ArticleNature genetics2020
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication.
Article in Nature genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 172 papers, 1 of them a synthesis that pooled it.
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172 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
- The heterozygous pineapple genome demonstrates the importance of haplotype-resolved plant genomes.Horticulture research · 2026Article
- Molecular insights and integrated management of Glomerella leaf spot in apple.Horticulture research · 2026Review
- Development of a low-coverage whole genome sequencing screen for apomixis using a diverse set of Malus germplasm.PLoS genetics · 2026Article
- Haplotype-resolved regulation of secondary metabolism in cannabis.Horticulture research · 2026Article
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Article
- Assembly and annotation of the 'Golden Delicious' Doubled-Haploid GDDH18 apple genome.G3 (Bethesda, Md.) · 2026Article
- Article
- Population genomic analysis and genome-wide association mapping of leaf morphology in Phyllanthus emblica L.BMC plant biology · 2026Article
- Identifying the contributions of progenitor Malus species to cultivated apple (M. domestica) using 20K SNP array data.BMC genomics · 2026Article
- A Super-Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution.Plant biotechnology journal · 2026Article
- Haplotype-resolved telomere-to-telomere assembly and haplotype-aware annotation pipeline enable high-quality reannotation of threeHorticulture research · 2026Article
- Genome-Wide Analysis of thePlants (Basel, Switzerland) · 2026Article
- A telomere-to-telomere gap-free genome of the new cultivar 'Zhongtian No. 5', combined with pan-genome analysis, aids in exploration and genetic enhancement of red clover (Horticulture research · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Unveiling genetic diversity and population structure in jackfruit (Artocarpus heterophyllus) through SNP markers for enhanced breeding and conservation.BMC plant biology · 2026Article
- Fine-mapping, candidate gene identification, and marker development for the apple scab resistance gene Rvi2.Journal of experimental botany · 2026Article
- Harnessing genomic resources for passion fruit improvement: Progress and prospects.The plant genome · 2026Review
- Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding.The plant genome · 2026Article
112 more citing papers are in PubMed but not listed here.
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12 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Domestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality.
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