ArticlePlant communications2021
Phasing analysis of the transcriptome and epigenome in a rice hybrid reveals the inheritance and difference in DNA methylation and allelic transcription regulation.
Article in Plant communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 20 citations in OpenAlex.
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Genetic Analysis of Genomic and Methylomic Variation and Identification of Multi-Trait Mutants in Rice Carried on Chang'e-5.Plants (Basel, Switzerland) · 2026Article
- DNA methylation in plant heterosis: mechanisms and prospects.Functional & integrative genomics · 2025Review
- Nei 6 You 7075, a hybrid rice cultivar, exhibits enhanced disease resistance and drought tolerance traits.BMC plant biology · 2024Article
- Allele-specific DNA methylation and gene expression during shoot organogenesis in tissue culture of hybrid poplar.Horticulture research · 2024Article
- Two haplotype-resolved genome assemblies for AAB allotriploid bananas provide insights into banana subgenome asymmetric evolution and Fusarium wilt control.Plant communications · 2024Article
- Paternal DNA methylation is remodeled to maternal levels in rice zygote.Nature communications · 2023Article
- Ribosome profiling reveals the translational landscape and allele-specific translational efficiency in rice.Plant communications · 2023Article
- CG and CHG Methylation Contribute to the Transcriptional Control of OsPRR37-Output Genes in Rice.Frontiers in plant science · 2022Article
- Review
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hybrids are always a focus of botanical research and have a high practical value in agricultural production. To better understand allele regulation and differences in DNA methylation in hybrids, we developed a phasing pipeline for hybrid rice based on two parental genomes (PP2PG), which is applicable for Iso-Seq, RNA-Seq, and Bisulfite sequencing (BS-Seq). Using PP2PG, we analyzed differences in gene transcription, alternative splicing, and DNA methylation in an allele-specific manner between parents and progeny or different progeny alleles. The phasing of Iso-Seq data provided a great advantage in separating the whole gene structure and producing a significantly higher separation ratio than RNA-Seq. The interaction of hybrid alleles was studied by constructing an allele co-expression network that revealed the dominant allele effect in the network. The expression variation between parents and the parental alleles in progeny showed tissue- or environment-specific patterns, which implied a preference for
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