ArticleNature communications2019
A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 222 papers.
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222 citing papers in PubMed.
- Genome evolution of Mediterranean olives following DNA repeats diversification.The plant genome · 2026Article
- The heterozygous pineapple genome demonstrates the importance of haplotype-resolved plant genomes.Horticulture research · 2026Article
- A 32-bp deletion inHorticulture research · 2026Article
- Candidate genes with antagonistic roles in stomatal development are associated with population-wide variation in apple.Horticulture research · 2026Article
- Multifaceted mechanisms underlying species- and cultivar-associated differential anthocyanin accumulation in fruits.Horticulture research · 2026Article
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- Pangenome analysis reveals the genetic mechanism underlying high-altitude adaptation in Qinghai-Xizang (Tibet) Plateau Rhododendron.Journal of integrative plant biology · 2026Article
- De novo chromosome-level genome assembly and annotation of the Muscovy duck (Cairina moschata).Poultry science · 2026Article
- Assembly and comparative analysis of the complete mitochondrial genome of Polygonatum odoratum (Yuzhu), a medicine-food homologous plant.BMC plant biology · 2026Article
- Genome evolution and transposable element expansion reveal host-associated genomic features in Cladosporium cucumerinum.Communications biology · 2026Article
- Genome-wide association study combined with multi-assay phenotyping identifies a novel anthracnose resistance locus in apple.BMC plant biology · 2026Article
- Identifying the contributions of progenitor Malus species to cultivated apple (M. domestica) using 20K SNP array data.BMC genomics · 2026Article
- Expression dynamics of starch and proanthocyanidin biosynthesis genes during Quercus glauca fruit development.BMC plant biology · 2026Article
- Characterization of the mitochondrial genome of the aquatic vegetable Eleocharis dulcis (Burm. f.) Trin. ex Hensch.: the first representative of genus Eleocharis with evolutionary insights in Cyperaceae.BMC plant biology · 2026Article
- The gene-like promoter and transcription of LTR retrotransposons.bioRxiv : the preprint server for biology · 2026Article
- Chromosome-level genome assembly of Youngia japonica reveals evolutionary dynamics underlying adaptation in a synanthropic Asteraceae species.BMC plant biology · 2026Article
- Pangenome Analysis Reveals Structural Variations Associated With Citric Acid Accumulation in Prunus mume.Plant biotechnology journal · 2026Article
- Fine-mapping, candidate gene identification, and marker development for the apple scab resistance gene Rvi2.Journal of experimental botany · 2026Article
- panHiTE: A comprehensive and accurate pipeline for TE detection in large-scale population genomes.Plant communications · 2026Article
162 more citing papers are in PubMed but not listed here.
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Authors and funding
21 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A complete and accurate genome sequence provides a fundamental tool for functional genomics and DNA-informed breeding. Here, we assemble a high-quality genome (contig N50 of 6.99 Mb) of the apple anther-derived homozygous line HFTH1, including 22 telomere sequences, using a combination of PacBio single-molecule real-time (SMRT) sequencing, chromosome conformation capture (Hi-C) sequencing, and optical mapping. In comparison to the Golden Delicious reference genome, we identify 18,047 deletions, 12,101 insertions and 14 large inversions. We reveal that these extensive genomic variations are largely attributable to activity of transposable elements. Interestingly, we find that a long terminal repeat (LTR) retrotransposon insertion upstream of MdMYB1, a core transcriptional activator of anthocyanin biosynthesis, is associated with red-skinned phenotype. This finding provides insights into the molecular mechanisms underlying red fruit coloration, and highlights the utility of this high-quality genome assembly in deciphering agriculturally important trait in apple.
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