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.