LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model

2005 ◽  
Vol 110 (1-4) ◽  
pp. 91-107 ◽  
Author(s):  
C. Vitte ◽  
O. Panaud
Keyword(s):  
Genome Size ◽  
Plant Genome ◽  
Flowering Plant ◽  
Ltr Retrotransposons

scholarly journals Variation and Evolution of Genome Size in Gymnosperms

2021 ◽  
Vol 70 (1) ◽  
pp. 156-169
Author(s):  
Deepak Ohri
Keyword(s):  
Transposable Elements ◽  
Genome Size ◽  
Narrow Range ◽  
Ltr Retrotransposons ◽  
General Survey ◽  
Efficient Mechanism ◽  
Repeat Sequences ◽  
Adaptive Value ◽  
Epigenetic Machinery ◽  
Large Genomes

Abstract Gymnosperms show a significantly higher mean (1C=18.16, 1Cx=16.80) and a narrow range (16.89-fold) of genome sizes as compared with angiosperms. Among the 12 families the largest ranges of 1C values is shown by Ephedraceae (4.73-fold) and Cupressaceae (4.45-fold) which are partly due to polyploidy as 1Cx values vary 2.41 and 1.37-fold respectively. In rest of the families which have only diploid taxa the range of 1C values is from 1.18-fold (Cycadaeae) to 4.36-fold (Podocarpaceae). The question is how gymnosperms acquired such big genome sizes despite the rarity of recent instances of polyploidy. A general survey of different families and genera shows that gymnosperms have experienced both increase and decrease in their genome size during evolution. Various genomic components which have accounted for these large genomes have been discussed. The major contributors are the transposable elements particularly LTR-retrotransposons comprising of Ty3gypsy, Ty1copia and gymny superfamilies which are most widespread. The genomes of gymnosperms have been acquiring diverse LTR-RTs in their long evolution in the absence of any efficient mechanism of their elimination. The epigenetic machinery which silences these large tracts of repeat sequences into the stretches of heterochromatin and the adaptive value of these silenced repeat sequences need further investigation.

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 The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
D. Blaine Marchant ◽  
Emily B. Sessa ◽  
Paul G. Wolf ◽  
Kweon Heo ◽  
W. Brad Barbazuk ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Green Plant ◽  
Land Plant ◽  
Plant Genome ◽  
Flowering Plant ◽  
Ceratopteris Richardii ◽  
Repeat Elements ◽  
Homosporous Fern ◽  
Homosporous Ferns ◽  
Large Genomes

AbstractFerns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.

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>

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