title: Transcriptome analysis in sheepgrass (Leymus chinensis): a dominant perennial grass of the Eurasian Steppe.
abstract: 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.
authors.affiliation: Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, PR China. sychen@ibcas.ac.cn
authors.forename: Shuangyan
authors.initials: S
authors.lastname: Chen
authors.forename: Xin
authors.initials: X
authors.lastname: Huang
authors.forename: Xueqing
authors.initials: X
authors.lastname: Yan
authors.forename: Ye
authors.initials: Y
authors.lastname: Liang
authors.forename: Yuezhu
authors.initials: Y
authors.lastname: Wang
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Li
authors.forename: Xianjun
authors.initials: X
authors.lastname: Peng
authors.forename: Xingyong
authors.initials: X
authors.lastname: Ma
authors.forename: Lexin
authors.initials: L
authors.lastname: Zhang
authors.forename: Yueyue
authors.initials: Y
authors.lastname: Cai
authors.forename: Tian
authors.initials: T
authors.lastname: Ma
authors.forename: Liqin
authors.initials: L
authors.lastname: Cheng
authors.forename: Dongmei
authors.initials: D
authors.lastname: Qi
authors.forename: Huajun
authors.initials: H
authors.lastname: Zheng
authors.forename: Xiaohan
authors.initials: X
authors.lastname: Yang
authors.forename: Xiaoxia
authors.initials: X
authors.lastname: Li
authors.forename: Gongshe
authors.initials: G
authors.lastname: Liu
mesh_terms: D001208:Asia; D030541:Databases, Genetic; D005060:Europe; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D001467:Hordeum / Q000145:classification / Q000235:genetics; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D058889:Molecular Typing; D010802:Phylogeny; D006109:Poaceae / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA; D059467:Transcriptome; D014908:Triticum / Q000145:classification / Q000235:genetics