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

文献类型：期刊论文

作者Chen, Shuangyan; Huang, Xin1; Yan, Xueqing1; Liang, Ye1; Wang, Yuezhu4; Li, Xiaofeng; Peng, Xianjun; Ma, Xingyong1; Zhang, Lexin1; Cai, Yueyue1
刊名PLOS ONE
出版日期2013
卷号8期号:7
ISSN号1932-6203
DOI10.1371/journal.pone.0067974
文献子类Article
英文摘要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.
学科主题Multidisciplinary Sciences
出版地SAN FRANCISCO
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)
语种英语
WOS记录号WOS:000323350700067
出版者PUBLIC LIBRARY SCIENCE
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
源URL[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.Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA
3.Chinese Natl Human Genome Ctr Shanghai, Shanghai MOST Key Lab Hlth & Dis Genom, Shanghai, Peoples R China
4.Chinese Acad Sci, Grad Schoo1, Beijing, Peoples R China
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).

入库方式： OAI收割

来源：植物研究所

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