Transcriptome analysis in sheepgrass (Leymus chinensis): a dominant perennial grass of the Eurasian Steppe.
Transcriptome analysis in sheepgrass (Leymus chinensis): a dominant perennial grass of the Eurasian Steppe.
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DOI：
10.1371/journal.pone.0067974
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Liu G
中科院分区：
文献类型：
--
作者：
Chen S;Huang X;Yan X;Liang Y;Wang Y;Li X;Peng X;Ma X;Zhang L;Cai Y;Ma T;Cheng L;Qi D;Zheng H;Yang X;Li X;Liu G
羊草[Leymus chinensis (Trin.) Tzvel.]是欧亚草原上重要的多年生牧草，以其对各种环境条件的适应性而闻名。然而，羊草公共数据库数据资源不足限制了我们对环境适应、基因发现和分子标记开发机制的理解。使用Roche 454焦磷酸测序技术对羊草的转录组进行测序。我们将 952,328 个高质量的读段组装到 87,214 个 unigene 中，包括 32,416 个重叠群和 54,798 个单基因。有 15,450 个长度超过 500 bp 的重叠群。对我们的数据库与 Swiss-Prot 和 NCBI 非冗余蛋白质序列 (nr) 数据库进行 BLAST 搜索，结果注释了 54,584 个 (62.6%) 的 unigene。基因本体 (GO) 分析为 17,463 个 unigene 分配了 89,129 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 11,675 个核心禾本科特异性单基因和 12,811 个假定的羊草特异性单基因。从该 RNAseq 数据集中总共发现了 2,979 个特定的冷冻响应性 unigene。我们在 3,597 个 unigene 中鉴定了 3,818 个 EST-SSR，并且一些 SSR 包含的 unigene 也是冷冻反应基因的候选基因。还对羊草中 SSR 的核苷酸重复和显性基序进行了表征。相似性和系统发育分析表明，羊草与大麦和小麦密切相关。该研究极大丰富了羊草转录组资源。已确定的与胁迫相关的基因将帮助我们破译该物种环境和生态适应的遗传基础，并将用于通过杂交或遗传转化来改良小麦和大麦作物。这里报道的 EST-SSR 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。
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.
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