An emerging role beyond genetics: DNA methylation in horticultural quality shaping DOI Creative Commons
Yanpei Chen, Dong Li,

Zhaobo Lang

et al.

The Innovation Life, Journal Year: 2024, Volume and Issue: 2(1), P. 100050 - 100050

Published: Jan. 1, 2024

<p>Horticultural products play an increasingly vital role in addressing the nutritional needs of world’s expanding population, which has surpassed 8 billion. The global trend towards health-oriented diets motivated consumers to seek high-quality natural horticultural food consumption. This highlights pressing requirement for updated guidance and strategies sustainable quality upgrading. Meanwhile, DNA methylation, epigenetic modification having transcriptional-regulation potential, is emerging as a crucial dominator food. In this current investigation, we integrate valuable methylation loci regulating traits fruit vegetable, elucidating underlying mechanisms emphasizing impressive species-specificity. At early stage, most extensively studied aspects include promoter transposable elements. Additionally, delve into locus-specific methylation-editing techniques, whose achievable genetic-modification-free advantages are promising alleviate consumer concerns regarding genetic-modification products. Overall, review devoted providing insights development produce design response security challenges.</p>

Language: Английский

The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees DOI Creative Commons
Tingting Shi, Xinxin Zhang,

Yukang Hou

et al.

Molecular Plant, Journal Year: 2024, Volume and Issue: 17(5), P. 725 - 746

Published: March 13, 2024

Understanding the underlying mechanisms and links between genome evolution adaptive innovations stands as a key goal in evolutionary studies. Poplars, among world's most widely distributed cultivated trees, exhibit extensive phenotypic diversity environmental adaptability. In this study, we present genus-level super-pangenome comprising 19 Populus genomes, revealing likely pivotal role of private genes facilitating local climate adaptation. Through integration pangenomes with transcriptomes, methylomes, chromatin accessibility mapping, unveil that trajectories pangenes duplicated are closely linked to genomic landscapes regulatory epigenetic architectures, notably CG methylation gene-body regions. Further comparative analyses have enabled identification 142 202 structural variants across species intersect significant number contribute substantially both divergence. We experimentally validated ∼180-bp presence/absence variant affecting expression CUC2 gene, crucial for leaf serration formation. Finally, developed user-friendly web-based tool encompassing multi-omics resources associated (http://www.populus-superpangenome.com). Together, pioneering resource forest trees not only aids advancement breeding efforts globally important tree genus but also offers valuable insights into potential avenues comprehending biology.

Language: Английский

Citations

22
Exploring the crop epigenome: a comparison of DNA methylation profiling techniques DOI Creative Commons

Dolores Rita Agius,

Aliki Kapazoglou, Evangelia V. Avramidou

et al.

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: May 30, 2023

Epigenetic modifications play a vital role in the preservation of genome integrity and regulation gene expression. DNA methylation, one key mechanisms epigenetic control, impacts growth, development, stress response adaptability all organisms, including plants. The detection methylation marks is crucial for understanding underlying these processes developing strategies to improve productivity resistance crop There are different methods detecting plant such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide analysis, methylated immunoprecipitation reduced representation MS immuno-based techniques. These profiling approaches vary many aspects, input, resolution, genomic region coverage, bioinformatics analysis. Selecting an appropriate screening approach requires This review provides overview plants, along with comparisons efficacy techniques between model strengths limitations each methodological outlined, importance considering both technical biological factors highlighted. Additionally, modulating species presented. Overall, this will assist scientists making informed decisions when selecting method.

Language: Английский

Citations

26
Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations DOI Creative Commons
Samuel N. Bogan, Soojin V. Yi

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(2)

Published: Feb. 1, 2024

Abstract There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that alter gene regulation and subsequently impact phenotypes. We first discuss origins variation nature, which may arise from genetic variation, spontaneous epimutations, drift, or capacitors. then review synthesize literature addressing three facets the aforementioned model: (i) causal effects on at level, (ii) divergence patterns natural populations distributed gradients, (iii) relationship between environmentally induced expression molecular level. focus DNA methylation, most extensively studied modification. find support for associated structure selection stable variants, inhibition enzymes frequently bears plasticity. However, there are pervasive confounding issues literature. Effects chromatin-modifying phenotype be independent marks, alternatively resulting functions protein interactions extrinsic epigenetics. Associations methylation strong plants mammals but notably absent invertebrates nonmammalian vertebrates. Given these challenges, we describe emerging approaches better investigate how affect regulation, plasticity, among populations.

Language: Английский

Citations

14
Phased Assembly of Neo-Sex Chromosomes Reveals Extensive Y Degeneration and Rapid Genome Evolution in Rumex hastatulus DOI Creative Commons
Bianca M. Sacchi, Zoë Humphries,

Jana Kružlicová

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(4)

Published: April 1, 2024

Abstract Y chromosomes are thought to undergo progressive degeneration due stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales evolutionary forces driving remain unclear. To investigate evolution sex on multiple timescales, we generated a high-quality phased genome assembly massive older (&lt;10 MYA) neo (&lt;200,000 yr) XYY cytotype dioecious plant Rumex hastatulus hermaphroditic outgroup salicifolius. Our assemblies, supported by fluorescence situ hybridization, confirmed that neo-sex were formed two key events: an X-autosome fusion reciprocal translocation between homologous autosome chromosome. The enormous sex-linked regions X (296 Mb) (503 both evolved from large repeat-rich genomic with low recombination; however, complete still led over 30% gene major rearrangements. In region, there has been significant increase transposable element abundance, even into near genes. neo-sex-linked regions, observed evidence extensive rearrangements without loss. Overall, inferred during first 10 million years chromosome but not very short timescales. results indicate when emerge repetitive already-low recombination, leads substantial content degeneration.

Language: Английский

Citations

12
The emerging trends and prospects of DNA methylomics for abiotic stress tolerance in legumes DOI

Sheel Yadav,

Ambika B. Gaikwad,

Gopal Kalwan

et al.

Journal of Plant Biochemistry and Biotechnology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 7, 2025

Language: Английский

Citations

1
DNA methylation dynamics in gymnosperm duplicate genes: implications for genome evolution and stress adaptation DOI
Kai‐Yuan Huang, Yuanyuan Feng, Hong Du

et al.

The Plant Journal, Journal Year: 2025, Volume and Issue: 121(4)

Published: Feb. 1, 2025

SUMMARY Duplicate genes are pivotal in driving evolutionary innovation, often exhibiting expression divergence that offers a system to investigate the role of DNA methylation transcriptional regulation. However, previous studies have predominantly focused on angiosperms, leaving patterns major lineages land plants still unclear. This study explores evolution duplicate across representative gymnosperm species with large genomes, spanning over 300 million years, using genomic, transcriptomic, and high‐depth methylomic data. We observed variations levels along gene bodies, flanking regions, statuses coding regions different duplication types. Biased divergences frequently occurred between copies. Specifically, 2‐kb downstream negatively correlated expression. Both CG CHG bodies were positively length, suggesting these types may function as an epigenomic buffer mitigate adverse impact length both notably enriched adaptation‐related biological processes, aid adaptive gymnosperms by regulating stress response genes. Changes switches status within transposed duplicates. depletion for or enrichment non‐CG significantly reduced translocated correlation suggests reduce genetic redundancy silencing Our highlights significance plant genome adaptation.

Language: Английский

Citations

1
Growth, physiological parameters and DNA methylation in Spirodela polyrhiza (L.) Schleid exposed to PET micro-nanoplastic contaminated waters DOI Creative Commons
Marco Dainelli, Maria Beatrice Castellani, Sara Pignattelli

et al.

Plant Physiology and Biochemistry, Journal Year: 2024, Volume and Issue: 207, P. 108403 - 108403

Published: Jan. 27, 2024

The effects of polyethylene terephthalate micro-nanoplastics (PET-MNPs) were tested on the model freshwater species Spirodela polyrhiza (L.) Schleid., with focus possible particle-induced epigenetic (i.e. alteration DNA methylation status). MNPs (size ∼ 200-300 nm) produced as water dispersions from PET bottles through repeated cycles homogenization and used to prepare N-medium at two environmentally relevant concentrations (∼0.05 g L

Language: Английский

Citations

7
Dynamic DNA Methylation Regulates Season-Dependent Secondary Metabolism in the New Shoots of Tea Plants DOI

Mengxue Han,

Shijia Lin, Biying Zhu

et al.

Journal of Agricultural and Food Chemistry, Journal Year: 2024, Volume and Issue: 72(8), P. 3984 - 3997

Published: Feb. 15, 2024

Plant secondary metabolites are critical quality-conferring compositions of plant-derived beverages, medicines, and industrial materials. The accumulations highly variable among seasons; however, the underlying regulatory mechanism remains unclear, especially in epigenetic regulation. Here, we used tea plants to explore an important mark DNA methylation (5mC)-mediated regulation plant metabolism different seasons. Multiple omics analyses were performed on spring summer new shoots. results showed that flavonoids theanine dominated metabolic response seasons In shoots, genes encoding methyltransferases demethylases up-regulated, global CG CHG reduced CHH increased. 5mC promoter gene body regions influenced seasonal expression; amplitude was correlated with transcriptions. These differentially methylated included those enzymes transcription factors which play roles flavonoid pathways. role further verified by applying a inhibitor. findings highlight dynamic plays seasonal-dependent provide insights for improving quality.

Language: Английский

Citations

7
DNA methylation: an emerging paradigm of gene regulation under drought stress in plants DOI

Sheel Yadav,

Shashi Meena,

Gopal Kalwan

et al.

Molecular Biology Reports, Journal Year: 2024, Volume and Issue: 51(1)

Published: Feb. 19, 2024

Language: Английский

Citations

7
DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus DOI

Julien Vigneaud,

Annegret Kohler, Mamadou Dia Sow

et al.

New Phytologist, Journal Year: 2023, Volume and Issue: 238(6), P. 2561 - 2577

Published: Feb. 20, 2023

Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level expression chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) two demethylases DEMETER-LIKE (DML) in Populus tremula × alba lines, we examined how host methylation modulates multiple parameters root colonization with fungus Laccaria bicolor. We compared ectomycorrhizas formed between transgenic wild-type (WT) trees analyzed their methylomes transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded hypomethylated overexpressing DML or RNAi-ddm1 lines. found 86 genes 288 transposable elements (TEs) differentially methylated WT (common both OX-dml RNAi-ddm1) 120 genes/1441 TEs fungal genome suggesting a host-induced remodeling methylome. Hypomethylated displayed 205 expressed (cis trans effects) common 17 being (cis). Our findings suggest central role ability form including not only involved initiation, ethylene jasmonate-mediated pathways, immune response but also terpenoid metabolism.

Language: Английский

Citations

15