School of Biological Sciences, University of Bristol, Woodland Road,
Bristol, BS8 1UG
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The genomic basis of adaptation and species divergence in Senecio
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. The fact that speciation events in the genus 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 alternative to more conventional plant models, such as Arabidopsis, for studies of plant evolution 'in action'. Previous work in this laboratory, carried out by Dr Matthew Hegarty, found evidence of rapid extreme changes to gene expression associated with homoploid and allopolyploid speciation in Senecio. More recently, he identified candidate genes potentially involved in physiological adaptation of S. aethnensis to elevated UV regimes on Mt Etna, and of S. squalidus to low sulphur soils typical of the UK. We have also set up, and host, the website SenecioDB, providing a new resource of 12,000 ESTs to the research community and a UK contribution to the US-based Compositae Genome Project.
The molecular bases of our observed changes to gene expression in Senecio have, however, proved difficult to address in the absence of a reference genome. For instance, it is not clear to what extent different gene expression is the result of adaptation to different environmental conditions (as opposed to phenotypic plasticity), and what genomic factors (coding regions and/or regulatory regions) are involved in the relatively rapid evolution of expression differences. Changes to gene expression are recognized as an important mechanism of evolutionary change, but few studies have made explicit correlations between gene expression change, adaptation and phenotypic divergence. We are making use of recent advances in sequencing technology to screen the genomes of different species for differences in coding and regulatory regions potentially associated with adaptation and species divergence. Initially, we are working on the production of a reference genome for Senecio. Future work will include miRNA profiling and ChIP-seq using core transcriptional machinery to look at changes in regulatory processes that are potentially involved in adaptation and species divergence. Analysis of this data in conjunction with investigations into the variation and selection of protein coding sequences by our collaborators in Oxford should then allow us to begin to gain some insight into the relative importance of regulatory and coding genomic changes to speciation and adaptation.
1. Establish a partial reference genome by 454 sequencing of the gene-space (non-repetitive fraction of the genome) of Senecio squalidus to enable a genome-wide evolutionary genetic analysis of coding and regulatory regions.
2. Interrogate the Senecio gene-space to identify protein- and microRNA-binding regulatory sites for evolutionary genetic analysis.
3. Analyse patterns of DNA polymorphism to identify protein coding and protein- and miRNA binding regulatory regions that may have been involved in local adaptation and speciation, and to investigate the evolutionary history of the three Senecio species.
4. Test whether altered gene expression/regulation, potentially involved in adaptation, is determined by species divergence or phenotypic plasticity.