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

<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 r...

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Autores principales: Da Cheng Hao, GuangBo Ge, PeiGen Xiao, YanYan Zhang, Ling Yang
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Publicado: Public Library of Science (PLoS) 2011
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spelling oai:doaj.org-article:9882602e83504e0187225cc21ac4fbb62021-11-18T06:51:33ZThe first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing.1932-620310.1371/journal.pone.0021220https://doaj.org/article/9882602e83504e0187225cc21ac4fbb62011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21731678/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<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 association between the plant transcriptome and metabolome with respect to the plant tissue type.<h4>Methodology/principal findings</h4>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.<h4>Conclusions/significance</h4>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.Da Cheng HaoGuangBo GePeiGen XiaoYanYan ZhangLing YangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 6, p e21220 (2011)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Da Cheng Hao
GuangBo Ge
PeiGen Xiao
YanYan Zhang
Ling Yang
The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing.
description <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 association between the plant transcriptome and metabolome with respect to the plant tissue type.<h4>Methodology/principal findings</h4>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.<h4>Conclusions/significance</h4>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.
format article
author Da Cheng Hao
GuangBo Ge
PeiGen Xiao
YanYan Zhang
Ling Yang
author_facet Da Cheng Hao
GuangBo Ge
PeiGen Xiao
YanYan Zhang
Ling Yang
author_sort Da Cheng Hao
title The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing.
title_short The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing.
title_full The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing.
title_fullStr The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing.
title_full_unstemmed The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing.
title_sort first insight into the tissue specific taxus transcriptome via illumina second generation sequencing.
publisher Public Library of Science (PLoS)
publishDate 2011
url https://doaj.org/article/9882602e83504e0187225cc21ac4fbb6
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