ArticleProceedings of the National Academy of Sciences of the United States of America2015
Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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97 citing papers in PubMed, 190 citations in OpenAlex.
- Polyploidization Redirects Carbon Flux to Diterpenoid Biosynthesis inPlants (Basel, Switzerland) · 2026Article
- HSP101-encoding NEO-TETRAPLOID RICE FERTILITY GENE 1 regulates tapetum development through interaction with SAPK2 in polyploid rice.Journal of integrative plant biology · 2026Article
- Genomic and population analyses reveal asymmetric subgenome evolution and local adaptation in the polyploid Lycopus lucidus.Communications biology · 2026Article
- Transcriptomic and DNA methylation insights into polyploidy-enhanced heat tolerance in rice (Oryza sativa L.).Plant physiology · 2026Article
- Autopolyploidization-Induced Chromatin Remodeling Regulates Leaf Size Variation in Brassica rapa.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Harnessing polyploidy and nitric oxide for improved arsenic tolerance in Oryza sativa.BMC plant biology · 2025Article
- Characteristics and Molecular Mechanism of Slow Vegetative Growth in Hexaploid Transgenic Poplar 741 With an Insect-Resistance Gene.Plant biotechnology journal · 2025Article
- Comparative phenotypic and transcriptomic analyses reveal the potential molecular basis of forming bigger leaf blade in autotetraploid castor bean.BMC plant biology · 2025Article
- Haplotype-resolved, gap-free genome assemblies provide insights into the divergence between Asian and European pears.Nature genetics · 2025Article
- Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome.Plants (Basel, Switzerland) · 2025Review
- Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi.Molecular horticulture · 2025Article
- Testing the potential of zebularine to induce heritable changes in crop growth and development.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Regional active transcription associates with homoeologous exchange breakpoints in synthetic Brassica tetraploids.Plant physiology · 2024Article
- Chromatin Accessibility and Gene Expression Vary Between a New and Evolved Autopolyploid of Arabidopsis arenosa.Molecular biology and evolution · 2024Article
- Comparative Morphological, Physiological, and Transcriptomic Analyses of Diploid and Tetraploid Wucai (Plants (Basel, Switzerland) · 2024Article
- Differentially methylated genes involved in reproduction and ploidy levels in recent diploidized and tetraploidized Eragrostis curvula genotypes.Plant reproduction · 2024Article
- Gene expression analysis of drought tolerance and cuticular wax biosynthesis in diploid and tetraploid induced wallflowers.BMC plant biology · 2024Article
- The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies.Nature ecology & evolution · 2024Article
- Expression and localization of HPG axis-related genes in Carassius auratus with different ploidy.Frontiers in endocrinology · 2024Article
- In vitro induction of tetraploidy and its effects on phenotypic variations in Populus hopeiensis.BMC plant biology · 2023Article
37 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Polyploidy, or whole-genome duplication (WGD), serves as a key innovation in plant evolution and is an important genomic feature for all eukaryotes. Neopolyploids have to overcome difficulties in meiosis, genomic alterations, changes of gene expression, and epigenomic reorganization. However, the underlying mechanisms for these processes are poorly understood. One of the most interesting aspects is that genome doubling events increase the dosage of all genes. Unlike allopolyploids entangled by both hybridization and polyploidization, autopolyploids, especially artificial lines, in relatively uniform genetic background offer a model system to understand mechanisms of genome-dosage effects. To investigate DNA methylation effects in response to WGD rather than hybridization, we produced autotetraploid rice with its diploid donor, Oryza sativa ssp. indica cv. Aijiaonante, both of which were independently self-pollinated over 48 generations, and generated and compared their comprehensive transcriptomes, base pair-resolution methylomes, and siRNAomes. DNA methylation variation of transposable elements (TEs) was observed as widespread in autotetraploid rice, in which hypermethylation of class II DNA transposons was predominantly noted in CHG and CHH contexts. This was accompanied by changes of 24-nt siRNA abundance, indicating the role of the RNA-directed DNA methylation pathway. Our results showed that the increased methylation state of class II TEs may suppress the expression of neighboring genes in autotetraploid rice that has obtained double alleles, leading to no significant differences in transcriptome alterations for most genes from its diploid donor. Collectively, our findings suggest that chromosome doubling induces methylation variation in TEs that affect gene expression and may become a "genome shock" response factor to help neoautopolyploids adapt to genome-dosage effects.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.