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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., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Transposable elements (TEs) are major components of eukaryotic genomes and represent approximately 45% of the human genome. TEs can be important sources of novelty in genomes and there is increasing evidence that TEs contribute to the evolution of gene regulation in mammals. Gene duplication is an evolutionary mechanism that also provides new genetic material and opportunities to acquire new functions. To investigate how duplicated genes are maintained in genomes, here, we explored the TE environment of duplicated and singleton genes. We found that singleton genes have more short-interspersed nuclear elements and DNA transposons in their vicinity than duplicated genes, whereas long-interspersed nuclear elements and long-terminal repeat retrotransposons have accumulated more near duplicated genes. We also discovered that this result is highly associated with the degree of essentiality of the genes with an unexpected accumulation of short-interspersed nuclear elements and DNA transposons around the more-essential genes. Our results underline the importance of taking into account the TE environment of genes to better understand how duplicated genes are maintained in genomes., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)