Data Mining: SenecioDB - development of existing EST data into a publicly available web resource for the Asteraceae community.

数据挖掘：千里光数据库 - 将现有 EST 数据开发为菊科社区的公开可用网络资源。

• 批准号: NE/F001207/1
• 负责人: Simon Hiscock
• 金额: $ 3.28万
• 依托单位: University of Bristol
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2008
• 资助国家: 英国
• 起止时间: 2008 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FF001207%2F1
• 关键词: Data; Mining; SenecioDB; development; existing

The Asteraceae family (daisies) is one of the largest plant families, containing around 10% of the world's flowering plants. It is also one of the most diverse families and contains many examples of hybridisation between species, many of which have occurred recently. The Asteraceae therefore represent a model group for investigation of hybridisation and adaptive radiation in flowering plants, yet it is unlikely that genome sequencing of any family member will occur in the near future. Expressed sequence tags (ESTs) represent a possible answer to this problem. It has been noted that EST collections are increasingly being used as the foundation of genome-scale analyses, using EST contig assemblies and singletons as 'gene collections'. Various resources, such as protein databases and the GO ontologies, can and have been used to tentatively annotate these collections with gene function. Such collections are useful for selection of common genes between different family members and can be used to estimate the percentage of conserved genes between genomes. Furthermore, by comparing data sets between libraries prepared from different tissues, it is possible to identify candidate genes involved in a range of developmental and/or stress responses, allowing these to be taken forward for functional analysis. Finally, a proportion (~2-5%) of ESTs are known to contain simple-sequence repeats (SSRs), and it has been demonstrated that these are generally better conserved between plant family members than those found in non-coding regions of the genome. The availability of EST collections within families is therefore useful as it becomes possible to develop SSR primer sets for one genus which stand a relatively high chance of successfully amplifying corresponding genetic regions in another, enabling basic genotyping analysis. At present, large-scale EST sequencing within the Asteraceae family has only been performed within a small number of family members, including lettuce and sunflower. The most substantial collection to date is the Compositae EST database (http://cgpdb.ucdavis.edu), a collaborative effort between several institutions in the United States. This proposal aims to develop an existing collection of ESTs from Senecio (ragwort) into a publicly available online resource for the Asteraceae research community. This will add around 11,000 sequences to the existing Asteraceae collection and provide important computational tools to enable researchers to identify regions of commonality/divergence between Asteraceae family members.

菊科（雏菊）是最大的植物家族之一，约占世界显花植物的10%。它也是最多样化的科之一，包含许多物种之间杂交的例子，其中许多是最近发生的。因此，菊科代表了一个模式组的调查杂交和适应性辐射在开花植物，但它是不可能的，基因组测序的任何家庭成员将在不久的将来发生。表达序列标签（EST）代表了这个问题的可能答案。人们已经注意到，EST集合越来越多地被用作基因组规模分析的基础，使用EST重叠群组装和单例作为“基因集合”。各种资源，如蛋白质数据库和GO本体，可以并且已经被用来尝试性地用基因功能注释这些集合。这样的集合对于选择不同家族成员之间的共同基因是有用的，并且可以用于估计基因组之间的保守基因的百分比。此外，通过比较从不同组织制备的文库之间的数据集，可以鉴定参与一系列发育和/或应激反应的候选基因，从而使这些基因能够用于功能分析。最后，已知一部分EST（~2-5%）含有简单序列重复（SSR），并且已经证明这些在植物家族成员之间通常比在基因组的非编码区中发现的更保守。因此，家族内EST收集的可用性是有用的，因为它可以开发一个属的SSR引物组，其具有相对高的成功扩增另一个属中相应遗传区域的机会，从而能够进行基本的基因分型分析。目前，大规模EST测序仅在少数家族成员中进行，包括莴苣和向日葵。迄今为止，最丰富的收集是菊科EST数据库（http：cgpdb.ucdavis.edu），这是美国几个机构之间的合作成果。该提案旨在将现有的千里光（豚草）EST集合开发成供菊科研究社区使用的公开在线资源。这将为现有的菊科收集增加约11，000个序列，并提供重要的计算工具，使研究人员能够识别菊科家族成员之间的共同/分歧区域。