Leymus chinensis
Omics
Epigenomics
| Species | Categorization | Article Overview | Tissue | Stress | Growth Stage | Source |
|---|---|---|---|---|---|---|
| DNA methylation | Abiotic stresses (warming, nitrogen addition, and their combination) induced significant cytosine methylation alterations (hypermethylation and hypomethylation) in Leymus chinensis, particularly around transposable elements. These stress-induced changes, confirmed as primarily epigenetic due to minimal genetic variation in clonally propagated plants, included targeted modifications at specific loci linked to stress response genes and resulted in epigenetic differentiation between treated and control groups, suggesting a mechanism for rapid plant adaptation to environmental changes like global warming and nitrogen deposition. | leaf | warming, N addition and warming+N addition | maturation | Yin et al., 2023 | |
Leymus chinensis | Non-coding RNA | Saline-alkali and drought stresses induced differential expression of specific microRNAs (miRNAs) in Leymus chinensis, including 15 and 19 altered miRNAs respectively. Key stress-responsive miRNAs like miR319 (downregulated) and miR393 (downregulated under saline-alkali) targeted genes encoding stress-related proteins such as ribulose bisphosphate carboxylase and MYB transcription factors. These findings indicate miRNA-mediated epigenetic regulation underpins L. chinensis adaptation to abiotic stress. | leaf | control; saline-alkali stress; drought | seedling | Zhai et al., 2014 |
Aegilops tauschii | DNA methylation | Bgt infection in Aegilops tauschii suppresses AGO4a expression and reduces AGO4a-associated 24-nt siRNA levels, particularly near transposable elements (TAGs), leading to widespread CHH hypomethylation in differentially methylated regions (DMRs). These hypomethylated TAGs—enriched for stress-response genes like receptor kinases, peroxidases, and pathogenesis-related proteins—show upregulated expression, exemplified by a β-1,3-glucanase defense gene. Virus-induced silencing of DRM2 enhances resistance to Bgt, confirming that dynamic CHH hypomethylation represents an epigenetic regulatory layer in antifungal immunity. | leaf | seedling | Geng et al., 2019 | |
Aegilops tauschii | DNA methylation | This study reveals that while DNA methylation is predominantly conserved across all three sub-genomes of hexaploid wheat and highly stable over evolutionary time, particularly for tri-genome methylated sites compared to the diploid progenitor Aegilops tauschii, significant sub-genome-specific methylation exists. Crucially, such sub-genome-specific promoter methylation correlates with decreased expression of the affected genome. Although altered growth temperature had only a minor global impact on methylation, the identified temperature-sensitive sites were functionally relevant, associated with stress-responsive genes and small expression changes. Transposable elements were consistently hypermethylated. This work establishes sub-genome-specific methylation as a contributor to gene regulation in polyploid wheat. | leaf | seedling | Laura-Jayne et al., 2015 | |
Aegilops tauschii | DNA methylation | Transposable elements (TEs) drive significant epigenetic regulation in Aegilops tauschii, with nearly half of all genes containing TE insertions. These insertions elevate DNA methylation (particularly in introns) and suppress gene expression. Genome-wide methylation profiling revealed high CG (89.7%) and CHG (59.1%) levels, with distinct epigenetic features: 1) Reduced CG methylation near transcriptional start/end sites of expressed genes; 2) Enriched CHG methylation in non-expressed genes; 3) Critical "mCHH islands" flanking gene boundaries, proposed to insulate genes from TE silencing. These results establish TEs as key determinants of methylation-mediated gene regulation. | leaf | seedling | Zhao et al., 2017 | |
Aegilops tauschii | DNA methylation | Reduced chromatin accessibility—not DNA methylation—drives widespread gene expression suppression in hexaploid wheat’s chromosome 3DL compared to its diploid progenitor (Aegilops tauschii 3L). ATAC-seq revealed globally compacted chromatin architecture in the polyploid context, particularly in promoters/5′UTRs, correlating with proportionally reduced expression (70% of syntenic genes expressed at ~40% of diploid levels). Despite similar methylation patterns (CG: 89.9% in wheat vs. 87.1% in Ae. tauschii), differential methylation explained only 11% of expression changes. Chromatin compaction thus emerges as the dominant epigenetic mechanism reprogramming gene expression post-polyploidization. | leaf,root | seedling | Lu et al., 2020 | |
Aegilops tauschii | DNA methylation | DNA methylation heavily targets repetitive elements, particularly retrotransposons (Ty3-gypsy, Ty1-copia) and DNA transposons (CACTA), in the large Triticeae genome. Methylation filtration enriched gene-rich sequences but was less efficient than in smaller genomes like maize, leaving 74.8% repeats. Crucially, despite higher methylation levels, Ty3-gypsy and CACTA elements showed greater transcriptional activity than less methylated Ty1-copia, linked to heterogeneous methylation within these families. Methylation significantly reduced GC content and increased C-to-T transitions, especially in CG/CNG motifs. Active TE transcription, potentially facilitated by comparatively lower global methylation, contributes to genome expansion. | leaf | seedling | Li et al., 2004 | |
Aegilops tauschii | DNA methylation | This study demonstrates that Cot filtration (CF) is a highly effective gene enrichment strategy for wheat, achieving 13.7-fold gene enrichment and a 3-fold reduction in repetitive DNA by exploiting DNA renaturation kinetics rather than epigenetic features like methylation. Unlike methylation filtration (MF)—which relies on differential methylation patterns and only enriched genes 2.2-fold in Aegilops tauschii—CF is independent of methylation status, avoids biases from methylation dynamics during development/stress, and is twice as efficient as MF for wheat gene sequencing. This positions CF as a superior epigenetic-neutral tool for sequencing the wheat gene space. | leaf,root | seedling | Lamoureux, et al., 2005 |
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