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The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing.

ABSTRACT: BACKGROUND: Illumina second generation sequencing is now an efficient route for generating enormous sequence collections that represent expressed genes and quantitate expression level. Taxus is a world-wide endangered gymnosperm genus and forms an important anti-cancer medicinal resource, but the large and complex genomes of Taxus have hindered the development of genomic resources. The research of its tissue-specific transcriptome is absent. There is also no study concerning the association between the plant transcriptome and metabolome with respect to the plant tissue type. METHODOLOGY/PRINCIPAL FINDINGS: We performed the de novo assembly of Taxus mairei transcriptome using Illumina paired-end sequencing technology. In a single run, we produced 13,737,528 sequencing reads corresponding to 2.03 Gb total nucleotides. These reads were assembled into 36,493 unique sequences. Based on similarity search with known proteins, 23,515 Unigenes were identified to have the Blast hit with a cut-off E-value above 10??. Furthermore, we investigated the transcriptome difference of three Taxus tissues using a tag-based digital gene expression system. We obtained a sequencing depth of over 3.15 million tags per sample and identified a large number of genes associated with tissue specific functions and taxane biosynthetic pathway. The expression of the taxane biosynthetic genes is significantly higher in the root than in the leaf and the stem, while high activity of taxane-producing pathway in the root was also revealed via metabolomic analyses. Moreover, many antisense transcripts and novel transcripts were found; clusters with similar differential expression patterns, enriched GO terms and enriched metabolic pathways with regard to the differentially expressed genes were revealed for the first time. CONCLUSIONS/SIGNIFICANCE: Our data provides the most comprehensive sequence resource available for Taxus study and will help define mechanisms of tissue specific functions and secondary metabolism in non-model plant organisms.

SUBMITTER: Hao da C

PROVIDER: S-EPMC3120849 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing.

Hao Da Cheng da C Ge GuangBo G Xiao PeiGen P Zhang YanYan Y Yang Ling L

PloS one 20110622 6

<h4>Background</h4>Illumina second generation sequencing is now an efficient route for generating enormous sequence collections that represent expressed genes and quantitate expression level. Taxus is a world-wide endangered gymnosperm genus and forms an important anti-cancer medicinal resource, but the large and complex genomes of Taxus have hindered the development of genomic resources. The research of its tissue-specific transcriptome is absent. There is also no study concerning the associati ...[more]

PMID: 21731678

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Project description:BACKGROUND: Switchgrass (Panicum virgatum L.) is a C4 perennial grass and widely popular as an important bioenergy crop. To accelerate the pace of developing high yielding switchgrass cultivars adapted to diverse environmental niches, the generation of genomic resources for this plant is necessary. The large genome size and polyploid nature of switchgrass makes whole genome sequencing a daunting task even with current technologies. Exploring the transcriptional landscape using next generation sequencing technologies provides a viable alternative to whole genome sequencing in switchgrass. PRINCIPAL FINDINGS: Switchgrass cDNA libraries from germinating seedlings, emerging tillers, flowers, and dormant seeds were sequenced using Roche 454 GS-FLX Titanium technology, generating 980,000 reads with an average read length of 367 bp. De novo assembly generated 243,600 contigs with an average length of 535 bp. Using the foxtail millet genome as a reference greatly improved the assembly and annotation of switchgrass ESTs. Comparative analysis of the 454-derived switchgrass EST reads with other sequenced monocots including Brachypodium, sorghum, rice and maize indicated a 70-80% overlap. RPKM analysis demonstrated unique transcriptional signatures of the four tissues analyzed in this study. More than 24,000 ESTs were identified in the dormant seed library. In silico analysis indicated that there are more than 2000 EST-SSRs in this collection. Expression of several orphan ESTs was confirmed by RT-PCR. SIGNIFICANCE: We estimate that about 90% of the switchgrass gene space has been covered in this analysis. This study nearly doubles the amount of EST information for switchgrass currently in the public domain. The celerity and economical nature of second-generation sequencing technologies provide an in-depth view of the gene space of complex genomes like switchgrass. Sequence analysis of closely related members of the NAD(+)-malic enzyme type C4 grasses such as the model system Setaria viridis can serve as a viable proxy for the switchgrass genome.

Project description:BackgroundThe safflower, Carthamus tinctorius L., is a worldwide oil crop, and its flowers, which have a high flavonoid content, are an important medicinal resource against cardiovascular disease in traditional medicine. Because the safflower has a large and complex genome, the development of its genomic resources has been delayed. Second-generation Illumina sequencing is now an efficient route for generating an enormous volume of sequences that can represent a large number of genes and their expression levels.Methodology/principal findingsTo investigate the genes and pathways that might control flavonoids and other secondary metabolites in the safflower, we used Illumina sequencing to perform a de novo assembly of the safflower tubular flower tissue transcriptome. We obtained a total of 4.69 Gb in clean nucleotides comprising 52,119,104 clean sequencing reads, 195,320 contigs, and 120,778 unigenes. Based on similarity searches with known proteins, we annotated 70,342 of the unigenes (about 58% of the identified unigenes) with cut-off E-values of 10(-5). In total, 21,943 of the safflower unigenes were found to have COG classifications, and BLAST2GO assigned 26,332 of the unigenes to 1,754 GO term annotations. In addition, we assigned 30,203 of the unigenes to 121 KEGG pathways. When we focused on genes identified as contributing to flavonoid biosynthesis and the biosynthesis of unsaturated fatty acids, which are important pathways that control flower and seed quality, respectively, we found that these genes were fairly well conserved in the safflower genome compared to those of other plants.Conclusions/significanceOur study provides abundant genomic data for Carthamus tinctorius L. and offers comprehensive sequence resources for studying the safflower. We believe that these transcriptome datasets will serve as an important public information platform to accelerate studies of the safflower genome, and may help us define the mechanisms of flower tissue-specific and secondary metabolism in this non-model plant.

Dataset Information

The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing.

Publications

The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing.

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