Analysis and annotation of the hexaploid oat seed transcriptome.
Analysis and annotation of the hexaploid oat seed transcriptome.
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DOI：
10.1186/1471-2164-14-471
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发表时间：
2013-07-11
期刊：
影响因子：
4.4
通讯作者：
Garvin DF
中科院分区：
文献类型：
--
作者：
Gutierrez-Gonzalez JJ;Tu ZJ;Garvin DF
下一代测序为探索转录本提供了新的机会。然而，对于同源等位基因和同源等位基因的准确区分仍然存在挑战，特别是在没有支持基因组序列的多倍体生物中。本研究利用RNA-Seq技术构建并鉴定了第一个六倍体燕麦基因表达图谱。三一和OASS软件包被用来从来自发育中的燕麦种子的近1.34亿个100bp的成对末端读数中产生转录本组件。根据所采用的质量参数，OASS组装是更好的。OASS的67kmer组装，被称为dnOST(De Novo Oat Seed Transcriptome)，长度超过5500万个核苷酸，平均转录长度为1043个核苷酸。74.8倍的测序深度足以区分很大比例的假定的同源等位基因和平行等位基因。为了评估dnOST的稳定性，我们成功地鉴定了与三种具有促进健康特性的化合物(文冠酰胺、甲醇、β-葡聚糖)的生物合成途径相关的基因转录本，并对它们的表达进行了量化。据我们所知，这项研究首次提供了多倍体生物体中两个主要组装者之间的直接性能比较。我们开发的工作流程为其他生物体的可比分析提供了有用的指南。这里开发的成绩单组装是一个重大进步。它将燕麦EST的数量扩大了3倍，并构成了燕麦中第一个全面的转录组研究。这一资源将是一个有用的新工具，无论是分析与燕麦营养增强相关的基因，还是总体上改良燕麦。
Next generation sequencing provides new opportunities to explore transcriptomes. However, challenges remain for accurate differentiation of homoeoalleles and paralogs, particularly in polyploid organisms with no supporting genome sequence. In this study, RNA-Seq was employed to generate and characterize the first gene expression atlas for hexaploid oat. The software packages Trinity and Oases were used to produce a transcript assembly from nearly 134 million 100-bp paired-end reads from developing oat seeds. Based on the quality-parameters employed, Oases assemblies were superior. The Oases 67-kmer assembly, denoted dnOST (de novo Oat Seed Transcriptome), is over 55 million nucleotides in length and the average transcript length is 1,043 nucleotides. The 74.8× sequencing depth was adequate to differentiate a large proportion of putative homoeoalleles and paralogs. To assess the robustness of dnOST, we successfully identified gene transcripts associated with the biosynthetic pathways of three compounds with health-promoting properties (avenanthramides, tocols, β-glucans), and quantified their expression. To our knowledge, this study provides the first direct performance comparison between two major assemblers in a polyploid organism. The workflow we developed provides a useful guide for comparable analyses in other organisms. The transcript assembly developed here is a major advance. It expands the number of oat ESTs 3-fold, and constitutes the first comprehensive transcriptome study in oat. This resource will be a useful new tool both for analysis of genes relevant to nutritional enhancement of oat, and for improvement of this crop in general.
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影响因子：
14.9
作者：
Benson DA;Karsch-Mizrachi I;Lipman DJ;Ostell J;Sayers EW
通讯作者：
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