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首页> 外文期刊>Agronomy >Characterisation of Faba Bean ( Vicia faba L.) Transcriptome Using RNA-Seq: Sequencing, De Novo Assembly, Annotation, and Expression Analysis
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Characterisation of Faba Bean ( Vicia faba L.) Transcriptome Using RNA-Seq: Sequencing, De Novo Assembly, Annotation, and Expression Analysis

机译：利用RNA序列表征蚕豆（Vicia faba L.）转录组：测序，从头组装，注释和表达分析

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RNA sequencing (RNA-Seq) is a deep sequencing method used for transcriptome profiling. RNA-Seq assemblies have successfully been used for a broad variety of applications, such as gene characterisation, functional genomic studies, and gene expression analysis, particularly useful in the absence of a well-studied genome reference sequence. This study reports on the development of reference unigene sets from faba bean using RNA-Seq. Two Australian faba bean cultivars (Doza and Farah) that differ in terms of disease resistance, breeding habit, and adaptation characteristics, and have been extensively used in breeding programs, were utilised in this study. The de novo assembly resulted in a total of 58,962 and 53,275 transcripts with approximately 67 Mbp (1588 bp N50) and 61 Mbp (1629 bp N50) for Doza and Farah, respectively. The generated transcripts have been compared to the protein and nucleotide databases of NCBI, as well as to the gene complements of several related legume species such as Medicago truncatula , soybean, and chickpea. Both assemblies were compared to previously-published faba bean transcriptome reference sets for the degree of completeness and utility. Annotation of unigenes has been performed, and patterns of tissue-specific expression identified. The gene complement derived from this comprehensive transcriptome analysis shows that faba bean, despite its complex 13 Gbp genome, compares well to other legumes in expressed gene content. This study in faba bean represents the most comprehensive reference transcriptomes from two different Australian cultivars available to date and it provides a valuable resource for future genomics-assisted breeding activities in this species.
机译：RNA测序（RNA-Seq）是用于转录组分析的一种深度测序方法。 RNA-Seq组件已成功用于各种应用，例如基因表征，功能基因组研究和基因表达分析，特别是在缺少经过充分研究的基因组参考序列的情况下尤其有用。这项研究报告了使用RNA-Seq从蚕豆开发参考单基因集的过程。在这项研究中，使用了两种澳大利亚蚕豆品种（Doza和Farah），它们在抗病性，育种习性和适应性特征方面有所不同，并已广泛用于育种程序中。从头开始的装配总共产生了58,962和53,275个转录本，其中Doza和Farah分别约为67 Mbp（1588 bp N50）和61 Mbp（1629 bp N50）。已将生成的转录本与NCBI的蛋白质和核苷酸数据库进行了比较，并与几种相关豆科植物物种（例如紫花苜蓿，大豆和鹰嘴豆）的基因补体进行了比较。将这两个程序集与以前发布的蚕豆转录组参考集进行了比较，以了解其完整性和实用性。已经对单基因进行了注释，并确定了组织特异性表达的模式。从这种全面的转录组分析得出的基因补体表明，尽管蚕豆具有复杂的13 Gbp基因组，但其表达的基因含量却与其他豆类相比很好。蚕豆的这项研究代表了迄今为止来自两个不同澳大利亚品种的最全面的参考转录组，它为该物种未来的基因组学辅助育种活动提供了宝贵的资源。

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