Release 57 saw the release of a 5-way EPO alignment across the telost fish – Zebrafish, Stickleback, Medaka, Tetraodon and Fugu. Just recently I’ve spent some time browsing through them. They are very interesting, with the ancestral duplication in Fish showing more complex homology relationships than in mammals. Here’s a nice, clean example
Here is a far more complex region, when ENREDO has clearly picked up the ancestral duplication but is struggling to make it colinear across the entire region
One thing which I don’t think most people appreciate is the incredible phylogenetic depth in the telost linage. In terms of “millions of years of evolution” or “sequence divergence” actually the deepest splits in the telosts – such as ZebraFish to Stickleback – are almost as deep as telosts to mammals – certainly deeper than birds to mammals. So this is asking alot to find good, clearly co linear stretches, in particular when you think of the draft nature of these genomes.
Chatting to Javier, it might be much better to also look at a 4-way EPO on the “Stickleback” side of the telost linage, in other words, Medaka/Stickleback/Fugu/Tetraodon. This I think will come together better (in fact most of the “nice” regions in the 5-way EPO are actually regions without ZebraFish) and we might be able to look at taking that ancestral chromosome ordering and perhaps sequence in comparisons to Zebrafish.