scholarly journals The Plant DNA C‐values database (release 7.1): an updated online repository of plant genome size data for comparative studies

2019 ◽  
Vol 226 (2) ◽  
pp. 301-305 ◽  
Author(s):  
Jaume Pellicer ◽  
Ilia J. Leitch
Keyword(s):  
Genome Size ◽  
Comparative Studies ◽  
Plant Genome ◽  
Plant Dna ◽  
Size Data

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 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 From Pixels to Picograms

2002 ◽  
Vol 50 (6) ◽  
pp. 735-749 ◽  
Author(s):  
David C. Hardie ◽  
T. Ryan Gregory ◽  
Paul D.N. Hebert
Keyword(s):  
Image Analysis ◽  
Genome Size ◽  
Genome Structure ◽  
Size Variation ◽  
Background Information ◽  
Genome Size Variation ◽  
Cell Staining ◽  
Theoretical Perspectives ◽  
C Value ◽  
Size Data

The study of genome size variation is important from a number of practical and theoretical perspectives. For example, the long-standing “C-value enigma” relating to the more than 200,000-fold range in eukaryotic genome sizes is best studied from a broad comparative standpoint. Genome size data are also required in detailed analyses of genome structure and evolution. The choice of future genome sequencing projects will be dependent on knowledge regarding the sizes of genomes to be sequenced, and so on. To date, genome size data have been acquired primarily by Feulgen microdensitometry or flow cytometry. Each has several advantages but also important limitations. In this review, we provide a practical guide to the new technique of Feulgen image analysis densitometry. The review is designed for those interested in genome size measurements but not extensively experienced in histochemistry, densitometry, or microscopy. Therefore, relevant historical and technical background information is included. For easy reference, we provide recipes for required reagents, guidelines for cell staining, and a checklist of steps for successful image analysis. We hope that the accuracy, rapidity, and cost-effectiveness of Feulgen image analysis demonstrated here will stimulate further surveys of genome sizes in a variety of taxa.

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>

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