De Novo Foliar Transcriptome of Chenopodium amaranticolor and Analysis of Its Gene Expression During Virus-Induced Hypersensitive Response

doi:10.1371/journal.pone.0045953

	De Novo Foliar Transcriptome of Chenopodium amaranticolor and Analysis of Its Gene Expression During Virus-Induced Hypersensitive Response
	Zhang, YQ; Pei, XW; Zhang, C; Lu, ZF; Wang, ZX; Jia, SR; Li, WM; Li, WM (reprint author), Chinese Acad Agr Sci, Biotechnol Res Inst, Beijing 100193, Peoples R China.
	2012-09-28
Source Publication	PLoS One Impact Factor & Quartile
ISSN	1932-6203
Volume	7 Issue:9 Pages:-
Abstract	Background: The hypersensitive response (HR) system of Chenopodium spp. confers broad-spectrum virus resistance. However, little knowledge exists at the genomic level for Chenopodium, thus impeding the advanced molecular research of this attractive feature. Hence, we took advantage of RNA-seq to survey the foliar transcriptome of C. amaranticolor, a Chenopodium species widely used as laboratory indicator for pathogenic viruses, in order to facilitate the characterization of the HR-type of virus resistance. Methodology and Principal Findings: Using Illumina HiSeq (TM) 2000 platform, we obtained 39,868,984 reads with 3,588,208,560 bp, which were assembled into 112,452 unigenes (3,847 clusters and 108,605 singletons). BlastX search against the NCBI NR database identified 61,698 sequences with a cut-off E-value above 10(-5). Assembled sequences were annotated with gene descriptions, GO, COG and KEGG terms, respectively. A total number of 738 resistance gene analogs (RGAs) and homology sequences of 6 key signaling proteins within the R proteins-directed signaling pathway were identified. Based on this transcriptome data, we investigated the gene expression profiles over the stage of HR induced by Tobacco mosaic virus and Cucumber mosaic virus by using digital gene expression analysis. Numerous candidate genes specifically or commonly regulated by these two distinct viruses at early and late stages of the HR were identified, and the dynamic changes of the differently expressed genes enriched in the pathway of plant-pathogen interaction were particularly emphasized. Conclusions: To our knowledge, this study is the first description of the genetic makeup of C. amaranticolor, providing deep insight into the comprehensive gene expression information at transcriptional level in this species. The 738 RGAs as well as the differentially regulated genes, particularly the common genes regulated by both TMV and CMV, are suitable candidates which merit further functional characterization to dissect the molecular mechanisms and regulatory pathways of the HR-type of virus resistance in Chenopodium.
Subject Area	Science & Technology - Other Topics
Publisher	PLOS
DOI	10.1371/journal.pone.0045953
Publication Place	SAN FRANCISCO
Indexed By	SCIE
Language	英语
First Inst	否
Funding Project	国家科技重大专项 ; 公益性行业科研专项 ; 转基因生物新品种培育科技重大专项
Project Number	National Major Special Project of China on New Varieties Cultivation for Transgenic Organisms [2011ZX08001-002, 2011ZX08004-004] ; Special Fund for Agro-scientific Research in the Public Interest [201103026-2]
WOS ID	WOS:000309973900067
Funding Organization	MOST ; MOA
Subtype	Article
Department	[Zhang, Yongqiang; Pei, Xinwu; Zhang, Chao; Wang, Zhixing; Jia, Shirong; Li, Weimin] Chinese Acad Agr Sci, Biotechnol Res Inst, Beijing 100193, Peoples R China; [Lu, Zifeng] Lanzhou Univ, Coll Pastoral Agr Sci & Technol, State Key Lab Grassland Agroecosyst, Lanzhou 730000, Peoples R China
Citation statistics	Cited Times:13[WOS] [WOS Record] [Related Records in WOS]
Document Type	期刊论文
Identifier	https://ir.lzu.edu.cn/handle/262010/113684
Collection	草地农业科技学院
Corresponding Author	Li, WM (reprint author), Chinese Acad Agr Sci, Biotechnol Res Inst, Beijing 100193, Peoples R China.
Recommended Citation GB/T 7714	Zhang, YQ,Pei, XW,Zhang, C,et al. De Novo Foliar Transcriptome of Chenopodium amaranticolor and Analysis of Its Gene Expression During Virus-Induced Hypersensitive Response[J]. PLoS One,2012,7(9):-.
APA	Zhang, YQ.,Pei, XW.,Zhang, C.,Lu, ZF.,Wang, ZX.,...&Li, WM .(2012).De Novo Foliar Transcriptome of Chenopodium amaranticolor and Analysis of Its Gene Expression During Virus-Induced Hypersensitive Response.PLoS One,7(9),-.
MLA	Zhang, YQ,et al."De Novo Foliar Transcriptome of Chenopodium amaranticolor and Analysis of Its Gene Expression During Virus-Induced Hypersensitive Response".PLoS One 7.9(2012):-.

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