Friday, September 16, 2011

Finally, the lamprey is there!

Today, the Ensembl genome database released the new version 64. Finally, this version includes the sea lamprey, Petromyzon marinus, in addition to the other new species, Tasmanian devil.

It has been a big interest, at least to me, if they handled molecular phylogeny of lamprey genes well or not. Here I am writing about orthology identification between lamprey genes and jawed vertebrate genes. It should not be so simple as they experienced for many of other species in Ensembl. Lampreys occupy a unique phylogenetic position relative to the so-called two-round (2R) whole genome duplications. As far as I have tried so far, there seems a lot of tricky issues in this resource. I am not criticizing the quality of work done for this. My point is that the lamprey genome has a lot of unique features that are hard to cope with based on traditional approaches of genome sequencing and annotation.

I have just realized that I have not written a lot about the 2R whole genome duplications in this blog. Actually, that was the main motivation to start this blog.

... more to follow.