De Novo Sequencing and Comparative Analysis of Schima superba Seedlings to Explore the Response to Drought Stress

doi:10.1371/journal.pone.0166975

	De Novo Sequencing and Comparative Analysis of Schima superba Seedlings to Explore the Response to Drought Stress
	Han, Bao-cai ; Wei, Wei ; Mi, Xiang-cheng ; Ma, Ke-ping
	2016
发表期刊	PLOS ONE
ISSN	1932-6203
卷号	11 期号:12
摘要	Schima superba is an important dominant species in subtropical evergreen broadleaved forests of China, and plays a vital role in community structure and dynamics. However, the survival rate of its seedlings in the field is low, and water shortage could be a factor that limits its regeneration. In order to better understand the response of its seedlings to drought stress on a functional genomics scale, RNA-seq technology was utilized in this study to perform a large-scale transcriptome sequencing of the S. superba seedlings under drought stress. More than 320 million clean reads were generated and 72218 unique transcripts were obtained through de novo assembly. These unigenes were further annotated by blasting with different public databases and a total of 53300 unique transcripts were annotated. A total of 31586 simple sequence repeat (SSR) loci were presented. Through gene expression profiling analysis between drought treatment and control, 11038 genes were found to be significantly enriched in drought-stressed seedlings. Based on these differentially expressed genes (DEGs), Gene Ontology (GO) terms enrichment and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analysis indicated that drought stress caused a number of changes in the types of sugars, enzymes, secondary mechanisms, and light responses, and induced some potential physical protection mechanisms. In addition, the expression patterns of 18 transcripts induced by drought, as determined by quantitative real-time PCR, were consistent with their transcript abundance changes, as identified by RNA-seq. This transcriptome study provides a rapid method for understanding the response of S. superba seedlings to drought stress and provides a number of gene sequences available for further functional genomics studies.
学科领域	Multidisciplinary Sciences
DOI	10.1371/journal.pone.0166975
收录类别	SCI
语种	英语
WOS关键词	RNA-SEQ ; GENE ONTOLOGY ; EXPRESSION ; BIOSYNTHESIS ; MECHANISMS ; TOLERANCE ; FOREST ; KEGG ; TOOL
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000389580900018
出版者	PUBLIC LIBRARY SCIENCE
文献子类	Article
出版地	SAN FRANCISCO
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31261120579] ; Direct For Biological SciencesNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [1643052] Funding Source: National Science Foundation
作者邮箱	kpma@ibcas.ac.cn
作品OA属性	Green Submitted, Green Published, gold
引用统计	被引频次：3[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/25124
专题	植被与环境变化国家重点实验室
作者单位	1.[Han, Bao-cai 2.Wei, Wei 3.Mi, Xiang-cheng 4.Chinese Acad Sci, Inst Bot, State Key Lab Vegetat & Environm Change, Beijing, Peoples R China 5.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Han, Bao-cai,Wei, Wei,Mi, Xiang-cheng,et al. De Novo Sequencing and Comparative Analysis of Schima superba Seedlings to Explore the Response to Drought Stress[J]. PLOS ONE,2016,11(12).
APA	Han, Bao-cai,Wei, Wei,Mi, Xiang-cheng,&Ma, Ke-ping.(2016).De Novo Sequencing and Comparative Analysis of Schima superba Seedlings to Explore the Response to Drought Stress.PLOS ONE,11(12).
MLA	Han, Bao-cai,et al."De Novo Sequencing and Comparative Analysis of Schima superba Seedlings to Explore the Response to Drought Stress".PLOS ONE 11.12(2016).

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