ArticleGigaScience2016
Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica).
Article in GigaScience, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed.
- Haplotype-resolved chromosome-level genome assemblies of nineteen apple (Malus domestica Borkh.) cultivars.Scientific data · 2026Article
- Apple Waste/By-Products and Microbial Resources to Promote the Design of Added-Value Foods: A Review.Foods (Basel, Switzerland) · 2025Review
- Pan-genome analysis reveals the evolution and diversity of Malus.Nature genetics · 2025Article
- A Haplotype-resolved, Chromosome-scale Genome for Malus domestica Borkh. 'WA 38'.G3 (Bethesda, Md.) · 2024Article
- A Chromosome-Level Genome of 'Xiaobaixing' (Plants (Basel, Switzerland) · 2023Article
- Article
- Expression Characteristics in Roots, Phloem, Leaves, Flowers and Fruits of Apple circRNA.Genes · 2022Article
- Research Progress on Genetic Basis of Fruit Quality Traits in Apple (Frontiers in plant science · 2022Review
- A phased, chromosome-scale genome of 'Honeycrisp' apple (GigaByte (Hong Kong, China) · 2022Article
- The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas.Scientific reports · 2021Article
- Study on the differences of gene expression between pear and apple wild cultivation materials based on RNA-seq technique.BMC plant biology · 2021Article
- Genome-Wide Identification of PRP Genes in Apple Genome and the Role ofInternational journal of molecular sciences · 2021Article
- An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals.Frontiers in plant science · 2021Review
- Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication.Nature genetics · 2020Article
- Identification of Phytochrome-Interacting Factor Family Members and Functional Analysis ofInternational journal of molecular sciences · 2020Article
- SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation.Communications biology · 2020Article
- Draft Genome of the European Mouflon (Frontiers in genetics · 2020Article
- Sequencing of a Wild Apple (G3 (Bethesda, Md.) · 2019Article
- A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour.Nature communications · 2019Article
- Insight on Rosaceae Family with Genome Sequencing and Functional Genomics Perspective.BioMed research international · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDomesticated apple (Malus × domestica Borkh) is a popular temperate fruit with high nutrient levels and diverse flavors. In 2012, global apple production accounted for at least one tenth of all harvested fruits. A high-quality apple genome assembly is crucial for the selection and breeding of new cultivars. Currently, a single reference genome is available for apple, assembled from 16.9 × genome coverage short reads via Sanger and 454 sequencing technologies. Although a useful resource, this assembly covers only ~89 % of the non-repetitive portion of the genome, and has a relatively short (16.7 kb) contig N50 length. These downsides make it difficult to apply this reference in transcriptive or whole-genome re-sequencing analyses.
findingsHere we present an improved hybrid de novo genomic assembly of apple (Golden Delicious), which was obtained from 76 Gb (~102 × genome coverage) Illumina HiSeq data and 21.7 Gb (~29 × genome coverage) PacBio data. The final draft genome is approximately 632.4 Mb, representing ~ 90 % of the estimated genome. The contig N50 size is 111,619 bp, representing a 7 fold improvement. Further annotation analyses predicted 53,922 protein-coding genes and 2,765 non-coding RNA genes.
conclusionsThe new apple genome assembly will serve as a valuable resource for investigating complex apple traits at the genomic level. It is not only suitable for genome editing and gene cloning, but also for RNA-seq and whole-genome re-sequencing studies.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.