High-throughput sequencing and De Novo assembly of the Isatis indigotica transcriptome

Xiaoqing Tang; Yunhua Xiao; Tingting Lv; Fangquan Wang; QianHao Zhu; Tianqing Zheng; Jie Yang

doi:10.1371/journal.pone.0102963

High-throughput sequencing and De Novo assembly of the Isatis indigotica transcriptome

PLoS One. 2014 Sep 26;9(9):e102963. doi: 10.1371/journal.pone.0102963. eCollection 2014.

Authors

Xiaoqing Tang¹, Yunhua Xiao¹, Tingting Lv¹, Fangquan Wang², QianHao Zhu³, Tianqing Zheng⁴, Jie Yang²

Affiliations

¹ College of Horticulture, Nanjing Agricultural University, Nanjing, The People's Republic of China.
² Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, The People's Republic of China.
³ CSIRO Plant Industry, Canberra, Australia.
⁴ Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, The People's Republic of China.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology
Gene Expression Profiling
Gene Expression Regulation, Plant*
High-Throughput Nucleotide Sequencing
Isatis / genetics*
Isatis / metabolism
Microsatellite Repeats
Molecular Sequence Annotation
Plants, Medicinal / genetics
Signal Transduction
Transcriptome*

Grants and funding

This work was supported by the National Natural Science Foundation of China (Grant no. 31171486). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.