ArticleBMC genomics2011
De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed.
- Transcriptome dataset of different carrot genotypes during various developmental stages of callus.Data in brief · 2026Article
- Cell-Type Specific miRNA Regulatory Network Responses to ABA Stress Revealed by Time Series Transcriptional Atlases in Arabidopsis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots.Nature plants · 2023Article
- De novo transcriptome analysis and identification of defensive genes in garlic (Allium sativum L.) using high-throughput sequencing.Journal, genetic engineering & biotechnology · 2023Article
- CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota).Database : the journal of biological databases and curation · 2022Article
- Single-Cell RNA Sequencing for Plant Research: Insights and Possible Benefits.International journal of molecular sciences · 2022Review
- Origin, evolution, breeding, and omics of Apiaceae: a family of vegetables and medicinal plants.Horticulture research · 2022Article
- Article
- Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies.International journal of molecular sciences · 2021Review
- Mantis: flexible and consensus-driven genome annotation.GigaScience · 2021Article
- A de novo transcriptome analysis revealed that photomorphogenic genes are required for carotenoid synthesis in the dark-grown carrot taproot.Molecular genetics and genomics : MGG · 2020Article
- Insights into genetic diversity and population structure of Indian carrot (Daucus carota L.) accessions.Journal of applied genetics · 2020Article
- Article
- Classification of "Kintoki ninjin" and other groups of carrot (Breeding science · 2019Article
- A draft genome assembly of halophyte Suaeda aralocaspica, a plant that performs C4 photosynthesis within individual cells.GigaScience · 2019Article
- Selection of reference genes for flowering pathway analysis in the masting plants, Celmisia lyallii and Chionochloa pallens, under variable environmental conditions.Scientific reports · 2019Article
- De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing.Scientific reports · 2019Article
- Identification of an SCPL Gene Controlling Anthocyanin Acylation in Carrot (Frontiers in plant science · 2019Article
- Advances in research on the carrot, an important root vegetable in the Apiaceae family.Horticulture research · 2019Review
- iTRAQ-Based Quantitative Proteomics and Transcriptomics Provide Insights Into the Importance of Expansins During Root Development in Carrot.Frontiers in genetics · 2019Article
28 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAmong next generation sequence technologies, platforms such as Illumina and SOLiD produce short reads but with higher coverage and lower cost per sequenced nucleotide than 454 or Sanger. A challenge now is to develop efficient strategies to use short-read length platforms for de novo assembly and marker development. The scope of this study was to develop a de novo assembly of carrot ESTs from multiple genotypes using the Illumina platform, and to identify polymorphisms.
resultsA de novo assembly of transcriptome sequence from four genetic backgrounds produced 58,751 contigs and singletons. Over 50% of these assembled sequences were annotated allowing detection of transposable elements and new carrot anthocyanin genes. Presence of multiple genetic backgrounds in our assembly allowed the identification of 114 computationally polymorphic SSRs, and 20,058 SNPs at a depth of coverage of 20× or more. Polymorphisms were predominantly between inbred lines except for the cultivated x wild RIL pool which had high intra-sample polymorphism. About 90% and 88% of tested SSR and SNP primers amplified a product, of which 70% and 46%, respectively, were of the expected size. Out of verified SSR and SNP markers 84% and 82% were polymorphic. About 25% of SNPs genotyped were polymorphic in two diverse mapping populations.
conclusionsThis study confirmed the potential of short read platforms for de novo EST assembly and identification of genetic polymorphisms in carrot. In addition we produced the first large-scale transcriptome of carrot, a species lacking genomic resources.
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