The First Insight into the Tissue Specific Taxus Transcriptome via Illumina Second Generation Sequencing

Biotechnology Institute, Dalian Jiaotong University, Dalian, China.
PLoS ONE (Impact Factor: 3.23). 06/2011; 6(6):e21220. DOI: 10.1371/journal.pone.0021220
Source: PubMed


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.
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 10⁻⁵. 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.
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.

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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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    • "Species Explant Profiling method Number of transcripts Reference T. chinensis MeJA elicited cells Illumina deep sequencing 46,581 unigenes Li et al. (2012a, 2012b) T. chinensis MeJA elicited cells Illumina deep sequencing 1,256,425 sRNAs Qiu et al. (2009) T. chinensis MeJA elicited cells Random Sanger sequencing of cDNA library 3563 unigenes Jennewein et al. (2004) T. cuspidata MeJA elicited cells Sanger sequencing of subtractive hybridization library 331 unigenes Lenka et al. (2012) T. cuspidata (Cambial) cells 454 deep sequencing 26,906 unigenes Lee et al. (2010) T. cuspidata Needles 454 deep sequencing 20,557 unigenes Wu et al. (2011) T. mairei Roots, leaves, stems Illumina deep sequencing 36,493 unigenes Hao et al. (2011a, 2011b "
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    • "e l s e v i e r . c o m / l o c a t e / g e n e (Hao et al., 2011; Li et al., 2011; Sandmann et al., 2011; Iseli et al., 1999). In the current study, we compared transcriptome sequences of above-and underground tissues of R. algida to obtain a profile of molecular mechanisms involved in synthesis of bioactive compounds . "
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