ArticleGenome biology and evolution2023
Insights into the Evolution of Ohnologous Sequences and Their Epigenetic Marks Post-WGD in Malus Domestica.
Article in Genome biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 8 citations in OpenAlex.
- Molecular Evolution and Expression Analysis of the ADH Gene Family in Apple Bud Mutants.Biology · 2026Article
- Assembly and annotation of the 'Golden Delicious' Doubled-Haploid GDDH18 apple genome.G3 (Bethesda, Md.) · 2026Article
- Genome-wide identification and characterization of theFrontiers in plant science · 2026Article
- Genome-Wide Identification, Evolutionary Expansion, and Expression Analyses of Aux/IAA Gene Family inBiology · 2025Article
- Phytocytokine genes newly discovered in Malus domestica and their regulation in response to Erwinia amylovora and acibenzolar-S-methyl.The plant genome · 2025Article
- doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.Bioinformatics (Oxford, England) · 2025Article
- Accurate Inference of the Polyploid Continuum Using Forward-Time Simulations.Molecular biology and evolution · 2024Article
- Fade into you: genetic control of pigmentation patterns in red-flesh apple (Frontiers in plant science · 2024Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A Whole Genome Duplication (WGD) event occurred several Ma in a Rosaceae ancestor, giving rise to the Maloideae subfamily which includes today many pome fruits such as pear (Pyrus communis) and apple (Malus domestica). This complete and well-conserved genome duplication makes the apple an organism of choice to study the early evolutionary events occurring to ohnologous chromosome fragments. In this study, we investigated gene sequence evolution and expression, transposable elements (TE) density, and DNA methylation level. Overall, we identified 16,779 ohnologous gene pairs in the apple genome, confirming the relatively recent WGD. We identified several imbalances in QTL localization among duplicated chromosomal fragments and characterized various biases in genome fractionation, gene transcription, TE densities, and DNA methylation. Our results suggest a particular chromosome dominance in this autopolyploid species, a phenomenon that displays similarities with subgenome dominance that has only been described so far in allopolyploids.
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