De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data

doi:10.1371/journal.pone.0131455

CORC > 中国农业科学院 > 植物保护研究所

	De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data
	Tian, Xin-jie 1; Long, Yan 2; Wang, Jiao 2; Zhang, Jing-wen 2; Wang, Yan-yan 2; Li, Wei-min 2; Peng, Yu-fa 3; Yuan, Qian-hua 1; Pei, Xin-wu 2
刊名	PLOS ONE
	2015
卷号	10 期号:7 页码:-
ISSN号	1932-6203
DOI	10.1371/journal.pone.0131455
通讯作者	Tian, Xin-jie
英文摘要	BackgroundThe perennial O. rufipogon (common wild rice), which is considered to be the ancestor of Asian cultivated rice species, contains many useful genetic resources, including drought resistance genes. However, few studies have identified the drought resistance and tissuespecific genes in common wild rice.ResultsIn this study, transcriptome sequencing libraries were constructed, including droughttreated roots (DR) and control leaves (CL) and roots (CR). Using Illumina sequencing technology, we generated 16.75 million bases of high-quality sequence data for common wild rice and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 119,332 unigenes with an average length of 715 bp. A total of 88,813 distinct sequences (74.42% of unigenes) significantly matched known genes in the NCBI NT database. Differentially expressed gene (DEG) analysis showed that 3617 genes were up-regulated and 4171 genes were down-regulated in the CR library compared with the CL library. Among the DEGs, 535 genes were expressed in roots but not in shoots. A similar comparison between the DR and CR libraries showed that 1393 genes were up-regulated and 315 genes were down-regulated in the DR library compared with the CR library. Finally, 37 genes that were specifically expressed in roots were screened after comparing the DEGs identified in the above-described analyses.ConclusionThis study provides a transcriptome sequence resource for common wild rice plants and establishes a digital gene expression profile of wild rice plants under drought conditions using the assembled transcriptome data as a reference. Several tissue-specific and drought-stress-related candidate genes were identified, representing a fully characterized transcriptome and providing a valuable resource for genetic and genomic studies in plants.
学科主题	Multidisciplinary Sciences
语种	英语
出版者	PUBLIC LIBRARY SCIENCE
WOS记录号	WOS:000358154400049
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/11673]
专题	植物保护研究所
作者单位	1.Hainan Univ, Coll Agr, Hainan Key Lab Sustainable Utilizat Trop Bioresou, Haikou 570228, Peoples R China 2.Chinese Acad Agr Sci, Inst Biotechnol, Beijing 100081, Peoples R China 3.Chinese Acad Agr Sci, Inst Plant Protect, Beijing 100094, Peoples R China
推荐引用方式 GB/T 7714	Tian, Xin-jie,Long, Yan,Wang, Jiao,et al. De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data[J]. PLOS ONE,2015,10(7):-.
APA	Tian, Xin-jie.,Long, Yan.,Wang, Jiao.,Zhang, Jing-wen.,Wang, Yan-yan.,...&Pei, Xin-wu.(2015).De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data.PLOS ONE,10(7),-.
MLA	Tian, Xin-jie,et al."De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data".PLOS ONE 10.7(2015):-.