Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.)

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.

• Publication year

  2014

• Venue

  DNA Research

• Publication date

  2014-10-31

• Fields of study

  Biology, Medicine, Materials Science, Environmental Science

• Identifiers
  DOI 10.1093/dnares/dsu035PMID 25362073PMCID 4379974
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Transcriptome analyses and differential gene expression in a non-model fish species with alternative mating tactics

  2014cited by this paper
• InterProScan 5: genome-scale protein function classification

  2014cited by this paper
• Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

  2014cited by this paper
• Assessment of transcript reconstruction methods for RNA-seq

  2013cited by this paper
• Long noncoding RNAs regulate adipogenesis

  2013cited by this paper
• Transcriptome sequencing to produce SNP-based genetic maps of onion

  2013cited by this paper
• De Novo Transcriptome Assembly in Chili Pepper (Capsicum frutescens) to Identify Genes Involved in the Biosynthesis of Capsaicinoids

  2013cited by this paper
• A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration

  2013cited by this paper
• Sequencing and De Novo Assembly of the Asian Clam (Corbicula fluminea) Transcriptome Using the Illumina GAIIx Method

  2013cited by this paper
• De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana

  2013cited by this paper
• Sequence assembly demystified

  2013cited by this paper
• The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

  2013cited by this paper
• Transcript Assembly and Quantification by RNA-Seq Reveals Differentially Expressed Genes between Soft-Endocarp and Hard-Endocarp Hawthorns

  2013cited by this paper
• Transcriptome Sequencing and Expression Analysis of Terpenoid Biosynthesis Genes in Litsea cubeba

  2013cited by this paper
• Transcriptome Analysis of Litopenaeus vannamei in Response to White Spot Syndrome Virus Infection

  2013cited by this paper
• Activities at the Universal Protein Resource (UniProt)

  2013cited by this paper
• Next generation sequencing and de novo transcriptome analysis of Costus pictus D. Don, a non-model plant with potent anti-diabetic properties

  2012cited by this paper
• De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes

  2012cited by this paper
• Update on activities at the Universal Protein Resource (UniProt) in 2013

  2012cited by this paper
• SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

  2012cited by this paper
• Current challenges in de novo plant genome sequencing and assembly

  2012cited by this paper
• De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing

  2012cited by this paper
• A beginner's guide to eukaryotic genome annotation

  2012cited by this paper
• A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

  2012cited by this paper
• Fast gapped-read alignment with Bowtie 2

  2012cited by this paper
• Control of somatic tissue differentiation by the long non-coding RNA TINCR

  2012cited by this paper
• The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

  2012cited by this paper
• Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

  2012cited by this paper
• Analyses of pig genomes provide insight into porcine demography and evolution

  2012cited by this paper
• RNA sequencing: advances, challenges and opportunities

  2011cited by this paper
• Next-generation transcriptome assembly

  2011cited by this paper
• RNA-Seq improves annotation of protein-coding genes in the cucumber genome

  2011cited by this paper
• Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing

  2011cited by this paper
• NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

  2011cited by this paper
• Defining the Transcriptome Assembly and Its Use for Genome Dynamics and Transcriptome Profiling Studies in Pigeonpea (Cajanus cajan L.)

  2011cited by this paper
• High-throughput illumina strand-specific RNA sequencing library preparation.

  2011cited by this paper
• Computational methods for transcriptome annotation and quantification using RNA-seq

  2011cited by this paper
• Genome sequencing and analysis of the model grass Brachypodium distachyon

  2010cited by this paper
• Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq.

  2010cited by this paper
• De Novo Transcriptome Sequencing in Anopheles funestus Using Illumina RNA-Seq Technology

  2010cited by this paper
• The genome of the cucumber, Cucumis sativus L.

  2009cited by this paper
• The Sorghum bicolor genome and the diversification of grasses

  2009cited by this paper
• Additional file 6

  2009cited by this paper
• The Sequence Alignment/Map format and SAMtools

  2009cited by this paper
• Annotating genomes with massive-scale RNA sequencing

  2008cited by this paper
• Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

  2008cited by this paper
• Onions: a source of unique dietary flavonoids.

  2007cited by this paper
• AUGUSTUS: ab initio prediction of alternative transcripts

  2006cited by this paper
• The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information

  2005cited by this paper
• Automated generation of heuristics for biological sequence comparison

  2005cited by this paper
• Total phenol, flavonoid, proanthocyanidin and vitamin C levels and antioxidant activities of Mauritian vegetables

  2004cited by this paper
• Varietal differences in phenolic content and antioxidant and antiproliferative activities of onions.

  2004cited by this paper
• Onions and Other Vegetable Alliums

  1994cited by this paper

• Analysis of crossover frequency and development of an optimal marker set for cultivar identification using a high-resolution linkage map in onion (Allium cepa L.)

  2026cites this paper
• Identification of a gene coding for a pentatricopeptide repeat protein as a candidate responsible for the Ms2, a novel restorer-of-fertility locus in onion (Allium cepa L.)

  2025cites this paper
• Purification and Characterization of α-Mannosidase from Onion, Allium cepa

  2024cites this paper
• Recent Advances in Molecular Genetics of Onion

  2024cites this paper
• Turning Garlic into a Modern Crop: State of the Art and Perspectives

  2023cites this paper
• Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion

  2023cites this paper
• Genetic analysis of the interaction between G and R loci involved in the determination of bulb colors in onion (Allium cepa L.)

  2023cites this paper
• Comparative mitochondrial genome analysis reveals a candidate ORF for cytoplasmic male sterility in tropical onion

  2023cites this paper
• Using Transcriptome Analysis to Explore Gray Mold Resistance-Related Genes in Onion (Allium cepa L.)

  2022cites this paper
• Systematic Identification and Validation of Housekeeping and Tissue-Specific Genes in Allotetraploid Chenopodium quinoa

  2021cites this paper
• Identification of Ms2, a novel locus controlling male-fertility restoration of cytoplasmic male-sterility in onion (Allium cepa L.), and development of tightly linked molecular markers

  2021cites this paper
• Genotyping-by-Sequencing Derived Genetic Linkage Map and Quantitative Trait Loci for Sugar Content in Onion (Allium cepa L.)

  2021cites this paper
• Construction of a high-resolution linkage map and chromosomal localization of the loci determining major qualitative traits in onion (Allium cepa L.)

  2021cites this paper
• Insights from the first genome assembly of Onion (Allium cepa)

  2021cites this paper
• Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper

  2021influential citation
• Development of Single Nucleotide Polymorphism Markers Linked to Quantitative Trait Loci Controlling Anthocyanin Content in Red Bulb Onion (Allium cepa L.)

  2021cites this paper
• Identification of a novel haplotype of the Ms locus controlling restoration of male-fertility and its implication in origination of cytoplasmic male-sterility in onion (Allium cepa L.)

  2021cites this paper
• Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling

  2021cites this paper
• Comprehensive Transcriptome and Metabolic Profiling of Petal Color Development in Lycoris sprengeri

  2021cites this paper
• Omics approaches in Allium research: Progress and way ahead

  2020cites this paper
• Functional Allium fistulosum Centromeres Comprise Arrays of a Long Satellite Repeat, Insertions of Retrotransposons and Chloroplast DNA

  2020cites this paper
• tgfam‐finder: a novel solution for target‐gene family annotation in plants

  2020cites this paper
• Construction of an Onion (Allium cepa L.) Genetic Linkage Map Using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and Content

  2020influential citation
• Construction of a linkage map flanking the I locus controlling dominant white bulb color and analysis of differentially expressed genes between dominant white and red bulbs in onion (Allium cepa L.)

  2020cites this paper
• Transcriptome Analysis and Metabolic Profiling of Lycoris Radiata

  2019cites this paper
• 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.)

  2019cites this paper
• The Power of Genomic in situ Hybridization (GISH) in Interspecific Breeding of Bulb Onion (Allium cepa L.) Resistant to Downy Mildew (Peronospora destructor [Berk.] Casp.)

  2019cites this paper
• Interplay between Jasmonic Acid, Phosphate Signaling and the Regulation of Glycerolipid Homeostasis in Arabidopsis.

  2019cites this paper
• Comparative Tyramide-FISH mapping of the genes controlling flavor and bulb color in Allium species revealed an altered gene order

  2019cites this paper
• Genetics of bulb colour variation and flavonoids in onion

  2018cites this paper
• Impact of the Allium Genomes on Plant Breeding

  2018cites this paper
• TGFam-Finder: An optimal solution for target-gene family annotation in eukaryotic genomes

  2018cites this paper
• Gene Family Evolution in Allium Species

  2018cites this paper
• Molecular Mapping of Genes and QTL: Progress to Date and Development of New Population Resources for NGS Genetics

  2018cites this paper
• SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing

  2018cites this paper
• Multiple reference genome sequences of hot pepper reveal the massive evolution of plant disease resistance genes by retroduplication

  2017cites this paper
• Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination

  2017cites this paper
• Selection and validation of reference genes for quantitative real-time PCR analysis under different experimental conditions in the leafminer Liriomyza trifolii (Diptera: Agromyzidae)

  2017cites this paper
• Tat-protein disulfide-isomerase A3: a possible candidate for preventing ischemic damage in the spinal cord

  2017cites this paper
• New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication

  2017cites this paper
• Development of a molecular marker tightly linked to the C locus conferring a white bulb color in onion (Allium cepa L.) using bulked segregant analysis and RNA-Seq

  2017cites this paper
• Persistent Shallot virus X infection correlates with transcriptional repression of plant cell RNA-dependent RNA polymerase and DCL proteins in plant roots

  2017cites this paper
• Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit development

  2017cites this paper
• Enhancing onion breeding using molecular tools

  2016cites this paper
• Construction of a draft reference transcripts of onion (Allium cepa) using long-read sequencing

  2016cites this paper
• Development of a simple PCR marker tagging the Allium roylei fragment harboring resistance to downy mildew (Peronospora destructor) in onion (Allium cepa L.)

  2016cites this paper
• Completion of the mitochondrial genome sequence of onion (Allium cepa L.) containing the CMS-S male-sterile cytoplasm and identification of an independent event of the ccmFN gene split

  2016cites this paper
• Doubled Haploid ‘CUDH2107’ as a Reference for Bulb Onion (Allium cepa L.) Research: Development of a Transcriptome Catalogue and Identification of Transcripts Associated with Male Fertility

  2016cites this paper
• Lessons from 25 years of genetic mapping in onion, where next?

  2016cites this paper
• De Novo Assembly and Annotation of the Chinese Chive (Allium tuberosum Rottler ex Spr.) Transcriptome Using the Illumina Platform

  2015cites this paper
• An RNA-Seq-based reference transcriptome for Citrus.

  2015cites this paper
• DNA Sequencing, Other Omics and Synthetic Biology

  2015cites this paper
• Plant Breeding in the Omics Era

  2015cites this paper
• Major Quantitative Trait Loci and Putative Candidate Genes for Powdery Mildew Resistance and Fruit-Related Traits Revealed by an Intraspecific Genetic Map for Watermelon (Citrullus lanatus var. lanatus)

  2015cites this paper
• De novo assembly and characterization of the Welsh onion (Allium fistulosum L.) transcriptome using Illumina technology

  2015cites this paper
• Identification of candidate genes associated with fertility restoration of cytoplasmic male-sterility in onion (Allium cepa L.) using a combination of bulked segregant analysis and RNA-seq

  2015cites this paper