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High-Throughput Sequencing and De Novo Assembly of the Isatis indigotica Transcriptome

BACKGROUND: Isatis indigotica, the source of the traditional Chinese medicine Radix isatidis (Ban-Lan-Gen), is an extremely important economical crop in China. To facilitate biological, biochemical and molecular research on the medicinal chemicals in I. indigotica, here we report the first I. indigo...

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Autores principales: Tang, Xiaoqing, Xiao, Yunhua, Lv, Tingting, Wang, Fangquan, Zhu, QianHao, Zheng, Tianqing, Yang, Jie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178013/
https://www.ncbi.nlm.nih.gov/pubmed/25259890
http://dx.doi.org/10.1371/journal.pone.0102963
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author Tang, Xiaoqing
Xiao, Yunhua
Lv, Tingting
Wang, Fangquan
Zhu, QianHao
Zheng, Tianqing
Yang, Jie
author_facet Tang, Xiaoqing
Xiao, Yunhua
Lv, Tingting
Wang, Fangquan
Zhu, QianHao
Zheng, Tianqing
Yang, Jie
author_sort Tang, Xiaoqing
collection PubMed
description BACKGROUND: Isatis indigotica, the source of the traditional Chinese medicine Radix isatidis (Ban-Lan-Gen), is an extremely important economical crop in China. To facilitate biological, biochemical and molecular research on the medicinal chemicals in I. indigotica, here we report the first I. indigotica transcriptome generated by RNA sequencing (RNA-seq). RESULTS: RNA-seq library was created using RNA extracted from a mixed sample including leaf and root. A total of 33,238 unigenes were assembled from more than 28 million of high quality short reads. The quality of the assembly was experimentally examined by cDNA sequencing of seven randomly selected unigenes. Based on blast search 28,184 unigenes had a hit in at least one of the protein and nucleotide databases used in this study, and 8 unigenes were found to be associated with biosynthesis of indole and its derivatives. According to Gene Ontology classification, 22,365 unigenes were categorized into 48 functional groups. Furthermore, Clusters of Orthologous Group and Swiss-Port annotation were assigned for 7,707 and 18,679 unigenes, respectively. Analysis of repeat motifs identified 6,400 simple sequence repeat markers in 4,509 unigenes. CONCLUSION: Our data provide a comprehensive sequence resource for molecular study of I. indigotica. Our results will facilitate studies on the functions of genes involved in the indole alkaloid biosynthesis pathway and on metabolism of nitrogen and indole alkaloids in I. indigotica and its related species.
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spelling pubmed-41780132014-10-02 High-Throughput Sequencing and De Novo Assembly of the Isatis indigotica Transcriptome Tang, Xiaoqing Xiao, Yunhua Lv, Tingting Wang, Fangquan Zhu, QianHao Zheng, Tianqing Yang, Jie PLoS One Research Article BACKGROUND: Isatis indigotica, the source of the traditional Chinese medicine Radix isatidis (Ban-Lan-Gen), is an extremely important economical crop in China. To facilitate biological, biochemical and molecular research on the medicinal chemicals in I. indigotica, here we report the first I. indigotica transcriptome generated by RNA sequencing (RNA-seq). RESULTS: RNA-seq library was created using RNA extracted from a mixed sample including leaf and root. A total of 33,238 unigenes were assembled from more than 28 million of high quality short reads. The quality of the assembly was experimentally examined by cDNA sequencing of seven randomly selected unigenes. Based on blast search 28,184 unigenes had a hit in at least one of the protein and nucleotide databases used in this study, and 8 unigenes were found to be associated with biosynthesis of indole and its derivatives. According to Gene Ontology classification, 22,365 unigenes were categorized into 48 functional groups. Furthermore, Clusters of Orthologous Group and Swiss-Port annotation were assigned for 7,707 and 18,679 unigenes, respectively. Analysis of repeat motifs identified 6,400 simple sequence repeat markers in 4,509 unigenes. CONCLUSION: Our data provide a comprehensive sequence resource for molecular study of I. indigotica. Our results will facilitate studies on the functions of genes involved in the indole alkaloid biosynthesis pathway and on metabolism of nitrogen and indole alkaloids in I. indigotica and its related species. Public Library of Science 2014-09-26 /pmc/articles/PMC4178013/ /pubmed/25259890 http://dx.doi.org/10.1371/journal.pone.0102963 Text en © 2014 Tang et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Tang, Xiaoqing
Xiao, Yunhua
Lv, Tingting
Wang, Fangquan
Zhu, QianHao
Zheng, Tianqing
Yang, Jie
High-Throughput Sequencing and De Novo Assembly of the Isatis indigotica Transcriptome
title High-Throughput Sequencing and De Novo Assembly of the Isatis indigotica Transcriptome
title_full High-Throughput Sequencing and De Novo Assembly of the Isatis indigotica Transcriptome
title_fullStr High-Throughput Sequencing and De Novo Assembly of the Isatis indigotica Transcriptome
title_full_unstemmed High-Throughput Sequencing and De Novo Assembly of the Isatis indigotica Transcriptome
title_short High-Throughput Sequencing and De Novo Assembly of the Isatis indigotica Transcriptome
title_sort high-throughput sequencing and de novo assembly of the isatis indigotica transcriptome
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178013/
https://www.ncbi.nlm.nih.gov/pubmed/25259890
http://dx.doi.org/10.1371/journal.pone.0102963
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