ArticlePlant physiology2024
High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar.
Article in Plant physiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Article
- Mapping structural variants in Populus tomentosa reveals adaptive signatures and improves prediction of wood properties.Nature communications · 2026Article
- Artificial Intelligence Methods in Forest Biotechnology: Current Status and Future Prospects.International journal of molecular sciences · 2026Review
- PcabHLH58/PcabHLH151 regulates adventitious root development and nitrogen uptake in poplar.Nature communications · 2026Article
- Identification and intra-genus conservation analysis of non-conventional peptides in hybrid poplar 84K.Forestry research · 2026Article
- Inheritance of DNA Methylation Patterns and Its Role in Modulating Allelic Expression inPlants (Basel, Switzerland) · 2025Article
- Natural variants ofScience advances · 2025Article
- A near-complete reassembled haplotype-resolved reference genome of Acer truncatum.Scientific data · 2025Article
- Diploid assembly of the Mexican lime genome.G3 (Bethesda, Md.) · 2025Article
- Chromosome-level and haplotype resolved genome assembly of Populus × euramericana cv. '74/76'.Scientific data · 2025Article
- Characterization and Role of AP2/EREBP Genes with Decreasing Expression During Leaf Development in 84K Poplar.Plants (Basel, Switzerland) · 2025Article
- A visual monitoring DNA-free multi-gene editing system excised via LoxP::FRT/FLP in poplar.Plant biotechnology journal · 2025Article
- Genomic selection for growth and wood properties in multi-generation hybrid populations ofHorticulture research · 2025Article
- A nearly complete haplotype-phased genome assembly of nerve plant (Horticulture research · 2025Article
- A gap-free reference genome of Populus deltoides provides insights into karyotype evolution of Salicaceae.BMC biology · 2025Article
- Synergistic optimization enhancing the precision and efficiency of cytosine base editors in poplar.Communications biology · 2025Article
- Potential risk of dipterocarps in the marginal Asian rainforests: low population size and high genomic erosion.BMC biology · 2025Article
- Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus.Genome research · 2025Article
- Chromosome-scale and haplotype-resolved genome assembly ofHorticulture research · 2025Article
- Genome-Wide Identification and Functional Analysis ofInternational journal of molecular sciences · 2025Article
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23 authors.
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Abstract
Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid "84K" (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.
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