological variability was stated. Chromosome numbers in diploids ranged 2n = 8-24 in L. nivea and L. luzuloides and 2n = 12-84 in hexaploid L. multiflora. Karyological variability resulted mainly from chromosome fission (agmatoploidy) and aneusomaty; chromosome fusion (symploidy) and polyploidy were also involved. Flow cytometric determination of nuclear genome size using propidium iodide staining gave values of 1.584 pg in L. luzuloides, 1.566 pg in L. nivea, and 3.034 pg in L. multiflora. Variability in relative nuclear genome size within species was measured by 4',6-diamidino-2-phenylindole staining. In contrast with previous reports, variability was fairly small and ranged from 1.796 to 1.864 pg in L. luzuloides, from 1.783 to 1.847 pg and from 1.737 to 1.808 pg in two populations (S and F) of L. nivea, respectively, and from 3.125 to 3.271 pg in L. multiflora. An intraplant (interleaf) genome size variation was also observed and its possible causes are discussed.Key words: Luzula, holokinetic chromosomes, agmatoploidy, symploidy, polyploidy, nuclear DNA amount, intraplant genome size variability, flow cytometry.

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Genome size variation in the Artemisia arborescens complex (Asteraceae, Anthemideae) and its cultivars

Genome ◽

10.1139/g05-105 ◽

2006 ◽

Vol 49 (3) ◽

pp. 244-253 ◽

Cited By ~ 23

Author(s):

Sònia Garcia ◽

Teresa Garnatje ◽

John D Twibell ◽

Joan Vallès

Keyword(s):

Flow Cytometry ◽

Genome Size ◽

Nuclear Dna ◽

Size Variation ◽

Interspecific Variation ◽

Dna Amount ◽

Genome Size Variation ◽

Artemisia Absinthium ◽

Mediterranean Populations ◽

C Value

Different wild Mediterranean populations of Artemisia arborescens from diverse locations representing its geographical distribution, as well as some of its well-known cultivars and some specimens cultivated as ornamentals in gardens, streets, roads and nurseries, were analysed for genome size. Other closely related species endemic to Macaronesia, Artemisia canariensis, Artemisia argentea, and Artemisia gorgonum, were also analysed, and their nuclear DNA amount has been related to the biogeography of this group of species. Additionally, 5 populations of the closely related Artemisia absinthium were analysed to establish comparisons. Measurements acquired by flow cytometry ranged from 8.29 to 11.61 pg for 2C values. Statistically significant differences of 2C nuclear DNA amounts with respect to factors such as insularity or domestication have been detected. However, quite a low intraspecific genome size variation has been found in these species. Furthermore, the study also addressed the possible hybrid origins and possible misidentifications of some of the supposed cultivars of A. arborescens.Key words: Artemisia arborescens, Artemisia absinthium, Artemisia argentea, Artemisia canariensis, Artemisia gorgonum, C value, Compositae, cultivar, domestication, flow cytometry, genome size, hybridization, interspecific variation, intraspecific variation, speciation.

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Miscanthus: Inter- and Intraspecific Genome Size Variation Among M. × Giganteus, M. Sinensis, M. Sacchariflorus Accessions

Acta Biologica Cracoviensia s Botanica ◽

10.1515/abcsb-2015-0013 ◽

2015 ◽

Vol 57 (1) ◽

pp. 104-113

Author(s):

Sandra Cichorz ◽

Maria Gośka ◽

Monika Rewers

Keyword(s):

Genome Size ◽

Dna Content ◽

Nuclear Dna ◽

Size Variation ◽

Nuclear Dna Content ◽

Interspecific Variation ◽

Genome Size Variation ◽

2C Dna Content ◽

Cytological Characteristics ◽

Stomatal Length

AbstractSinceM. sinensisAnderss.,M. sacchariflorus(Maxim.) Hack. andM. ×giganteusJ.M.Greef & Deuter ex Hodk. and Renvoize have considerably the highest potential for biomass production amongMiscanthusAnderss. species, there is an urgent need to broaden the knowledge about cytological characteristics required for their improvement. In this study our objectives were to assess the genome size variation among eighteenMiscanthusaccessions, as well as estimation of the monoploid genome size (2C and Cx) of theM. sinensiscultivars, which have not been analyzed yet. The characterization of threeMiscanthusspecies was performed with the use of flow cytometry and analysis of the stomatal length. The triploid (2n = 3x = 57)M. sinensis‘Goliath’ andM. ×giganteusclones possessed the highest 2C DNA content (8.34 pg and 7.43 pg, respectively). The intermediate 2C-values were found in the nuclei of the diploid (2n = 2x = 38)M. sinensisaccessions (5.52–5.72 pg), whereas they were the lowest in the diploid (2n = 2x = 38)M. sacchariflorusecotypes (4.58–4.59 pg). The presented study revealed interspecific variation of nuclear DNA content (P<0.01) and therefore allowed for recognition of particular taxa, inter- and intraspecific hybrids and prediction of potential parental components. Moreover, intraspecific genome size variation (P<0.01) was observed inM. sinensiscultivars at 3.62%. The values of the stomatal size obtained for the triploidM. ×giganteus‘Great Britain’ (mean 30.70 μm) or ‘Canada’ (mean 29.67 μm) and diploidM. sinensis‘Graziella’ (mean 29.96 μm) did not differ significantly, therefore this parameter is not recommended for ploidy estimation.

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The genome sizes of Hordeum species show considerable variation

Genome ◽

10.1139/g96-092 ◽

1996 ◽

Vol 39 (4) ◽

pp. 730-735 ◽

Cited By ~ 18

Author(s):

Juha Kankanpää ◽

Alan H. Schulman ◽

Leena Mannonen

Keyword(s):

Flow Cytometry ◽

Hordeum Vulgare ◽

Genome Size ◽

Nuclear Dna ◽

Size Variation ◽

Nuclear Dna Content ◽

Meiotic Pairing ◽

Genome Size Variation ◽

Dapi Staining ◽

Hordeum Vulgare Ssp

Hordeum, distributed worldwide in temperate zones, is the second largest genus in the tribe Triticeae and includes diploid, tetraploid, and hexaploid species. We determined, by DAPI staining and flow cytometry, the nuclear DNA content for 35 accessions of the genus Hordeum, from a total of 19 species, including specimens of 2 cultivars and 2 landraces of Hordeum vulgare ssp. vulgare as well as samples of 12 Hordeum vulgare ssp. spontaneum populations. Genome sizes ranged from 5.69 to 9.41 pg for the G1 nuclei of the diploids, and from 13.13 to 18.36 pg for those of the tetraploids. This constitutes a 1.7-fold variation for the diploids, contrasting with a 4% variation previously reported. For H. vulgare ssp. vulgare (barley), the accessions examined differed by 18%. These variations in genome size cannot be correlated with meiotic pairing groups (I, H, X, Y) or with proposed phylogenetic relationships within the genus. Genome size variation between barley accessions cannot be related to status as cultivated or wild, or to climatic or geological gradients. We suggest these data may indicate rapid but sporadic changes in genome size within the genus. Key words : barley, Hordeum, Triticeae, genome size, flow cytometry.

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Nuclear DNA content in Sinningia (Gesneriaceae); intraspecific genome size variation and genome characterization in S. speciosa

Genome ◽

10.1139/g10-077 ◽

2010 ◽

Vol 53 (12) ◽

pp. 1066-1082 ◽

Cited By ~ 14

Author(s):

David Zaitlin ◽

Andrew J. Pierce

Keyword(s):

Genome Size ◽

Nuclear Dna ◽

Size Variation ◽

Nuclear Genome ◽

Nuclear Dna Content ◽

Size Estimation ◽

Cell Nuclei ◽

Genome Size Variation ◽

Genome Survey ◽

Size Estimates

The Gesneriaceae (Lamiales) is a family of flowering plants comprising >3000 species of mainly tropical origin, the most familiar of which is the cultivated African violet ( Saintpaulia spp.). Species of Gesneriaceae are poorly represented in the lists of taxa sampled for genome size estimation; measurements are available for three species of Ramonda and one each of Haberlea , Saintpaulia, and Streptocarpus , all species of Old World origin. We report here nuclear genome size estimates for 10 species of Sinningia , a neotropical genus largely restricted to Brazil. Flow cytometry of leaf cell nuclei showed that holoploid genome size in Sinningia is very small (approximately two times the size of the Arabidopsis genome), and is small compared to the other six species of Gesneriaceae with genome size estimates. We also documented intraspecific genome size variation of 21%–26% within a group of wild Sinningia speciosa (Lodd.) Hiern collections. In addition, we analyzed 1210 genome survey sequences from S. speciosa to characterize basic features of the nuclear genome such as guanine–cytosine content, types of repetitive elements, numbers of protein-coding sequences, and sequences unique to S. speciosa. We included several other angiosperm species as genome size standards, one of which was the snapdragon ( Antirrhinum majus L.; Veronicaceae, Lamiales). Multiple measurements on three accessions indicated that the genome size of A. majus is ∼633 × 106 base pairs, which is approximately 40% of the previously published estimate.

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Substantial intraspecific genome size variation in golden-brown algae and its phenotypic consequences

Annals of Botany ◽

10.1093/aob/mcaa133 ◽

2020 ◽

Vol 126 (6) ◽

pp. 1077-1087

Author(s):

Dora Čertnerová ◽

Pavel Škaloud

Keyword(s):

Growth Rate ◽

Genome Size ◽

Cell Size ◽

Nuclear Dna ◽

Gc Content ◽

Size Variation ◽

Nuclear Dna Content ◽

Genome Size Variation ◽

Adaptive Consequences ◽

Genomic Gc Content

Abstract Background and Aims While nuclear DNA content variation and its phenotypic consequences have been well described for animals, vascular plants and macroalgae, much less about this topic is known regarding unicellular algae and protists in general. The dearth of data is especially pronounced when it comes to intraspecific genome size variation. This study attempts to investigate the extent of intraspecific variability in genome size and its adaptive consequences in a microalgal species. Methods Propidium iodide flow cytometry was used to estimate the absolute genome size of 131 strains (isolates) of the golden-brown alga Synura petersenii (Chrysophyceae, Stramenopiles), identified by identical internal transcribed spacer (ITS) rDNA barcodes. Cell size, growth rate and genomic GC content were further assessed on a sub-set of strains. Geographic location of 67 sampling sites across the Northern hemisphere was used to extract climatic database data and to evaluate the ecogeographical distribution of genome size diversity. Key Results Genome size ranged continuously from 0.97 to 2.02 pg of DNA across the investigated strains. The genome size was positively associated with cell size and negatively associated with growth rate. Bioclim variables were not correlated with genome size variation. No clear trends in the geographical distribution of strains of a particular genome size were detected, and strains of different genome size occasionally coexisted at the same locality. Genomic GC content was significantly associated only with genome size via a quadratic relationship. Conclusions Genome size variability in S. petersenii was probably triggered by an evolutionary mechanism operating via gradual changes in genome size accompanied by changes in genomic GC content, such as, for example, proliferation of transposable elements. The variation was reflected in cell size and relative growth rate, possibly with adaptive consequences.

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Nuclear DNA amount and genome downsizing in natural and synthetic allopolyploids of the genera Aegilops and Triticum

Genome ◽

10.1139/g08-043 ◽

2008 ◽

Vol 51 (8) ◽

pp. 616-627 ◽

Cited By ~ 52

Author(s):

T. Eilam ◽

Y. Anikster ◽

E. Millet ◽

J. Manisterski ◽

M. Feldman

Keyword(s):

Genome Size ◽

Dna Sequences ◽

First Generation ◽

Nuclear Dna ◽

Chromosome Doubling ◽

Intergeneric Hybridization ◽

Dna Amount ◽

B Genome ◽

Nuclear Dna Amount ◽

Dna Amounts

Recent molecular studies in the genera Aegilops and Triticum showed that allopolyploidization (interspecific or intergeneric hybridization followed by chromosome doubling) generated rapid elimination of low-copy or high-copy, non-coding and coding DNA sequences. The aims of this work were to determine the amount of nuclear DNA in allopolyploid species of the group and to see to what extent elimination of DNA sequences affected genome size. Nuclear DNA amount was determined by the flow cytometry method in 27 natural allopolyploid species (most of which were represented by several lines and each line by several plants) as well as 14 newly synthesized allopolyploids (each represented by several plants) and their parental plants. Very small intraspecific variation in DNA amount was found between lines of allopolyploid species collected from different habitats or between wild and domesticated forms of allopolyploid wheat. In contrast to the constancy in nuclear DNA amount at the intraspecific level, there are significant differences in genome size between the various allopolyploid species, at both the tetraploid and hexaploid levels. In most allopolyploids nuclear DNA amount was significantly less than the sum of DNA amounts of the parental species. Newly synthesized allopolyploids exhibited a similar decrease in nuclear DNA amount in the first generation, indicating that genome downsizing occurs during and (or) immediately after the formation of the allopolyploids and that there are no further changes in genome size during the life of the allopolyploids. Phylogenetic considerations of the origin of the B genome of allopolyploid wheat, based on nuclear DNA amount, are discussed.

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Small, but surprisingly repetitive genomes: Transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

10.21203/rs.2.9135/v3 ◽

2019 ◽

Author(s):

Julie Blommaert ◽

Simone Riss ◽

Bette Hecox-Lea ◽

David B. Mark-Welch ◽

Claus-Peter Stelzer

Keyword(s):

Genome Size ◽

Species Complex ◽

Nuclear Dna ◽

Repetitive Element ◽

Size Variation ◽

Nuclear Dna Content ◽

Repetitive Elements ◽

Element Content ◽

Genome Size Variation ◽

Closely Related Species

Abstract Background: The causes and consequences of genome size variation across Eukaryotes, which spans five orders of magnitude, have been hotly debated since before the advent of genome sequencing. Previous studies have mostly examined variation among larger taxonomic units (e.g., orders, or genera), while comparisons among closely related species are rare. Rotifers of the Brachionus plicatilis species complex exhibit a seven-fold variation in genome size and thus represent a unique opportunity to study such changes on a relatively short evolutionary timescale. Here, we sequenced and analysed the genomes of four species of this complex with nuclear DNA contents spanning 110- 422 Mbp. To establish the likely mechanisms of genome size change, we analysed both sequencing read libraries and assemblies for signatures of polyploidy and repetitive element content. We also compared these genomes to that of B. calyciflorus, the closest relative with a sequenced genome (293 Mbp nuclear DNA content). Results summary: Despite the very large differences in genome size, we saw no evidence of ploidy level changes across the B. plicatilis complex. However, repetitive element content explained a large portion of genome size variation (at least 54%). The species with the largest genome, B. asplanchnoidis, has a strikingly high 44% repetitive element content, while the smaller B. plicatilis genomes contain between 14% and 25% repetitive elements. According to our analyses, the B. calyciflorus genome contains 39% repetitive elements, which is substantially higher than previously reported (21%), and suggests that high repetitive element load could be widespread in monogonont rotifers. Conclusions: Even though the genome sizes of these species are at the low end of the Metazoan spectrum, their genomes contain substantial amounts of repetitive elements. Polyploidy does not appear to play a role in genome size variations in these species, and these variations can be mostly explained by changes in repetitive element content. This contradicts the naïve expectation that small genomes are streamlined, or less complex, and that large variations in nuclear DNA content between closely related species are due to polyploidy.

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Intraspecific Genome Size Variation in Pumpkin (Cucurbita pepo subsp. pepo)

HortScience ◽

10.21273/hortsci.43.3.949 ◽

2008 ◽

Vol 43 (3) ◽

pp. 949-951 ◽

Cited By ~ 2

Author(s):

A. Lane Rayburn ◽

Mosbah M. Kushad ◽

Wanisari Wannarat

Keyword(s):

Flow Cytometry ◽

Genome Size ◽

Cucurbita Pepo ◽

Fruit Size ◽

Size Variation ◽

Fruit Morphology ◽

Genome Size Variation ◽

A Genome ◽

Size Variability

Genome size has recently been reported to vary 16% in pumpkins (Cucurbita spp.). The majority of this variation can be attributed to genome size differences in pumpkins of various taxonomical classes. The purpose of this study was to determine if intraspecific genome size variability could be detected by flow cytometry in Cucurbita pepo subsp. pepo pumpkin cultivars with similar fruit morphology. The pie pumpkins group was chosen for this study because of their similar fruit size, shape, and color. Genome sizes ranged from 1.109 pg in Spooktacular to 1.064 pg in Small Sugar. Spooktacular had a genome size larger than Small Sugar in all three experiments. Therefore, intraspecific genome size variation does exist in C. pepo subsp. pepo among pumpkin cultivars of similar fruit morphology.

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