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.
Molecular Breeding 01/2014; DOI:10.1007/s11032-014-0148-6 · 2.28 Impact Factor
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ABSTRACT: Seashore paspalum (Paspalum vaginatum O. Swartz) is a halophytic warm-season perennial grass, which plays an important role in protection of environment. However, very limited transcriptomic and genomic information are currently available for seashore paspalum. In this study, the seashore paspalum transcriptome were sequenced using Illumina paired-end sequencing technology. In total, 32,603 unigenes with an average length of 970 bp were obtained by de novo assembly. Of the unigenes, 25,411 unigenes (77.94 %) had significant similarity with known proteins in the NCBI non-redundant protein and Swiss-Prot databases. Of these annotated unigenes, 20,962 and 10,620 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. A total of 4,699 unigenes were mapped into 118 Kyoto Encyclopedia of Genes and Genomes pathways. In addition, 3,010 potential simple sequence repeats (SSRs) were predicted for microsatellite analyse. Tri-nucleotide was the dominant repeat (1,583, 52.58 %), followed by di-nucleotide (975, 32.39 %) and tetra-nucleotide (217, 7.21 %). Fifty SSR sites were randomly selected for validation and development of EST–SSR markers. This study provided the global sequence data for seashore paspalum and demonstrated that the Illumina paired-end sequencing is a fast and cost-effective approach to gene discovery and molecular marker development.Genes & genomics 01/2015; 37(1). DOI:10.1007/s13258-014-0231-8 · 0.57 Impact Factor
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ABSTRACT: Ipomoea nil is widely used as an ornamental plant due to its abundance of flower color, but the limited transcriptome and genomic data hinder research on it. Using illumina platform, transcriptome profiling of I. nil was performed through high-throughput sequencing, which was proven to be a rapid and cost-effective means to characterize gene content. Our goal is to use the resulting information to facilitate the relevant research on flowering and flower color formation in I. nil. In total, 268 million unique illumina RNA-Seq reads were produced and used in the transcriptome assembly. These reads were assembled into 220,117 contigs, of which 137,307 contigs were annotated using the GO and KEGG database. Based on the result of functional annotations, a total of 89,781 contigs were assigned 455,335 GO term annotations. Meanwhile, 17,418 contigs were identified with pathway annotation and they were functionally assigned to 144 KEGG pathways. Our transcriptome revealed at least 55 contigs as probably flowering-related genes in I. nil, and we also identified 25 contigs that encode key enzymes in the phenylpropanoid biosynthesis pathway. Based on the analysis relating to gene expression profiles, in the phenylpropanoid biosynthesis pathway of I. nil, the repression of lignin biosynthesis might lead to the redirection of the metabolic flux into anthocyanin biosynthesis. This may be the most likely reason that I. nil has high anthocyanins content, especially in its flowers. Additionally, 15,537 simple sequence repeats (SSRs) were detected using the MISA software, and these SSRs will undoubtedly benefit future breeding work. Moreover, the information uncovered in this study will also serve as a valuable resource for understanding the flowering and flower color formation mechanisms in I. nil.MGG Molecular & General Genetics 04/2015; DOI:10.1007/s00438-015-1034-6 · 2.83 Impact Factor