Abstract
BackgroundIllumina 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 FindingsWe 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 10−5. 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/SignificanceOur 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.
Highlights
Taxus is a genus of yews, small coniferous trees or shrubs in the gymnosperm family Taxaceae
With the alignment parameters E value #1e-5 and the sequence identity $80%, 44.6%, 43.8%, 75.3%, and 49.8% of T. mairei Unigenes were annotated with clone sequences and Unigenes of P. glauca, Unigenes of Korea T. cuspidata, and Unigenes of China T. cuspidata, respectively
Quality control comparisons to the Sanger-derived transcript sequences from Taxus, as well as multiple lines of evidence such as protein coding sequence (CDS) prediction (Fig. S4) and digital gene expression (DGE) tag mapping showed that the transcript assemblies are robust and that thousands of coding sequences and their respective 59 and/or 39 untranslated regions were successfully assembled (Table S2)
Summary
Taxus is a genus of yews, small coniferous trees or shrubs in the gymnosperm family Taxaceae. There are at least 14 species in Taxus [1,2], most of which are the sources of biological active compounds such as paclitaxel or Taxol, a chemotherapeutic drug used in the treatment of many types of cancer. Paclitaxel and its precursors belong to a group of typical secondary metabolites named the taxane diterpenoids or taxoids, but the distribution and content are highly varied with species and tissues. For that reason, choosing suitable Taxus species and screening the constituents in each tissue are essential to cost-effective production of taxane drugs. The biosynthesis pathway of paclitaxel and other taxanes is not fully elucidated and the underlying molecular mechanism of the metabolic difference between different Taxus tissues has not been studied, which hamper improvements in taxane drug production. There is no study concerning the association between the plant transcriptome and metabolome with respect to the plant tissue type
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