Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, PR China.
PLoS One. 2013 Jul 4;8(7):e67974. doi: 10.1371/journal.pone.0067974. Print 2013.
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.
羊草[Leymus chinensis (Trin.) Tzvel.]是欧亚草原上一种重要的多年生牧草，以适应各种环境条件而闻名。然而，公共数据库中羊草的数据资源不足，限制了我们对其环境适应机制、基因发现和分子标记开发的理解。
我们使用 Roche 454 焦磷酸测序技术对羊草的转录组进行了测序。我们将 952328 条高质量reads 组装成 87214 个非冗余基因，其中 32416 条为 contigs，54798 条为 singletons。长度超过 500bp 的 contigs 有 15450 个。将我们的数据库与 Swiss-Prot 和 NCBI non-redundant protein sequences (nr) 数据库进行 BLAST 搜索，结果注释了 54584 个（62.6%）非冗余基因。GO 分析为 17463 个非冗余基因分配了 89129 个 GO 术语注释。通过对所有植物基因组和转录组数据库进行 BLAST 搜索，我们鉴定了 11675 个核心禾本科特异性和 12811 个假定的羊草特异性非冗余基因。从这个 RNAseq 数据集中共发现了 2979 个特定的抗冻响应非冗余基因。我们在 3597 个非冗余基因中鉴定了 3818 个 EST-SSRs，一些 SSR 包含也是抗冻响应基因候选的非冗余基因。还对羊草核苷酸重复和 SSR 优势基序进行了特征分析。相似性和系统发育分析表明，羊草与大麦和小麦关系密切。
本研究极大地丰富了羊草转录组资源。鉴定出的与应激相关的基因将有助于我们揭示该物种环境和生态适应的遗传基础，并通过杂交或遗传转化应用于提高小麦和大麦作物的产量。本文报道的 EST-SSRs 将成为未来基因-表型研究以及羊草和其他禾本科物种分子育种的宝贵资源。
