Transcriptome analysis in sheepgrass (Leymus chinensis): a dominant perennial grass of the Eurasian Steppe

• Published in: PloS one 2013-07, Vol.8 (7), p.e67974-e67974
• Main Authors: Chen, Shuangyan, Huang, Xin, Yan, Xueqing, Liang, Ye, Wang, Yuezhu, Li, Xiaofeng, Peng, Xianjun, Ma, Xingyong, Zhang, Lexin, Cai, Yueyue, Ma, Tian, Cheng, Liqin, Qi, Dongmei, Zheng, Huajun, Yang, Xiaohan, Li, Xiaoxia, Liu, Gongshe
• Format: Article
• Language: English
• Subjects: Adaptability; Adaptation; Adaptations; Agriculture; Analysis; Annotations; Asia; Barley; BASIC BIOLOGICAL SCIENCES; Biology; Brachypodium; Brachypodium distachyon; Breeding; Cereal crops; Computer programs; Data bases; Databases, Genetic; Ecological adaptation; Environmental conditions; Europe; Expressed Sequence Tags; Forage; Forages; Freezing; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes; Genetic transformation; Genome, Plant; Genomes; Genomics; Grasses; Hordeum - classification; Hordeum - genetics; Hybridization; Laboratories; Leymus; Leymus chinensis; Microsatellite Repeats; Molecular Sequence Annotation; Molecular Typing; Ontology; Oryza; Phenotypes; Phylogenetics; Phylogeny; Physiological aspects; Plant breeding; Poaceae; Poaceae - classification; Poaceae - genetics; R&D; Research & development; Ryegrasses; Searching; Sequence Analysis, DNA; Steppes; Transcription factors; Transcriptome; Triticeae; Triticum; Triticum - classification; Triticum - genetics; Wheat
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0067974

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. 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. 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.