ArticleProceedings of the National Academy of Sciences of the United States of America2025
The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- Dissecting the genetic basis of climatic adaptation in wild relatives (Malus baccata) for climate-resilient apple breeding.Journal of integrative plant biology · 2026Article
- Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.G3 (Bethesda, Md.) · 2026Article
- Ancient wheat DNA: How and what for?Journal, genetic engineering & biotechnology · 2026Article
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- A dual genome-methylome map of clonal evolution in grapevine.Genome biology · 2026Article
- Phased T2T genome of a tetraploid grapevine reveals segmental allopolyploid origin and allele-specific alternative splicing during fruit development.Plant physiology · 2026Article
- Haplotype-Resolved 3D Genomic Landscapes and Their Impacts on Agronomic Traits in Grapevine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Haplotype-resolved T2T genome and population resequencing provide insights into the domestication and mogroside biosynthesis ofHorticulture research · 2026Article
- Hybridization footprint and the mechanism of leaf color differences inHorticulture research · 2026Article
- Kiwifruit genomics and applications: recent advances, current challenges, and future prospects.Horticulture research · 2026Article
- Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in China.Horticulture research · 2026Article
- Pangenome analyses of tea plants reveal structural variations driving gene expression alterations and agronomic trait diversification.Nature communications · 2025Article
- Pangenomics and single-cell transcriptomics uncover the genetic basis of continuous bearing trait in grapevine.Horticulture research · 2025Article
- Phased epigenomics and methylation inheritance in a historical Vitis vinifera hybrid.Genome biology · 2025Article
- Banana breeding by genome design.Journal of integrative plant biology · 2025Review
- The cytonuclear interactions during grapevine domestication.Journal of integrative plant biology · 2025Article
- Mango pangenome reveals dramatic impacts of reference bias on population genomic analyses.Horticulture research · 2025Article
- Chromosome-level reference genome ofHorticulture research · 2025Article
- The dynamics of wildHorticulture research · 2025Article
- The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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Abstract
Hemizygous genes, which are present on only one of the two homologous chromosomes of diploid organisms, have been mainly studied in the context of sex chromosomes and sex-linked genes. However, these genes can also occur on the autosomes of diploid plants due to structural variants (SVs), such as a deletion/insertion of one allele, and this phenomenon largely unexplored in plants. Here, we investigated the genomic and epigenomic landscapes of hemizygous genes across 22 genomes with varying propagation histories: eleven clonal lineages, seven outcrossed samples, and four inbred and putatively homozygous genomes. We identified SVs leading to genic hemizygosity. As expected, very few genes (0.01 to 1.2%) were hemizygous in the homozygous genomes, representing negative controls. Hemizygosity was appreciable among outcrossed lineages, averaging 8.7% of genes, but consistently elevated for the clonal samples at 13.8% genes, likely reflecting heterozygous SV accumulation during clonal propagation. Compared to diploid genes, hemizygous genes were more often situated in centromeric than telomeric regions and experienced weaker purifying selection. They also had reduced levels of expression, averaging ~20% of the expression levels of diploid genes, violating the evolutionary model of dosage compensation. We also detected higher DNA methylation levels in hemizygous genes and transposable elements, which may contribute to their reduced expression. Finally, expression profiles showed that hemizygous genes were more specifically expressed in contexts related to fruit development, organ differentiation, and stress responses. Overall, hemizygous genes accumulate in clonally propagated lineages and display distinct genetic and epigenetic features compared to diploid genes, shedding unique insights into genetic studies and breeding programs of clonal crops.
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