Existence of two histone H3 variants in dicotyledonous plants and correlation between their acetylation and plant genome size

1992 ◽  
Vol 18 (2) ◽  
pp. 181-187 ◽  
Author(s):  
Jakob H. Waterborg
Keyword(s):  
Genome Size ◽  
Histone H3 ◽  
Plant Genome ◽  
Dicotyledonous Plants

scholarly journals Maize centromeric chromatin scales with changes in genome size

Genetics ◽  
2021 ◽  
Vol 217 (4) ◽  
Author(s):  
Na Wang ◽  
Jianing Liu ◽  
William A Ricci ◽  
Jonathan I Gent ◽  
R Kelly Dawe
Keyword(s):  
Genome Size ◽  
Cell Size ◽  
Histone H3 ◽  
Limiting Factors ◽  
Positive Relationships ◽  
Satellite Sequence ◽  
Centromeric Chromatin ◽  
Protein Levels ◽  
Centromeric Satellite

Abstract Centromeres are defined by the location of Centromeric Histone H3 (CENP-A/CENH3) which interacts with DNA to define the locations and sizes of functional centromeres. An analysis of 26 maize genomes including 110 fully assembled centromeric regions revealed positive relationships between centromere size and genome size. These effects are independent of variation in the amounts of the major centromeric satellite sequence CentC. We also backcrossed known centromeres into two different lines with larger genomes and observed consistent increases in functional centromere sizes for multiple centromeres. Although changes in centromere size involve changes in bound CENH3, we could not mimic the effect by overexpressing CENH3 by threefold. Literature from other fields demonstrate that changes in genome size affect protein levels, organelle size and cell size. Our data demonstrate that centromere size is among these scalable features, and that multiple limiting factors together contribute to a stable centromere size equilibrium.

scholarly journals An enormous Paris polyphylla genome sheds light on genome size evolution and polyphyllin biogenesis

2020 ◽  
Author(s):  
Jing Li ◽  
Meiqi Lv ◽  
Lei Du ◽  
A Yunga ◽  
Shijie Hao ◽  
...  
Keyword(s):  
Genome Size ◽  
Single Molecule ◽  
Repetitive Sequences ◽  
Plant Genome ◽  
Growth Stages ◽  
Evolutionary Trend ◽  
Rna Seq ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
Paris Polyphylla

AbstractThe monocot family Melanthiaceae with varying genome sizes in a range of 230-fold is an ideal model to study the genome size fluctuation in plants. Its family member Paris genus demonstrates an evolutionary trend of bearing huge genomes characterized by an average c-value of 49.22 pg. Here, we report a 70.18 Gb genome assembly out of the 82.55 Gb genome of Paris polyphylla var. yunnanensis (PPY), which represents the biggest sequenced genome to date. We annotate 69.53% repetitive sequences in this genome and 62.50% of which are long-terminal repeat (LTR) transposable elements. Further evolution analysis indicates that the giant genome likely results from the joint effect of common and species-specific expansion of different LTR superfamilies, which might contribute to the environment adaptation after speciation. Moreover, we identify the candidate pathway genes for the biogenesis of polyphyllins, the PPY-specific medicinal saponins, by complementary approaches including genome mining, comprehensive analysis of 31 next-generation RNA-seq data and 55.23 Gb single-molecule circular consensus sequencing (CCS) RNA-seq reads, and correlation of the transcriptome and phytochemical data of five different tissues at four growth stages. This study not only provides significant insights into plant genome size evolution, but also paves the way for the following polyphyllin synthetic biology.

scholarly journals Strategies to produce T-DNA free CRISPRed fruit trees via Agrobacterium tumefaciens stable gene transfer

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Lorenza Dalla Costa ◽  
Stefano Piazza ◽  
Valerio Pompili ◽  
Umberto Salvagnin ◽  
Alessandro Cestaro ◽  
...  
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Gene Transfer ◽  
Genomic Dna ◽  
Fruit Trees ◽  
Plant Genome ◽  
Stable Gene ◽  
Binary Vectors ◽  
Exogenous Dna ◽  
Left Behind ◽  
Dicotyledonous Plants

AbstractGenome editing via CRISPR/Cas9 is a powerful technology, which has been widely applied to improve traits in cereals, vegetables and even fruit trees. For the delivery of CRISPR/Cas9 components into dicotyledonous plants, Agrobacterium tumefaciens mediated gene transfer is still the prevalent method, although editing is often accompanied by the integration of the bacterial T-DNA into the host genome. We assessed two approaches in order to achieve T-DNA excision from the plant genome, minimizing the extent of foreign DNA left behind. The first is based on the Flp/FRT system and the second on Cas9 and synthetic cleavage target sites (CTS) close to T-DNA borders, which are recognized by the sgRNA. Several grapevine and apple lines, transformed with a panel of CRISPR/SpCas9 binary vectors, were regenerated and characterized for T-DNA copy number and for the rate of targeted editing. As detected by an optimized NGS-based sequencing method, trimming at T-DNA borders occurred in 100% of the lines, impairing in most cases the excision. Another observation was the leakage activity of Cas9 which produced pierced and therefore non-functional CTS. Deletions of genomic DNA and presence of filler DNA were also noticed at the junctions between T-DNA and genomic DNA. This study proved that many factors must be considered for designing efficient binary vectors capable of minimizing the presence of exogenous DNA in CRISPRed fruit trees.

scholarly journals Towards completing understanding of genome size characters in plants. A commentary on: ‘Genome size and endopolyploidy evolution across the moss phylogeny’

2020 ◽  
Vol 125 (4) ◽  
pp. iv-v
Author(s):  
Jeff Duckett
Keyword(s):  
Genome Size ◽  
Vascular Plant ◽  
Plant Genome

Abstract Major differences between moss and vascular plant genome sizes have major implications for stomatal biology whilst an absence of endopolyploidy in Sphagnum is most probably related to the unique development of the capitulum.

scholarly journals Plant Genome Size Research: A Field In Focus

2005 ◽  
Vol 95 (1) ◽  
pp. 1-6 ◽  
Author(s):  
M. D. BENNETT
Keyword(s):  
Genome Size ◽  
Plant Genome

The effects of rapid desiccation on estimates of plant genome size

2011 ◽  
Vol 19 (6) ◽  
pp. 825-842 ◽  
Author(s):  
Jillian D. Bainard ◽  
Brian C. Husband ◽  
Sarah J. Baldwin ◽  
Aron J. Fazekas ◽  
T. Ryan Gregory ◽  
...  
Keyword(s):  
Genome Size ◽  
Plant Genome

scholarly journals Plant Genome Size Estimation by Flow Cytometry: Inter-laboratory Comparison

1998 ◽  
Vol 82 (suppl_1) ◽  
pp. 17-26 ◽  
Author(s):  
J. Doležel ◽  
J. Greilhuber ◽  
S. Lucretti ◽  
A. Meister ◽  
M. A. Lysák ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Genome Size ◽  
Plant Genome ◽  
Size Estimation

scholarly journals УРОВНИ ПЛОИДНОСТИ И ОТНОСИТЕЛЬНОГО СОДЕРЖАНИЯ ДНК В КУЛЬТУРЕ КЛЕТОК И ТКАНЕЙ РАСТЕНИЙ IN VITRO

2016 ◽  
Vol 6 (3) ◽  
pp. 33-38
Author(s):  
M. V. Skaptsov ◽  
M. A. Krasnoborodkina ◽  
M. G. Kutsev ◽  
S. V. Smirnov ◽  
A. I. Shmakov ◽  
...  
Keyword(s):  
Genome Size ◽  
Ploidy Level ◽  
Dna Content ◽  
Nuclear Dna Content ◽  
Callus Cultures ◽  
Plant Genome ◽  
Control Group ◽  
Ms Medium ◽  
Relative Dna Content

<p>We presented results of variations in the ploidy level and the genome size of the <em>R. acetosa</em> regenerants. These regenerants was obtained by indirect and direct morphogenesis in in vitro culture. Explants were prepared from seedlings on the three-leaf stage of plant development. More than 100 explants were used to stimulate the indirect and direct morphogenesis. Mesophilic explants were cultured on the MS nutrient medium containing auxin to callus proliferation (2 mg/L NAA, 1 mg/L BA). Cultivation of the callus was maintained for 4 weeks followed by an indirect morphogenes. Indirect morphogenesis stimulated on the MS medium with cytokinin and gibberellic acid predominance (0.5 mg/L BA, 0.2 mg/L GA3). Direct stimulate morphogenesis from the apical meristem of seedlings on nutrient media with a predominance of cytokinins (1 mg/L BA, 0.25 mg/L NAA). Rhizogenesis have stimulated by transferring of the regenerants to the ½MS medium supplemented with 0.2 mg/L of NAA. Research of a ploidy level and genome size was performed by flow cytometry used propidium iodide staining with <em>Vicia faba</em> cv “Innovec” (2C=26.90 pg) as internal DNA standard. We calculated the relative DNA content (2C) for <em>R. acetosa</em> equal to 6,98 pg. Cytogenetical analisis showed that the maximum genome size variation recorded for regenerants obtained through the indirect morphogenesis. Variations in the genome size of the regenerants obtained by direct morphogenesis deviates from the control group to 0.30 pg (2С=7.28 pg) and after indirect morphogenesis to 1.04 pg (2С=8.2 pg). Cytogenetical analysis of the regenerated plants showed the presence of different somatic chromosome numbers ranging from 2n = 14 to 2n = 28. The relative DNA content of tetraploid forms was 11.87 pg. In our study was shown, that the most effective method of plant conservation in the <em>in vitro</em> culture is a direct morphogenesis. Analysis of the relative nuclear DNA content and chromosome counts of regenerants obtained by indirect morphogenesis from the callus cultures showed significant variations in the DNA content, as well as the appearance of polyploid forms. Therefore, long-term cultivation of callus cultures increases the probability of genomic aberrations, which reduces the stability of the plant genome.</p>

scholarly journals Maize centromeric chromatin scales with changes in genome size

2020 ◽  
Author(s):  
Na Wang ◽  
Jianing Liu ◽  
William A. Ricci ◽  
Jonathan I. Gent ◽  
R. Kelly Dawe
Keyword(s):  
Genome Size ◽  
Cell Size ◽  
Histone H3 ◽  
Limiting Factors ◽  
Positive Relationships ◽  
Satellite Sequence ◽  
Centromeric Chromatin ◽  
Protein Levels ◽  
Centromeric Satellite

AbstractCentromeres are defined by the location of Centromeric Histone H3 (CENP-A/CENH3) which interacts with DNA to define the locations and sizes of functional centromeres. An analysis of 26 maize genomes including 110 fully assembled centromeric regions revealed positive relationships between centromere size and genome size. These effects are independent of variation in the amounts of the major centromeric satellite sequence CentC. We also backcrossed known centromeres into two different lines with larger genomes and observed consistent increases in functional centromere sizes for multiple centromeres. Although changes in centromere size involve changes in bound CENH3, we could not mimic the effect by overexpressing CENH3 by threefold. Literature from other fields demonstrate that changes in genome size affect protein levels, organelle size and cell size. Our data demonstrate that centromere size is among these scalable features, and that multiple limiting factors together contribute to a stable centromere size equilibrium.

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