The genome sizes of Hordeum species show considerable variation

Genome ◽  
1996 ◽  
Vol 39 (4) ◽  
pp. 730-735 ◽  
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.

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

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.

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

Genome ◽  
2010 ◽  
Vol 53 (12) ◽  
pp. 1066-1082 ◽  
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.

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

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.

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

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.

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

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.

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

2019 ◽  
Author(s):  
Julie Esmeralda 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.

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

Genome ◽  
2006 ◽  
Vol 49 (3) ◽  
pp. 244-253 ◽  
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.

Cryptic speciation in Pelobates fuscus (Anura, Pelobatidae): evidence from DNA flow cytometry

2001 ◽  
Vol 22 (4) ◽  
pp. 387-396 ◽  
Author(s):  
◽  
◽  
◽  
Keyword(s):  
Flow Cytometry ◽  
Eastern Europe ◽  
Genome Size ◽  
Nuclear Dna ◽  
Size Variation ◽  
Dna Flow Cytometry ◽  
Cryptic Speciation ◽  
Genome Size Variation ◽  
The West ◽  
Pelobates Fuscus

AbstractThe amount of nuclear DNA in 173 specimens of Pelobates f. fuscus from 34 localities in Russia, Ukraine, Moldavia and Latvia was determined by DNA flow cytometry. Two distinct groups with different genome sizes were identified. The ranges of the genome size variation in the two groups did not overlap. Geographically, these groups with smaller or larger genome size are distributed in the west and in the east of eastern Europe, respectively.

scholarly journals Analysis of Genome Size of Sixteen Coffea arabica Cultivars Using Flow Cytometry

HortScience ◽  
2019 ◽  
Vol 54 (6) ◽  
pp. 998-1004
Author(s):  
Josue Ortega-Ortega ◽  
Francisco Arturo Ramírez-Ortega ◽  
Roberto Ruiz-Medrano ◽  
Beatriz Xoconostle-Cázares
Keyword(s):  
Flow Cytometry ◽  
Genome Size ◽  
Dna Content ◽  
Coffea Arabica ◽  
Nuclear Dna ◽  
Nuclear Dna Content ◽  
Dapi Staining ◽  
Breeding Programs ◽  
Tropical Regions ◽  
Coffee Breeding

Coffee is an important crop worldwide, grown on about 10 million hectares in tropical regions including Latin America, Africa, and Asia. The genus Coffea includes more than 100 species; most are diploid, except for C. arabica, which is allotetraploid and autogamous. The genetic diversity of commercial coffee is low, likely due to it being self-pollinating, in addition, the widespread propagation of few selected cultivars, such as Caturra, Bourbon, and Typica. One approach is the analysis of genome size in these cultivars as a proxy to study its genetic variability. In the present work, genome size of 16 cultivars was assessed through high-resolution flow cytometry (FCM). Nuclear DNA was analyzed using a modified procedure that uses propidium iodide (PI) and 4′,6′-diamino-2-phenylindole dihydrochloride hydrate (DAPI) staining. The C. arabica cultivars investigated possessed a nuclear DNA content ranging from 2.56 ± 0.016 pg for Typica, to 3.16 ± 0.033 pg for ICATU, which had the largest genome size. All cultivars measured using both fluorochromes had greater estimates with DAPI than PI. The proportion of the genome composed of guanosine and cytosine (GC%) among the cultivars evaluated in this study ranged from 37.03% to 39.22%. There are few studies of genome size by FCM of distinct important C. arabica cultivars, e.g., hybrids and artificial crosses. Thus, this work could be valuable for coffee breeding programs. The data presented here are intended to expand the genomic understanding of C. arabica and could link nuclear DNA content with evolutionary relationships such as diversification, hybridization and polyploidy.

First estimates of genome size in ribbon worms (phylum Nemertea) using flow cytometry and Feulgen image analysis densitometry

2014 ◽  
Vol 92 (10) ◽  
pp. 847-851 ◽  
Author(s):  
Kelly L. Mulligan ◽  
Terra C. Hiebert ◽  
Nicholas W. Jeffery ◽  
T. Ryan Gregory
Keyword(s):  
Flow Cytometry ◽  
Image Analysis ◽  
Body Size ◽  
Genome Size ◽  
Positive Relationship ◽  
Nuclear Dna ◽  
Nuclear Dna Content ◽  
Size Estimation ◽  
Size Diversity ◽  
Size Estimates

Ribbon worms (phylum Nemertea) are among several animal groups that have been overlooked in past studies of genome-size diversity. Here, we report genome-size estimates for eight species of nemerteans, including representatives of the major lineages in the phylum. Genome sizes in these species ranged more than fivefold, and there was some indication of a positive relationship with body size. Somatic endopolyploidy also appears to be common in these animals. Importantly, this study demonstrates that both of the most common methods of genome-size estimation (flow cytometry and Feulgen image analysis densitometry) can be used to assess genome size in ribbon worms, thereby facilitating additional efforts to investigate patterns of variability in nuclear DNA content in this phylum.

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