Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish.
ABSTRACT 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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ABSTRACT: Radish (Raphanus sativus L., 2n = 2x = 18) is an economically important vegetable crop worldwide. A large collection of radish expressed sequence tags (ESTs) has been generated but remains largely uncharacterized. In this study, approximately 315,000 ESTs derived from 22 Raphanus cDNA libraries from 18 different genotypes were analyzed, for the purpose of gene and marker discovery and to evaluate large-scale genome duplication and phylogenetic relationships among Raphanus spp. The ESTs were assembled into 85,083 unigenes, of which 90%, 65%, 89% and 89% had homologous sequences in the GenBank nr, SwissProt, TrEMBL and Arabidopsis protein databases, respectively. A total of 66,194 (78%) could be assigned at least one gene ontology (GO) term. Comparative analysis identified 5,595 gene families unique to radish that were significantly enriched with genes related to small molecule metabolism, as well as 12,899 specific to the Brassicaceae that were enriched with genes related to seed oil body biogenesis and responses to phytohormones. The analysis further indicated that the divergence of radish and Brassica rapa occurred approximately 8.9-14.9 million years ago (MYA), following a whole-genome duplication event (12.8-21.4 MYA) in their common ancestor. An additional whole-genome duplication event in radish occurred at 5.1-8.4 MYA, after its divergence from B. rapa. A total of 13,570 simple sequence repeats (SSRs) and 28,758 high-quality single nucleotide polymorphisms (SNPs) were also identified. Using a subset of SNPs, the phylogenetic relationships of eight different accessions of Raphanus was inferred. Comprehensive analysis of radish ESTs provided new insights into radish genome evolution and the phylogenetic relationships of different radish accessions. Moreover, the radish EST sequences and the associated SSR and SNP markers described in this study represent a valuable resource for radish functional genomics studies and breeding.BMC Genomics 10/2013; 14(1):721. · 4.40 Impact Factor
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ABSTRACT: Liriodendron chinense (Hemsl.) Sarg is an endangered species and occupies a pivotal position in phylogenetic studies of flowering plants, while its genomic resources are limited. In this study, we performed transcriptome sequencing for L. chinense petals and leaves using the Illumina paired-end sequencing technique. Approximately 17.02-Gb clean reads were obtained, and de novo assembly generated 87,841 unigenes, with an average length of 778bp. Of these, there were 65,535 (74.61 %) unigenes with significant similarity to publically available plant protein sequences. There were 3,386 genes identified as significant differentially expressed between petals and leaves, among them 2,969 (87.68 %) were up-regulated and 417 (12.31 %) down-regulated in petals. Metabolic pathway analysis revealed that 25 unigenes were predicted to be responsible for the biosynthesis of carotenoids, with 7 genes differentially expressed between these two tissues. This report is the first to identify genes associated with carotenoid biosynthesis in Liriodendron and represents a valuable resource for future genomic studies on the endangered species L. chinense.Gene 11/2013; · 2.20 Impact Factor
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ABSTRACT: Radish (Raphanus sativus L.), is an important root vegetable crop worldwide. Glucosinolates in the fleshy taproot significantly affect the flavor and nutritional quality of radish. However, little is known about the molecular mechanisms underlying glucosinolate metabolism in radish taproots. The limited availability of radish genomic information has greatly hindered functional genomic analysis and molecular breeding in radish. In this study, a high-throughput, large-scale RNA sequencing technology was employed to characterize the de novo transcriptome of radish roots at different stages of development. Approximately 66.11 million paired-end reads representing 73,084 unigenes with a N50 length of 1,095 bp, and a total length of 55.73 Mb were obtained. Comparison with the publicly available protein database indicates that a total of 67,305 (about 92.09% of the assembled unigenes) unigenes exhibit similarity (e --value <= 1.0e-5) to known proteins. The functional annotation and classification including Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the main activated genes in radish taproots are predominately involved in basic physiological and metabolic processes, biosynthesis of secondary metabolite pathways, signal transduction mechanisms and other cellular components and molecular function related terms. The majority of the genes encoding enzymes involved in glucosinolate (GS) metabolism and regulation pathways were identified in the unigene dataset by targeted searches of their annotations. A number of candidate radish genes in the glucosinolate metabolism related pathways were also discovered, from which, eight genes were validated by T-A cloning and sequencing while four were validated by quantitative RT-PCR expression profiling. The ensuing transcriptome dataset provides a comprehensive sequence resource for molecular genetics research in radish. It will serve as an important public information platform to further understanding of the molecular mechanisms involved in biosynthesis and metabolism of the related nutritional and flavor components during taproot formation in radish.BMC Genomics 11/2013; 14(1):836. · 4.40 Impact Factor