Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish

Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
Plant Cell Reports (Impact Factor: 3.07). 04/2012; 31(8):1437-47. DOI: 10.1007/s00299-012-1259-3
Source: PubMed


The tuberous root of radish is an important vegetable, but insufficient transcriptomic and genomic data are currently available to understand the molecular mechanisms underlying tuberous root formation and development. High-throughput transcriptomic sequencing is essential to generate a large transcript sequence data set for gene discovery and molecular marker development. In this study, a total of 107.3 million clean reads were generated using Illumina paired-end sequencing technology. De novo assembly generated 61,554 unigenes with an average length of 820 bp. Based on a sequence similarity search with known proteins or nucleotides, 85.51 % (52,634), 90.18 % (55,507) and 54 % (33,242) consensus sequences showed homology with sequences in the Nr, Nt and Swiss-Prot databases, respectively. Of these annotated unigenes, 21,109 and 17,343 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. A total of 27,809 unigenes were assigned to 123 pathways in the Kyoto Encyclopedia of Genes and Genomes database. Analysis of transcript differences between libraries from the early and late seedling developmental stages demonstrated that starch and sucrose metabolism and phenylpropanoid biosynthesis may be the dominant metabolic events during tuberous root formation and plant hormones probably play critical roles in regulation of this developmental process. In total, 14,641 potential EST-SSRs were identified among the unigenes, and 12,733 primer pairs for 2,511 SSR were obtained. Summarily, this study gave us a clue to understand the radish tuberous root formation and development, and also provided us with a valuable sequence resource for novel gene discovery and marker-assisted selective breeding in radish. KEY MESSAGE: De novo assembled and characterized the radish tuberous root transcriptome; explored the mechanism of radish tuberous root formation; development of EST-SSR markers in radish.

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    • "RNA-Seq has been leveraged with de novo transcriptome assembly to learn about plant innovations including parasitism4567and C4 photosynthesis[8], plant processes including fruit ripening[9], drought response[10], and flavonoid biosynthesis[11], chemical defenses[12], and the evolution of sex chromosomes[13]. The recent boom of RNA-Seq studies involving de novo assembly has motivated innovations in assemblers developed specifically for RNA-Seq data (Velvet[14,15], Oases[16,17](includes Velvet[18]), SOAPdenovo1920212223242526272829, SOAPdenovo- Trans[30], CLC[31], ABySS[32], Trinity[5,13,333435363738). Comparison of de novo transcriptome assembler performance is hindered by lack of widely used standard quality metrics[39]or rigorous evaluation of a comprehensive selection of assemblers with a transcriptome from a high quality reference genome. "
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    Full-text · Article · Jan 2016 · PLoS ONE
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    • "Fortunately , with the advent of next-generation sequencing (NGS) technology in recent years, genomic information in previously uncharacterized systems can be generated (Grabherr et al. 2011). Currently, high-throughput RNA sequencing (RNA-Seq) has emerged as a powerful and cost-efficient tool for transcriptome analysis, and it has also been used for transcript profiling in various nonmodel plant species, including potato (Solanum tuberosum L.) (Zhang et al. 2014), pennycress (Thlaspi arvense) (Dorn et al. 2013), sweet potato (Ipomoea batatas) (Firon et al. 2013) and radish (Raphanus sativus L.) (Wang et al. 2012a). "
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    • "After removing the reads with adaptors, reads with unknown nucleotides larger than 5% and low quality reads, 66,110,340 clean PE reads consisting of 5,949,930,600 nucleotides (nt) were obtained with an average GC content of 47.34% (Table 1). The output was similar to a previous study on radish transcriptome from two root cDNA libraries, which generated a total of 53.6 million and 53.7 million clean reads, respectively [13]. All high-quality clean reads were assembled into 150,455 contigs with an average length of 299 bp, and the length distribution of the assembled contigs was as shown in Additional file 1A. "
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    Full-text · Article · Nov 2013 · BMC Genomics
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