Cytophotometric and biochemical analyses of DNA in pentaploid and diploid Agave species

Genome ◽  
1996 ◽  
Vol 39 (2) ◽  
pp. 266-271 ◽  
Author(s):  
A. Cavallini ◽  
L. Natali ◽  
G. Cionini ◽  
I. Castorena-Sanchez
Keyword(s):  
Genome Size ◽  
Chromatin Structure ◽  
Nuclear Dna ◽  
Repetitive Sequences ◽  
Point Mutations ◽  
Diploid Species ◽  
Nuclear Dna Content ◽  
Dapi Staining ◽  
Gene Copies ◽  
Biochemical Analyses

Nuclear DNA content, chromatin structure, and DNA composition were investigated in four Agave species: two diploid, Agave tequilana Weber and Agave angustifolia Haworth var. marginata Hort., and two pentaploid, Agave fourcroydes Lemaire and Agave sisalana Perrine. It was determined that the genome size of pentaploid species is nearly 2.5 times that of diploid ones. Cytophotometric analyses of chromatin structure were performed following Feulgen or DAPI staining to determine optical density profiles of interphase nuclei. Pentaploid species showed higher frequencies of condensed chromatin (heterochromatin) than diploid species. On the other hand, a lower frequency of A-T rich (DAPI stained) heterochromatin was found in pentaploid species than in diploid ones, indicating that heterochromatin in pentaploid species is made up of sequences with base compositions different from those of diploid species. Since thermal denaturation profiles of extracted DNA showed minor variations in the base composition of the genomes of the four species, it is supposed that, in pentaploid species, the large heterochromatin content is not due to an overrepresentation of G-C repetitive sequences but rather to the condensation of nonrepetitive sequences, such as, for example, redundant gene copies switched off in the polyploid complement. It is suggested that speciation in the genus Agave occurs through point mutations and minor DNA rearrangements, as is also indicated by the relative stability of the karyotype of this genus. Key words : Agave, DNA cytophotometry, DNA melting profiles, chromatin structure, genome size.

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 Genome size and identification of abundant repetitive sequences in Vallisneria spinulosa

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3982 ◽  
Author(s):  
RuiJuan Feng ◽  
Xin Wang ◽  
Min Tao ◽  
Guanchao Du ◽  
Qishuo Wang
Keyword(s):  
Genome Size ◽  
Aquatic Plant ◽  
Nuclear Dna ◽  
De Novo ◽  
Repetitive Sequences ◽  
Nuclear Dna Content ◽  
Ltr Retrotransposons ◽  
Sequencing Data ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Vallisneria spinulosa is a freshwater aquatic plant of ecological and economic importance. However, there is limited cytogenetic and genomics information on Vallisneria. In this study, we measured the nuclear DNA content of Vallisneria spinulosa by flow cytometry, performed a de novo assembly, and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. The genome size of Vallisneria spinulosa is approximately 3,595 Mbp, in which nearly 60% of the genome consists of repetitive sequences. The majority of the repetitive sequences are LTR-retrotransposons comprising 43% of the genome. Although the amount of sequencing data used in this study was not sufficient for a whole-genome assembly, it could generate an overview of representative elements in the genome. These results will lay a new foundation for further studies on various species that belong to the Vallisneria genus.

Genome size and genome evolution in diploid Triticeae species

Genome ◽  
2007 ◽  
Vol 50 (11) ◽  
pp. 1029-1037 ◽  
Author(s):  
T. Eilam ◽  
Y. Anikster ◽  
E. Millet ◽  
J. Manisterski ◽  
O. Sagi-Assif ◽  
...  
Keyword(s):  
Genome Size ◽  
Intraspecific Variation ◽  
Dna Content ◽  
Nuclear Dna ◽  
Diploid Species ◽  
Nuclear Dna Content ◽  
Dna Amount ◽  
Nuclear Dna Amount ◽  
Speciation Event ◽  
Close Temporal Proximity

One of the intriguing issues concerning the dynamics of plant genomes is the occurrence of intraspecific variation in nuclear DNA amount. The aim of this work was to assess the ranges of intraspecific, interspecific, and intergeneric variation in nuclear DNA content of diploid species of the tribe Triticeae (Poaceae) and to examine the relation between life form or habitat and genome size. Altogether, 438 plants representing 272 lines that belong to 22 species were analyzed. Nuclear DNA content was estimated by flow cytometry. Very small intraspecific variation in DNA amount was found between lines of Triticeae diploid species collected from different habitats or between different morphs. In contrast to the constancy in nuclear DNA amount at the intraspecific level, there are significant differences in genome size between the various diploid species. Within the genus Aegilops , the 1C DNA amount ranged from 4.84 pg in A. caudata to 7.52 pg in A. sharonensis; among genera, the 1C DNA amount ranged from 4.18 pg in Heteranthelium piliferum to 9.45 pg in Secale montanum . No evidence was found for a smaller genome size in annual, self-pollinating species relative to perennial, cross-pollinating ones. Diploids that grow in the southern part of the group’s distribution have larger genomes than those growing in other parts of the distribution. The contrast between the low variation at the intraspecific level and the high variation at the interspecific one suggests that changes in genome size originated in close temporal proximity to the speciation event, i.e., before, during, or immediately after it. The possible effects of sudden changes in genome size on speciation processes are discussed.

scholarly journals Estimating Nuclear DNA Content in Peach and Related Diploid Species Using Laser Flow Cytometry and DNA Hybridization

1994 ◽  
Vol 119 (6) ◽  
pp. 1312-1316 ◽  
Author(s):  
W. Vance Baird ◽  
Agnes S. Estager ◽  
John K. Wells
Keyword(s):  
Flow Cytometry ◽  
Chromosome Number ◽  
Genome Size ◽  
Dna Content ◽  
Nuclear Dna ◽  
Diploid Species ◽  
Nuclear Genome ◽  
Nuclear Dna Content ◽  
Gene Copy ◽  
Polyploid Series

Using laser flow cytometry, nuclear DNA amounts were estimated for 12 Prunus species, representing three subgenera [Prunophora (Prunus), Amygdalus, and Cerasus (Lithocerasus)], two interspecific hybrids, four cultivars, and a synthetic polyploid series of peach consisting of haploids, diploids, triploids, and tetraploids (periclinal cytochimeras). Peach nuclear DNA content ranged from 0.30 pg for the haploid nuclei to 1.23 pg for the tetraploid nuclei. The diploid genome of peach is relatively small and was estimated to be 0.60±0.03 pg (or 5.8×108 nucleotide base pairs). The polyploid series represented the expected arithmetic progression, as genome size positively correlated with ploidy level (i.e., DNA content was proportional to chromosome number). The DNA content for the 12 diploid species and two interspecific diploid hybrids ranged from 0.57 to 0.79 pg. Genome size estimates were verified independently by Southern blot analysis, using restriction fragment length polymorphism clones as gene-copy equivalents. Thus, a relatively small and stable nuclear genome typifies the Prunus species investigated, consistent with their low, basic chromosome number (× = 8).

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.

Genome size in cyclopoid copepods (Copepoda: Cyclopoida): chromatin diminution as a hypothesized mechanism of evolutionary constraint

2021 ◽  
Vol 41 (3) ◽  
Author(s):  
Emilly Schutt ◽  
Maria Hołyńska ◽  
Grace A Wyngaard
Keyword(s):  
Genome Size ◽  
Life Histories ◽  
Nuclear Dna ◽  
Cell Lineage ◽  
Fundamental Property ◽  
Nuclear Dna Content ◽  
Evolutionary Constraint ◽  
Chromatin Diminution ◽  
Somatic Genome ◽  
Copepoda Cyclopoida

Abstract Genome size is a fundamental property of organisms that impacts their molecular evolution and life histories. The hypothesis that somatic genome sizes in copepods in the order Cyclopoida are small and evolutionary constrained relative to those in the order Calanoida was proposed 15 years ago. Since then, the number of estimates has almost doubled and the taxon sampling has broadened. Here we add 14 new estimates from eight genera of freshwater cyclopoids that vary from 0.2 to 6.6 pg of DNA per nucleus in the soma; all except one are 2.0 pg DNA per nucleus or smaller. This new sample adds to the pattern of genome size in copepods and is remarkably similar to the distribution on which the original hypothesis was based, as well as those of subsequently published estimates. Embryonic chromatin diminution, during which large portions of DNA are excised from the presomatic cell lineage, is reported in Paracyclops affinis (G.O. Sars, 1863). This diminution results in a somatic genome that is one half the size of the germline genome. When the sizes of the germline genomes carried in presomatic cells of cyclopoid species that possess chromatin diminution are considered, the prediminuted germline genome sizes of cyclopoid embryos overlap with the distribution of calanoid somatic genome sizes, supporting the hypothesis that chromatin diminution has functioned as a mechanism to constrain somatic nuclear DNA content in cyclopoid copepods. Geographically based variation in genome size among populations is also reviewed.

scholarly journals Genome size mediates the effect of environmental filtering in determining plant β-diversity across temperate grasslands

2021 ◽  
Author(s):  
Hai-Yang Zhang ◽  
Xiaotao Lü ◽  
cunzheng wei ◽  
Jeff Powell ◽  
Xiaobo Wang ◽  
...  
Keyword(s):  
Genome Size ◽  
Community Assembly ◽  
Nuclear Dna ◽  
Environmental Filtering ◽  
Nuclear Dna Content ◽  
Mean Annual Precipitation ◽  
Mean Annual Temperature ◽  
Nitrogen And Phosphorus ◽  
Temperate Grasslands ◽  
Β Diversity

Elucidating mechanisms underlying community assembly and biodiversity patterns is central to ecology and evolution. Genome size (GS, i.e. nuclear DNA content) determines species’ capacity to tolerate environmental stress or to exploit new environments and therefore potentially drive community assembly. However, its role in driving β-diversity (i.e., the site-to-site variability in species composition) remains unclear. We measured GS for 169 plant species and investigated their occurrences within plant communities across 52 sites spanning a 3200-km transect in the temperate grasslands of China. We found environmental factors showed larger effects on β-diversity of large-GS than that of small-GS species. Community weighted mean GS increased with mean annual precipitation, soil total nitrogen and phosphorus concentrations, but decreased with mean annual temperature, suggesting a negative selection against species with large GS in resources-limited or warmer climates. These findings highlight the roles for GS in driving community assembly and predicting species responses to climate change.

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.

C-banding and DNA content in seven species of Tenebrionidae (Coleoptera)

Genome ◽  
1989 ◽  
Vol 32 (5) ◽  
pp. 834-839 ◽  
Author(s):  
C. Juan ◽  
E. Petitpierre
Keyword(s):  
Genome Size ◽  
X Chromosome ◽  
Dna Content ◽  
Nuclear Dna ◽  
Nuclear Dna Content ◽  
C Banding ◽  
Metaphase I

The relative amount of C-banded heterochromatin varies strikingly in seven species of tenebrionid beetles, from 25 to 58%, but most species show procentric bands only. Nevertheless, Gonocephalum patruele exhibits an almost completely heterochromatic X chromosome. The nuclear DNA content of Feulgen-stained spermatids has yielded up to a threefold difference, from 0.27 to 0.86 pg, which is not completely in accordance with the amount of C-banded heterochromatin. However, the genome sizes correlate significantly with the total chromosome areas at metaphase I and with the spermatid areas. Furthermore, the genome sizes agree with the subfamilial taxonomic groupings of these tenebrionids.Key words: Tenebrionidae, genome size, C-banding.

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