Japanese lamprey gene set now available at aLeaves

As announced in the change log, I have included the predicted gene set of the Japanese lamprey (Lethenteron japonicum) in the database #6 of aLeaves, the homolog collection tool I have been maintaining.

Complicated! - lamprey genome resource availability

I have been asked by many of people around me about publicly available resources of the sea lamprey genome. I have just written down some facts and information on an independent new page inside this blog, titled 'Lamprey genome guide'. The situation is somewhat complicated, I see.

I will try to keep this page updated for the lamprey researchers' convenience.
I believe this third-party guide does not interfere any database function and research activity by other researchers. But, please let me know if there is some problem.

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.