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

doi:10.1371/journal.pone.0102963

	High-Throughput Sequencing and De Novo Assembly of the Isatis indigotica Transcriptome
	Tang, Xiaoqing 1; Xiao, Yunhua 1; Lv, Tingting 1; Wang, Fangquan 2; Zhu, QianHao 3; Zheng, Tianqing 4; Yang, Jie 2
刊名	PLOS ONE
	2014
卷号	9 期号:9 页码:-
ISSN号	1932-6203
DOI	10.1371/journal.pone.0102963
通讯作者	Tang, Xiaoqing
英文摘要	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.
学科主题	Multidisciplinary Sciences
语种	英语
出版者	PUBLIC LIBRARY SCIENCE
WOS记录号	WOS:000342685600003
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/4837]
专题	作物科学研究所_分子生物学系
作者单位	1.Nanjing Agr Univ, Coll Hort, Nanjing, Jiangsu, Peoples R China 2.Jiangsu Acad Agr Sci, Inst Food Crops, Nanjing, Jiangsu, Peoples R China 3.CSIRO Plant Ind, Canberra, ACT, Australia 4.Chinese Acad Agr Sci, Inst Crop Sci, Beijing 100193, Peoples R China
推荐引用方式 GB/T 7714	Tang, Xiaoqing,Xiao, Yunhua,Lv, Tingting,et al. High-Throughput Sequencing and De Novo Assembly of the Isatis indigotica Transcriptome[J]. PLOS ONE,2014,9(9):-.
APA	Tang, Xiaoqing.,Xiao, Yunhua.,Lv, Tingting.,Wang, Fangquan.,Zhu, QianHao.,...&Yang, Jie.(2014).High-Throughput Sequencing and De Novo Assembly of the Isatis indigotica Transcriptome.PLOS ONE,9(9),-.
MLA	Tang, Xiaoqing,et al."High-Throughput Sequencing and De Novo Assembly of the Isatis indigotica Transcriptome".PLOS ONE 9.9(2014):-.