Tang Xiaoqing, Xiao Yunhua, Lv Tingting, Wang Fangquan, Zhu QianHao, Zheng Tianqing, Yang Jie
College of Horticulture, Nanjing Agricultural University, Nanjing, The People's Republic of China.
Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, The People's Republic of China.
PLoS One. 2014 Sep 26;9(9):e102963. doi: 10.1371/journal.pone.0102963. eCollection 2014.
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).
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.
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.
菘蓝是传统中药板蓝根的来源植物，在中国是一种极其重要的经济作物。为了促进对菘蓝中药用化学成分的生物学、生物化学和分子研究，我们在此报告通过RNA测序（RNA-seq）生成的首个菘蓝转录组。
使用从包括叶和根的混合样本中提取的RNA创建了RNA-seq文库。从超过2800万个高质量短读段中组装出总共33238个单基因。通过对7个随机选择的单基因进行cDNA测序，对组装质量进行了实验检验。基于比对搜索，28184个单基因在本研究使用的蛋白质和核苷酸数据库中至少有一个匹配，并且发现8个单基因与吲哚及其衍生物的生物合成相关。根据基因本体分类，22365个单基因被分为48个功能组。此外，分别为7707个和18679个单基因指定了直系同源簇和瑞士蛋白质数据库注释。对重复基序的分析在4509个单基因中鉴定出6400个简单序列重复标记。
我们的数据为菘蓝的分子研究提供了全面的序列资源。我们的结果将有助于研究参与吲哚生物碱生物合成途径的基因功能以及菘蓝及其相关物种中氮和吲哚生物碱的代谢。
