SQUEEEEEEEEE!!!!!!!!

The first sequenced carnivore genome shows complex host-endogenous retrovirus relationships.

ONE note of dismay: They did not include a picture of the boxer they sequenced. WTF???

Substitute picture:
funny dog pictures - Goggie ob teh Week: I Eated All the Cookies :(
see more dog and puppy pictures

Fun quickies!

  • Despite Arnies love of getting into the garbage, dogs have much less junk DNA via proviral ERVs than humans (them <0.15%, us 0.8%)
  • Of the 407 kinda ERVs, most are gammas (313) and betas (28)
  • Only 44 had potentially fully open gag-pol-env
  • Only 36 still had their LTRs
  • Their ERVs are backwards! With DNA, there really is no ‘wrong’ direction– like how the people in Australia dont feel like they are upside down, the ERVs dont know they are upside down… but being upside down means they cant alter gene expression the same way the ones that are rightside up, relative to the other genes, can. Apparently ERVs that are in the same orientation as the genes, in dogs, have been actively selected against. The older they are, the more likely they were to be backwards.
  • New word: putative + protein = PUTEINS LOL!!!
  • When they looked at all the putein pols… some of them clustered in a phylogenetic tree with HUMAN ERVs! HERV-Fc. They integrated in dogs and humans long before there was a dog + humans, so we probably didnt get them from each other. It was probably just a kind of virus that was sampling hosts, and was more successful in dogs than it was in primates, as humans just have a handful, and dogs have a bunch. I still like knowing I share a bit of ERV history with Arnieman.

Really neat paper. Needed a piccie of teh puppah, even if it was only in the supplemental. Probably going to email the authors for a piccie. :-D

Comments

  1. #1 Taki
    May 20, 2011
  2. #2 Sili
    May 20, 2011

    dog + humans

    Perhaps, but what about PYGMYS+DWARFS! ?

  3. #3 Poodle Stomper
    May 20, 2011

    Really neat paper. Needed a piccie of teh puppah, even if it was only in the supplemental. Probably going to email the authors for a piccie. :-D

    You may not want to do that without specifying “if the dog is alive”. A lab-mate of mine did a lot of cat genetics and they’d have freezers full of cats. They’d have to go chip off pieces of frozen cat when their stocks got low so I’d hate for the authors to mail you a photo of a chipped-away freezer-pooch.

  4. #4 herr doktor bimler
    May 20, 2011

    Needed a piccie of teh puppah

    But what about the anonymising black bar across the eyes? FOR SHAME.

    DO rodent geneticists have mice-blocks?

  5. #5 LordKhaine
    May 20, 2011

    No boxers were harmed in generating the dog genome. Simple blood draws were used. Her name was Tasha, but since the genome was published, she has passed away from natural causes!

  6. #6 LordKhaine
    May 20, 2011

    :(

  7. #7 LordKhaine
    May 20, 2011

    Oh, and if you’re interested, a pic of Tasha is in the upper right hand of this page:
    http://www.broadinstitute.org/mammals/dog

  8. #8 William Wallace
    May 21, 2011

    Which ones do our cousins have in common with us? Or did the whole ERV as “more proof of global warming” oops, sorry, wrong “science”. I meant ERVs as “more proof of evolution” argument get tossed down the memory hole?

  9. #9 Arkady
    May 21, 2011

    Recently heard at a conference of an interesting discovery of a dog virus: a new, closer relative of HepC. There’s a group at Columbia doing random PCR to find new viruses, and they found this in respiratory (!) samples from dog shelters. They haven’t found enough sources yet for a comprehensive evolutionary analysis, but the current hypothesis is that it’s more likely they got the virus from us rather than the other way around, between 400-1600 years ago depending on the analysis method used. Seems to be pre-publication still though, can’t find a paper yet.

  10. #10 Poodle Stomper
    May 21, 2011

    No boxers were harmed in generating the dog genome. Simple blood draws were used.

    Good. I happen to like dogs. =)

  11. #11 John Marley
    May 22, 2011

    @Willy Wally:

    At least read the post before making snide remakes, then you might not look quite as idiotic.

    some of them clustered in a phylogenetic tree with HUMAN ERVs! HERV-Fc. They integrated in dogs and humans long before there was a dog + humans, so we probably didnt get them from each other.

    Okay, that doesn’t say how many, but ERV is summarizing. Follow her link to read the paper.

  12. #12 W. Kevin Vicklund
    May 22, 2011

    John, that doesn’t actually address what Wallaids is asking. Those HERV-Fc and CtERV clusters represent independent insertions wrt the two species, and would not be useful for determining common descent of dogs and humans. However, they do serve as a falsification test for the current model of descent, as the ERV’s should not be homologous wrt location in the two genomes.

    Or to say it another way, we can create viral phylogenies from the data you referenced, but not metazoan phylogenies.

  13. #13 John Marley
    May 23, 2011

    @ W. Kevin Vicklund

    Okay, fair enough. I think you’re giving Willy Wally too much credit, though.

  14. #14 fnxtr
    May 23, 2011

    Layman question spawned from ERVs-in-backward: how does RNA know which strand to read? Linky to basics would be appreciated. Thanks.

  15. #15 ERV
    May 23, 2011

    They only looked at the youngest ERVs, the almost complete ones. They inserted long after humans and dogs diverged, but still before the Christian deity created the universe.

  16. #16 ERV
    May 23, 2011

    fnxtr– A lot goes into figuring out whether a gene (DNA) is transcribed (RNA), but learning about promoters would be a good place for a layman to start :)

    With retroviruses, the ‘LTR’ (see the link in my post) acts as a promoter. If a retrovirus is in the same direction as genes in the region, those LTRs can act as promoters for host genes. If they are in reverse, they might still make host genes RNA, but it will be backwards too, which might cause other problems. But for some reason, ‘the same direction’ has been selected against in dogs. That pattern hasnt been noticed in humans. Dunno why yet!

  17. #17 fnxtr
    May 23, 2011

    Fascinating. Many thanks, ERV.

  18. #18 W. Kevin Vicklund
    May 23, 2011

    They only looked at the youngest ERVs, the almost complete ones.

    I thought that was the case, but it wasn’t clear to me exactly how sensitive the test protocol was. With that info in hand:

    I predict that none of the CfERVs detected using this method will be homologous with HERVs, barring the possibility of certain known conserved sequences such as found in placental genes. Any similar sequences will not be located in matching segments, indicating independent insertion events.

  19. #19 Azkyroth
    May 24, 2011

    New word: putative + protein = PUTEINS LOL!!!

    If you find one that might produce lethal mutations in bears, I’m going to laugh.