Molecular Biology Reports, Год журнала: 2024, Номер 51(1)
Опубликована: Янв. 18, 2024
Язык: Английский
Mobile DNA, Год журнала: 2025, Номер 16(1)
Опубликована: Апрель 16, 2025
Язык: Английский
Процитировано
0
Nature Communications, Год журнала: 2025, Номер 16(1)
Опубликована: Май 4, 2025
Abstract Extrachromosomal circular DNAs (eccDNAs) have been identified in various eukaryotic organisms and are known to play crucial roles genomic plasticity. However, crop plants, the role of eccDNAs responses environmental cues, particularly nutritional stresses, remains unexplored. Rice ( Oryza sativa ssp. japonica ), a vital for over half world’s population an excellent model plant studies, faces numerous challenges during growth. Therefore, we conduct comprehensive studies investigating distribution, sequence, potential rice stresses. We describe changes eccDNA landscape at developmental stages optimal also identify overlapping with genes ecGenes transposable elements ecTEs full-length repeat units ecRepeatUnits whose prevalence responds nitrogen (N) phosphorus (P) deficiency. analyze multiple-fragment propose TE-mediated homologous recombination mechanism as origin rice’s eccDNAs. provide evidence genome plasticity under stresses underscore significance their abundance specificity.
Язык: Английский
Процитировано
0
Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2023, Номер 50(7), С. 462 - 472
Опубликована: Апрель 15, 2023
Since the discovery of first transposon by Dr. Barbara McClintock, prevalence and diversity transposable elements (TEs) have been gradually recognized. As fundamental genetic components, TEs drive organismal evolution not only contributing functional sequences (e.g., regulatory or "controllers" as phrased McClintock) but also shuffling genomic sequences. In latter respect, TE-mediated gene duplications contributed to origination new genes attracted extensive interest. response development this field, we herein attempt provide an overview duplication focusing on common rules emerging across generated different TE types. Specifically, despite huge divergence transposition machinery TEs, identify three features various mechanisms, including end bypass, template switching, recurrent transposition. These lead one outcome, namely, duplicates tend be subjected exon neofunctionalization. Therefore, intrinsic properties mutational mechanism constrain evolutionary trajectories these duplicates. We finally discuss future field in-depth characterization both mechanisms functions
Язык: Английский
Процитировано
7
Plant and Cell Physiology, Год журнала: 2024, Номер unknown
Опубликована: Май 18, 2024
Abstract Transposable elements (TEs) are mobile DNA that particularly abundant in the plant genomes. They have long been considered as junk DNA; however, a growing body of evidence suggests TE insertions promote genetic diversity is essential for adaptive evolution species. Thus far, studies mainly investigated cis-acting regulatory roles TEs generated by their nearby or within host genes. However, trans-acting effects TE-derived RNA and remained obscure to date. contain various sequences can accommodate binding specific RNAs proteins. Recently, it was suggested some these cellular regulators shared between genes, competition common factors underlies fine-tuned developmental reprogramming. In this review, we will highlight discuss latest discoveries on biological functions TEs, with particular focus competitive regulators.
Язык: Английский
Процитировано
2
Scientific Reports, Год журнала: 2022, Номер 12(1)
Опубликована: Дек. 14, 2022
Abstract Sparganium is an emergent aquatic macrophyte widely spread in temperate and subtropical zones. Taxa of this genus feature high phenotypic plasticity can produce interspecific hybrids. By means high-throughput sequencing the internal transcribed spacer (ITS1) 35S rDNA, status 15 Eurasian species subspecies was clarified role hybridization events recent evolution investigated. It has been shown that a number such as S. angustifolium, fallax subglobosum have homogenized rDNA represented by one major ribotype. The other taxa two or more ribotypes. Species with heterogeneity are apparently hybrid origin. Based on differences patterns, intraspecific diversity identified probatovae emersum . Thus, we concluded extensive at subgenus level, there may also be occasional between from different subgenera.
Язык: Английский
Процитировано
7
BMC Genomics, Год журнала: 2024, Номер 25(1)
Опубликована: Апрель 24, 2024
Abstract Transposable elements (TEs) are a major force in the evolution of plant genomes. Differences transposition activities and landscapes TEs can vary substantially, even closely related species. Interspecific hybridization, widely employed technique tomato breeding, results creation novel combinations from distinct The implications this process for TE activity have not been studied modern cultivars. In study, we used nanopore sequencing extrachromosomal circular DNA (eccDNA) identified two highly active Ty1/ Copia LTR retrotransposon families ( Solanum lycopersicum ), called Salsa Ketchup . Elements these produce thousands eccDNAs under controlled conditions epigenetic stress. EccDNA sequence analysis revealed that parts eccDNA produced by exhibited low similarity to S. genomic sequence. To trace origin TEs, whole-genome de novo genome assembly were performed. We found occurred breeding line via interspecific introgression peruvianum Our findings collectively show introgressions contribute both genetic phenotypic diversity only introducing variants, but also importing transposable other
Язык: Английский
Процитировано
1
Frontiers in Genetics, Год журнала: 2024, Номер 15
Опубликована: Апрель 29, 2024
Human extrachromosomal circular DNA, or eccDNA, has been the topic of extensive investigation in last decade due to its prominent regulatory role development disorders including cancer. With rapid advancement experimental, sequencing and computational technology, millions eccDNA records are now accessible. Unfortunately, literature databases only provide snippets this information, preventing us from fully understanding eccDNAs. Researchers frequently struggle with process selecting algorithms tools examine eccDNAs interest. To explain underlying formation mechanisms five basic classes eccDNAs, we categorized their characteristics functions summarized eight biogenesis theories. Most significantly, created a clear procedure help selection suitable techniques thoroughly examined most recent experimental bioinformatics methodologies data resources for identifying, measuring analyzing sequences. In conclusion, highlighted current obstacles prospective paths research, specifically discussing probable uses molecular diagnostics clinical prediction, an emphasis on potential contribution novel strategies.
Язык: Английский
Процитировано
1
The Plant Journal, Год журнала: 2024, Номер unknown
Опубликована: Ноя. 14, 2024
As a result of extensive selection, two polyploid grass weeds, Hordeum glaucum (northern barley grass; 2n = 4x 28) and Bromus diandrus (ripgut brome; 8x 56), have evolved resistance to glyphosate, in Australia. Previous research suggested amplification 5-enolpyruvylshikimate-3-Phosphate synthase (EPSPS) gene confers these weed species. The objective this was investigate the genomic organization EPSPS species through molecular cytogenetic analyses fluorescence situ hybridization (FISH) understand possible mechanism gene. copy number H. B. plants estimated via quantitative polymerase chain reaction. susceptible both had one EPSPS, whereas resistant 14-17 16-32 copies, respectively. FISH analysis glyphosate-susceptible (Hg-RWS) glaucum, revealed four faint signals pairs homologous chromosomes, at telomeric region. glyphosate-resistant (Hg-YP1) also showed regions but were brighter appeared as cluster genes. Similarly, (Bd-S) on position. However, samples glyphosate-resistant, diandrus, Bd-SA988 Bd-Vic much gene, located telomere suggesting an increase copies Overall, unequal crossover during meiosis may triggered initial duplication sparking evolution glyphosate resistance.
Язык: Английский
Процитировано
1
Canadian Journal of Plant Science, Год журнала: 2024, Номер unknown
Опубликована: Дек. 4, 2024
The coinciding increase in genomics resources for weedy plant species and herbicide resistance evolution has led to a rapid expansion of our understanding the relationship between genomic structural variation mechanisms. Since first discovery 5-enolpyruvylshikimate-3-phosphate synthase ( EPSPS) copy number conferring glyphosate Amaranthus palmeri, we have seen convergent same herbicide-resistance mechanism eleven diverse weed by variety unique variant-generating These mechanisms include extrachromosomal circular DNA replication, unequal crossing over, subtelomeric duplication. More recently, target-site duplication been found cause other herbicides with different modes action, including acetyl-CoA carboxylase (ACCase) inhibitors glutamine synthetase inhibitors. Additionally, transposon-generated variants that confer resistances are beginning be discovered. This review summarizes current agronomic genomes as it relates emphasizes necessary future research clarify size, nature, give rise variation. While limit traits, this work also highlights importance critical component total genetic diversity its novel traits.
Язык: Английский
Процитировано
1
PLANT PHYSIOLOGY, Год журнала: 2023, Номер 193(1), С. 172 - 173
Опубликована: Июль 3, 2023
Adapta on to environmental change is necessary in all organisms, especially sessile organisms such as plants.Increased gene expression one of the core stress responses, but there can be limits how much transcribed from a single locus.The obvious solu this problem duplicate needed genes, achieved within genera on?Gene amplifica through extrachromosomal circular DNA (eccDNA) form genome plas city capable driving process (Peng et al., 2022).These molecules have been observed kinds eukaryote cells where they vary size and c content.In plants, most eccDNA contain repe ve sequences, intergenic regions, genic fragments, it rare find full endogenous protein-coding genes.A well-known excep 400-kb ini ally found crop weed Amaranthus palmeri, which carries 59 proteincoding genes including enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), target herbicide glyphosate (Koo 2018).Remarkably, increased copy number EPSPS confers resistance.The sequence, structure, inheritance replicon were previously inves gated Fluorescence In Situ Hybridiza (FISH) 2018).The EPSPS-FISH signals showed that important resistance was not integrated presented elements, yet anchored chromosomes during metaphase.In soma cells, up 80 copies replicon, able transmi ed progeny via chromosome tethering.Crossing sensi resistant A. palmeri plants inherited by offspring, varied dras cally among F 1 individuals, ssues even cells.Once sexual transmission demonstrated, an interes ng ques whether could also passed other species.Plants for spinosus, another same genus (Nandula 2014).In over-expressed comparison with suscep ble sequence iden cal glyphosate-resistant plants.Thus, authors hypothesized
Язык: Английский
Процитировано
3