Would a gene by any other name smell as sweet?

I was thinking about blogging about the paper on metal tolerance evolution in Arabidopsis halleri via a cis-regulatory change (Hanikenne et al), but I see that gnxp has already done so here. So I thought in the vein of the 'cis-regulatory vs protein' evolution debate, I would point people towards a recent paper (Scalliet et al and here for a commentary) looking at a phenotypic change involving a coding change in roses. The plant in question is the Chinese rose, which apparently is where the garden variety hybrid tea rose (chinese x european) gets its scent from. The final part of the pathway which underlies the rose's scent involves two genes (OOMT1 and OOMT2), and the authors identify a single residual underlying the crucial difference in the specificity of the two proteins. OOMT1 appears to have arisen by a gene duplication in Chinese roses, as it is absent in other roses. So here is a case of recent gene duplication followed by protein divergence underlying a novel phenotype.

Interesting the Arabidopsis halleri paper identifies both a change in copy number and cis regulatory mutation underlying a phenotype. Changes in copy number can be considered regulatory mutations (as they can change the expression level of a protein), and can be selected for because of this; a recent example of this is the amalyse copy number variation (Perry et al, see the commentary on this paper by Coyne and Hoekstra). Subsequent selection pressures may favour the functionality of the duplicates to change, by amino-acid substitutions, or changes in where the two duplicates are expressed. Thus it is very likely that evolution proceeds by a combination of regulatory (cis and copy number) and protein changes (including mutations in trans factors etc) .


References:
Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4
Hanikenne et al. Nature 2008

Evolution of Protein Expression: New Genes for a New Diet
Jerry A. Coyne, Hopi E. Hoekstra. Current Biology 2007

Diet and the evolution of human amylase gene copy number variation
Perry et al 2007. Nature Genetics

Plant biology: Scent of a rose
Shadan S. Nature (News and Views) 2008

Scent evolution in Chinese roses
Scalliet et al. PNAS 2008