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

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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.