ArticleNature genetics2025
Pan-genome analysis reveals the evolution and diversity of Malus.
Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges.Molecular biology and evolution · 2026Article
- Dissecting the genetic basis of climatic adaptation in wild relatives (Malus baccata) for climate-resilient apple breeding.Journal of integrative plant biology · 2026Article
- The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.Advanced genetics (Hoboken, N.J.) · 2026Article
- Pan-species genome-wide evolution of the RGF peptide gene family and its impact on adventitious root regeneration in apple.Horticulture research · 2026Article
- Regulatory insights underlying apple to cold stress.Horticulture research · 2026Article
- Haplotype‑resolved comparison of transcription factor superfamilies between wild and cultivated autotetraploid green jujube and prioritization of candidate transcription factors via machine learning.The plant genome · 2026Article
- Pangenome and resequencing analyses reveal flowering evolution and genetic control in Cerasus.Nature communications · 2026Article
- BAT: an integrated pipeline for gene tree construction, annotation, and functional inference.bioRxiv : the preprint server for biology · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Pangenome Analysis Reveals Structural Variations Associated With Citric Acid Accumulation in Prunus mume.Plant biotechnology journal · 2026Article
- MT@SiOPlant biotechnology journal · 2026Article
- Dynamics of genome evolution in the era of pangenome analysis.Cell genomics · 2026Review
- Phylogenomic profile of exon-intron organization across angiosperms, their relationships with protein domains, and functional implications.Nature communications · 2026Article
- Pan-genomics of polyploid crops: from complexity to breeding.Frontiers in plant science · 2026Review
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2026Article
- 2b-RAD sequencing of Malus florentina populations reveals strong population structure and signals of balancing selection at disease resistance loci.BMC plant biology · 2025Article
- Article
- Transcriptomic and Metabolic Profiles of Apple Peels of Different Colors.Plants (Basel, Switzerland) · 2025Article
- Nuclear phylogeny of Malus with increased sampling provides new insights into biogeography and character evolution.BMC plant biology · 2025Article
- Multidimensional Transcriptomics Reveals the Key Genes and Pathways Regulating the Acidity of Apples.Current issues in molecular biology · 2025Article
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Authors and funding
27 authors.
Funding
Abstract
Malus Mill., a genus of temperate perennial trees with great agricultural and ecological value, has diversified through hybridization, polyploidy and environmental adaptation. Limited genomic resources for wild Malus species have hindered the understanding of their evolutionary history and genetic diversity. We sequenced and assembled 30 high-quality Malus genomes, representing 20 diploids and 10 polyploids across major evolutionary lineages and geographical regions. Phylogenomic analyses revealed ancient gene duplications and conversions, while six newly defined genome types, including an ancestral type shared by polyploid species, facilitated the detection of strong signals for extensive introgressions. The graph-based pan-genome captured shared and species-specific structural variations, facilitating the development of a molecular marker for apple scab resistance. Our pipeline for analyzing selective sweep identified a mutation in MdMYB5 having reduced cold and disease resistance during domestication. This study advances Malus genomics, uncovering genetic diversity and evolutionary insights while enhancing breeding for desirable traits.
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