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

Lead Research Organisation: University of Bristol
Department Name: Biological Sciences


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 (, 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.
Description SenecioDB is an expanding genomics resource for plant scientists, particularly those working on ragworts (Senecio) and the daisy family (Asteraceae) more generally. SenecioDB is the product of an extensive body of NERC-funded research on the evolutionary genetics of hybrid speciation in Senecio conducted by Simon Hiscock and Richard Abbott initiated under the NERC Environmental Genomics thematic programme, the aim of which was to "exploit existing and emerging genomic knowledge and technology to advance and test evolutionary and ecological theory". The "Senecio system" is rapidly becoming recognized as one of the most tractable plant models in which to study the process of speciation at a genetic, genomic, and ecological level. That speciation events in the genus, homoploid hybrid speciation and allopolyploid speciation, have occurred relatively recently and that the homoploid (diploid) hybrid species Senecio squalidus (Oxford ragwort) became invasive in the UK after its origin make Senecio a unique plant model for studies of plant evolution "in action".

Over the next few months this database will be augmented with a draft genome sequence for Oxford ragwort (Senecio squalidus) and approximately 25,000 expressed gene sequences - these data have been generated from an ongoing NERC-funded project.
Exploitation Route For such a specialist database its content is unlikely to be of use to non-academics except perhaps the background information on the homepage. The main scientific users of SenecioDB are the world community of plant scientists working on species of the Asteraceae, particularly those in the genus Senecio. The Asteraceae research community is composed of at least three groups of researchers: (i) those interested in economically important crop and weedy species, (ii) those interested in the evolutionary biology of this ecologically immensely important group, and (iii) those interested in the broad taxonomic aspects of this diverse family.
Sectors Environment

Description Grant application to NERC: NE/G017646/1 
Organisation University of Oxford
Department Department of Plant Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Collaborative research application involving Hiscock and Abbott and new collaborator Dr Dmitry Filatov (Department of Plant Sciences, University of Oxford)
Collaborator Contribution Hiscock, Filatov, Abbott and Hegarty Jointly wrote a grant application to NERC - 'The genomic basis of adaptation and species divergence in Senecio. The award was funded as a joint award to Bristol and Oxford - NE/G018448/1 and NE/G017646/1.
Impact The collaborative research proposal was funded as a joint award to Bristol and Oxford - NE/G018448/1 and NE/G017646/1.
Start Year 2009