ArticleNature communications2023
Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 2 of them syntheses that pooled it.
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Who cites it
29 citing papers in PubMed, 2 syntheses or guidelines pooled it, 60 citations in OpenAlex.
- Meta genetic analysis of melon sweetness.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Pooled it
- Research evolution of flat peach (Frontiers in plant science · 2025Pooled it
- Identification of ZmGLN5, a candidate gene for resistance to Gibberella ear rot in maize.Molecular biology reports · 2026Article
- Pangenomes aid accurate detection of large insertions and deletions from targeted sequencing: the case of cardiomyopathies.Genome medicine · 2026Article
- A chromosome-level genome assembly of Platycladus orientalis and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes.Plant communications · 2026Article
- Pangenome and resequencing analyses reveal flowering evolution and genetic control in Cerasus.Nature communications · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- TaHST2 silencing shapes basal heat tolerance in allohexaploid wheat.Nature plants · 2026Article
- Pangenome Analysis Reveals Structural Variations Associated With Citric Acid Accumulation in Prunus mume.Plant biotechnology journal · 2026Article
- Genome Assembly Revealed MdZAT5 Coordinates Anthocyanin Biosynthesis in Apple Fruit Peel and Flesh by Interacting With MdHY5.Plant biotechnology journal · 2026Article
- OsCPK9-mediated Thr105 phosphorylation activates OsCATC to enhance drought tolerance in rice.Journal of advanced research · 2026Article
- Genomic variation analysis and discovery of stable heterozygous loci in Loquat (Eriobotrya Japonica Lindl.).BMC plant biology · 2026Article
- A pangenome and pantranscriptome of hexaploid oat.Nature · 2026Article
- Pangenome analyses of tea plants reveal structural variations driving gene expression alterations and agronomic trait diversification.Nature communications · 2025Article
- An alpha/beta-hydrolase-like gene (GhABH) is identified to be responsible for fiber quality from a multi-effect quantitative trait locus (QTL) on chromosome A06 of upland cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Studies on the mother flower carnation: past, present, and future.Horticulture research · 2025Article
- Comprehensive Genome-Wide Characterization of L-Type Lectin Receptor-like Kinase (L-LecRLK) Genes in Wheat (Plants (Basel, Switzerland) · 2025Article
- Construction of the super pan-genome for the genusHorticulture research · 2025Article
- An intronic SNP in the Carotenoid Cleavage Dioxygenase 1 (CsCCD1) controls yellow flesh formation in cucumber fruit (Cucumis sativus L.).Plant biotechnology journal · 2025Article
- Pan-genome analysis reveals the evolution and diversity of Malus.Nature genetics · 2025Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structural variations (SVs) and copy number variations (CNVs) contribute to trait variations in fleshy-fruited species. Here, we assemble 10 genomes of genetically diverse Malus accessions, including the ever-green cultivar 'Granny Smith' and the widely cultivated cultivar 'Red Fuji'. Combining with three previously reported genomes, we assemble the pan-genome of Malus species and identify 20,220 CNVs and 317,393 SVs. We also observe CNVs that are positively correlated with expression levels of the genes they are associated with. Furthermore, we show that the noncoding RNA generated from a 209 bp insertion in the intron of mitogen-activated protein kinase homology encoding gene, MMK2, regulates the gene expression and affects fruit coloration. Moreover, we identify overlapping SVs associated with fruit quality and biotic resistance. This pan-genome uncovers possible contributions of CNVs to gene expression and highlights the role of SVs in apple domestication and economically important traits.
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