ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2015
Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 70 citations in OpenAlex.
- Identification of a gene coding for a pentatricopeptide repeat protein as a candidate responsible for theMolecular breeding : new strategies in plant improvement · 2025Article
- Purification and Characterization of α-Mannosidase from Onion,Journal of applied glycoscience · 2024Article
- Comparative mitochondrial genome analysis reveals a candidate ORF for cytoplasmic male sterility in tropical onion.3 Biotech · 2024Article
- Turning Garlic into a Modern Crop: State of the Art and Perspectives.Plants (Basel, Switzerland) · 2023Review
- Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion.Frontiers in plant science · 2023Article
- Article
- Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (Plants (Basel, Switzerland) · 2021Article
- Insights from the first genome assembly of Onion (Allium cepa).G3 (Bethesda, Md.) · 2021Article
- Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling.Scientific reports · 2021Article
- Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper.BMC plant biology · 2021Article
- Comprehensive Transcriptome and Metabolic Profiling of Petal Color Development inFrontiers in plant science · 2021Article
- TGFam-Finder: a novel solution for target-gene family annotation in plants.The New phytologist · 2020Article
- Construction of an Onion (Plants (Basel, Switzerland) · 2020Article
- Transposition of a non-autonomous DNA transposon in the gene coding for a bHLH transcription factor results in a white bulb color of onions (Allium cepa L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Omics approaches inPeerJ · 2020Article
- FunctionalFrontiers in plant science · 2020Article
- Transcriptome Analysis and Metabolic Profiling ofBiology · 2019Article
- Comparative Tyramide-FISH mapping of the genes controlling flavor and bulb color in Allium species revealed an altered gene order.Scientific reports · 2019Article
- The Power of GenomicPlants (Basel, Switzerland) · 2019Article
- SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing.PloS one · 2018Article
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12 authors at 5 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp.
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