Yes! After we had used a newly developed and very sensitive software tool called ADHoRe to detect all duplicated segments in the genome of Arabidopsis, it became clear that some duplicated segments lost all similarity between them, due to extreme gene loss. However, they can still be identified as being homologous by comparing them with a third segment, with which they both are still colinear.

Our paper shows that large-scale gene duplication events (such as genome doubling or polyploidy events) are most likely recurring events in the evolution of land plants and possibly in other eukaryotic organisms as well—in the meantime, we have also provided evidence for a genome duplication in ray-finned fishes (PNAS 101, 1638—43, 2004). Additionally, we have also demonstrated that, in order to find remnants of very old genome duplication events, simple pairwise comparisons of chromosomes are not sufficient, but more sophisticated bioinformatics approaches have to be adopted.

I had been studying gene and genome duplications in ray-finned fishes in the lab of Axel Meyer at the University of Konstanz, Germany, for some years before I became Professor and team leader of the Bioinformatics team of the Department of Plant Systems Biology at Ghent University, Belgium. Investigating the duplication past of the favorite genome of plant biologists simply was the logical next step.