Transcriptome Analysis in Sheepgrass (Leymus chinensis): A Dominant Perennial Grass of the Eurasian Steppe

doi:10.1371/journal.pone.0067974

	Transcriptome Analysis in Sheepgrass (Leymus chinensis): A Dominant Perennial Grass of the Eurasian Steppe
	Chen, Shuangyan ; Huang, Xin 1; Yan, Xueqing 1; Liang, Ye 1; Wang, Yuezhu 2; Li, Xiaofeng ; Peng, Xianjun ; Ma, Xingyong 1; Zhang, Lexin 1; Cai, Yueyue 1; Ma, Tian ; Cheng, Liqin ; Qi, Dongmei ; Zheng, Huajun 2; Yang, Xiaohan 3; Li, Xiaoxia 1; Liu, Gongshe
	2013
发表期刊	PLOS ONE
ISSN	1932-6203
卷号	8 期号:7
摘要	Background: Sheepgrass [Leymus chinensis (Trin.) Tzvel.] is an important perennial forage grass across the Eurasian Steppe and is known for its adaptability to various environmental conditions. However, insufficient data resources in public databases for sheepgrass limited our understanding of the mechanism of environmental adaptations, gene discovery and molecular marker development. Results: The transcriptome of sheepgrass was sequenced using Roche 454 pyrosequencing technology. We assembled 952,328 high-quality reads into 87,214 unigenes, including 32,416 contigs and 54,798 singletons. There were 15,450 contigs over 500 bp in length. BLAST searches of our database against Swiss-Prot and NCBI non-redundant protein sequences (nr) databases resulted in the annotation of 54,584 (62.6%) of the unigenes. Gene Ontology (GO) analysis assigned 89,129 GO term annotations for 17,463 unigenes. We identified 11,675 core Poaceae-specific and 12,811 putative sheepgrass-specific unigenes by BLAST searches against all plant genome and transcriptome databases. A total of 2,979 specific freezing-responsive unigenes were found from this RNAseq dataset. We identified 3,818 EST-SSRs in 3,597 unigenes, and some SSRs contained unigenes that were also candidates for freezing-response genes. Characterizations of nucleotide repeats and dominant motifs of SSRs in sheepgrass were also performed. Similarity and phylogenetic analysis indicated that sheepgrass is closely related to barley and wheat. Conclusions: This research has greatly enriched sheepgrass transcriptome resources. The identified stress-related genes will help us to decipher the genetic basis of the environmental and ecological adaptations of this species and will be used to improve wheat and barley crops through hybridization or genetic transformation. The EST-SSRs reported here will be a valuable resource for future gene-phenotype studies and for the molecular breeding of sheepgrass and other Poaceae species.
学科领域	Multidisciplinary Sciences
DOI	10.1371/journal.pone.0067974
收录类别	SCI
语种	英语
WOS关键词	FREEZING TOLERANCE ; SSR-MARKERS ; ARABIDOPSIS-THALIANA ; COLD-ACCLIMATION ; MICROSATELLITE MARKERS ; PHYLOGENETIC ANALYSIS ; GENOME ANNOTATION ; GENE DISCOVERY ; SALT TOLERANCE ; TRITICEAE
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000323350700067
出版者	PUBLIC LIBRARY SCIENCE
文献子类	Article
出版地	SAN FRANCISCO
资助机构	National High Technology Research and Development Program of China (863)(National High Technology Research and Development Program of China) ; National Natural Science Foundation of China(National Natural Science Foundation of China (NSFC)) ; Key Project of the Chinese Academy of Sciences(Chinese Academy of Sciences) ; Project of Ningxia Agricultural Comprehensive Development Office
作者邮箱	Yang, Xiaohan/AAM-2449-2020 ; Yang, Xiaohan/A-6975-2011
作品OA属性	gold, Green Submitted, Green Published
引用统计	被引频次：64[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/2S10CLM1/27800
专题	中科院北方资源植物重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, Key Lab Plant Resources, Beijing, Peoples R China 2.Chinese Acad Sci, Grad Schoo1, Beijing, Peoples R China 3.Chinese Natl Human Genome Ctr Shanghai, Shanghai MOST Key Lab Hlth & Dis Genom, Shanghai, Peoples R China 4.Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA
推荐引用方式 GB/T 7714	Chen, Shuangyan,Huang, Xin,Yan, Xueqing,et al. Transcriptome Analysis in Sheepgrass (Leymus chinensis): A Dominant Perennial Grass of the Eurasian Steppe[J]. PLOS ONE,2013,8(7).
APA	Chen, Shuangyan.,Huang, Xin.,Yan, Xueqing.,Liang, Ye.,Wang, Yuezhu.,...&Liu, Gongshe.(2013).Transcriptome Analysis in Sheepgrass (Leymus chinensis): A Dominant Perennial Grass of the Eurasian Steppe.PLOS ONE,8(7).
MLA	Chen, Shuangyan,et al."Transcriptome Analysis in Sheepgrass (Leymus chinensis): A Dominant Perennial Grass of the Eurasian Steppe".PLOS ONE 8.7(2013).

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