title: High-throughput sequencing and De Novo assembly of the Isatis indigotica transcriptome.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, The People's Republic of China.
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Tang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, The People's Republic of China.
authors.forename: Yunhua
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, The People's Republic of China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Lv
authors.affiliation: Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, The People's Republic of China.
authors.forename: Fangquan
authors.initials: F
authors.lastname: Wang
authors.affiliation: CSIRO Plant Industry, Canberra, Australia.
authors.forename: QianHao
authors.initials: Q
authors.lastname: Zhu
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, The People's Republic of China.
authors.forename: Tianqing
authors.initials: T
authors.lastname: Zheng
authors.affiliation: Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, The People's Republic of China.
authors.forename: Jie
authors.initials: J
authors.lastname: Yang
mesh_terms: D019295:Computational Biology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D031219:Isatis / Q000235:genetics* / Q000378:metabolism; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D010946:Plants, Medicinal / Q000235:genetics; D015398:Signal Transduction; D059467:Transcriptome