Fish on Friday
New browsers for a whole menagerie: Manatee, Squirrel Monkey, Atlantic Cod, Coelacanth, Budgerigar, Sloth, Hedgehog, Mouse Lemur, and more!
— UCSC Genome Browser (@GenomeBrowser) November 20, 2012
It’s very cool to see more and more genomes come through and become available here. Cod particularly caught my eye because in the last year I had read that biography of cod–as much as I love biographies, it was certainly the first biography of a species I had read (Cod by Mark Kurlansky; good review of it in The Smithsonian here.). I had no idea how far back in history the Atlantic cod had spawned a fishing industry, and how much cod was being shipped around Europe. The size of the fish in the past, and the abundance, was amazing to me. Mostly I’ve been aware of the current state of cod based on the New England fishing industry drama. As the prologue of the book notes:
“The problem for the people in Petty Harbor, out here on the headlands of North America, is that they are on the wrong end of a 1000-year fishing spree.”
This fish had enormous economic and social impact on the world. And the resulting overfishing has had biological impacts as well. Anyway–now you can browse the Atlantic cod genome in the UCSC Genome Browser.
Oh, the huge manatee
I looked around at the manatee genome as well. There aren’t a lot of tracks available for manatee at this point. But I’m glad they are being studied. The NCBI genome resource notes their interesting relationship to other species:
Manatees, along with whales and dolphins, are the only mammals that spend their entire life in water. However, manatees are not closely related to whales or dolphins but rather share an ancient ancestry with elephants and hyraxes.
You can examine the manatee genome here.
Oh–and there was also an announcement of a more well-characterized assembly that has become the default on the browser: the mouse GRCm38/mm10 has become the one that loads up when you start searching now. If you need the previous one you can still choose that from the assembly menu though.
So check out the new species additions. And follow UCSC Genome Browser’s tweets for news like that.
Star, B., Nederbragt, A., Jentoft, S., Grimholt, U., Malmstrøm, M., Gregers, T., Rounge, T., Paulsen, J., Solbakken, M., Sharma, A., Wetten, O., Lanzén, A., Winer, R., Knight, J., Vogel, J., Aken, B., Andersen, �., Lagesen, K., Tooming-Klunderud, A., Edvardsen, R., Tina, K., Espelund, M., Nepal, C., Previti, C., Karlsen, B., Moum, T., Skage, M., Berg, P., Gjøen, T., Kuhl, H., Thorsen, J., Malde, K., Reinhardt, R., Du, L., Johansen, S., Searle, S., Lien, S., Nilsen, F., Jonassen, I., Omholt, S., Stenseth, N., & Jakobsen, K. (2011). The genome sequence of Atlantic cod reveals a unique immune system Nature, 477 (7363), 207-210 DOI: 10.1038/nature10342
Arnason, U., Adegoke, J., Gullberg, A., Harley, E., Janke, A., & Kullberg, M. (2008). Mitogenomic relationships of placental mammals and molecular estimates of their divergences Gene, 421 (1-2), 37-51 DOI: 10.1016/j.gene.2008.05.024