[personal profile] rho posting in [community profile] science
Olivia Judson asks in her NYT column/blog ([syndicated profile] olivia_judson_feed):

If you could pick any organism to have its whole genome sequenced — what would it be?

She chose the coelacanth, which is a fine choice, but she got me thinking about other alternatives that I might choose, if I were in the position.

My first thought here was trichoplax, an amorphous little blob of an animal close to the base of the animal family tree, and with a relatively small genome to boot. I see that there’s a trichoplax project underway already though, so onto my next idea.

After a bit of thought I decided on the Tasmanian Devil for a few reasons:

1. Marsupial sequencing is much thinner on the ground than placental sequencing, and having more marsupials sequenced could be instructive when it comes to comparing us with our more distant mammalian cousins.

2. Devil Facial Tumour Disease is pretty terrifying. Or rather, the thought of a similar transmissible cancer that effected humans ever existing is terrifying. If we better understood the devils, we’d have a better chance of understanding their cancer.

3. There are conservation concerns here too, with DFTD threatening the devils as a species.

4. The Tasmanian devil is a charismatic and iconic animal that fires the public imagination. Science and conservation both desperately need to get the general public as interested as possible.

So what would you choose? And if you're an actual real biologist, why are my choices hopelessly naive and bad?

Date: 2009-09-03 03:15 pm (UTC)
yvi: Kaylee half-smiling, looking very pretty (Default)
From: [personal profile] yvi
So what would you choose?

None. I would choose to have the currently available genomes available in good quality first. I am working with insect genomes + a cnidarian at the moment and the quality of many of these is too horrible to work with even if they have been published for more than a year.

I am probably too jaded by now, having worked with several whole genomes and proteoms to get excited about genome sequencing - it's not as great as it looks until the data has been reviewed for a few years. Right now, its okay to work with Drosophila melanogaster or Arabidopsis thaliana, but I haven't seen many more really good genomes.

I'm also not sure that things like studying Devil Facial Tumour Disease would benefit greatly from a while genome sequecing, even if done at high quality.

More muti-cellular animals outside of the vertebrate and insect clades would be great, though. There's Nematostella vectensis and Hydra magnipapillata for cnidarians, a few nematodes and not that much else. More coverage of the other regions would be nice.

List of currently available or in-progess genomes.

Yvi, disillusioned Bioinformatician ;)
Edited Date: 2009-09-03 03:26 pm (UTC)

Date: 2009-09-03 04:56 pm (UTC)
troisroyaumes: Painting of a duck, with the hanzi for "summer" in the top left (Default)
From: [personal profile] troisroyaumes
Hey, I know a professor in my department who is working on the trichoplax project. (He presented some of the work at last year's departmental retreat. It is really weird.)

I work with yeast (which I would like to abandon for a less human-domesticated species), so my personal vote is for any exotic fungi. Some of them occupy really interesting ecological niches.

Date: 2009-09-03 05:47 pm (UTC)
holyschist: Image of a medieval crocodile from Herodotus, eating a person, with the caption "om nom nom" (Default)
From: [personal profile] holyschist
Not a biologist (I study fossils, not genetics), but I'd be interested in a monotreme (echidna or platypus)--they're more basal than marsupials, and it could be some fascinating data. I'm not sure how much work on monotreme genomes has been done already, although I know there's some.

Date: 2009-09-03 07:29 pm (UTC)
yvi: Kaylee half-smiling, looking very pretty (Default)
From: [personal profile] yvi
The platypus has been sequenced, and the sequences are being worked on. Not sure how good the sequencing was, though.

Date: 2009-09-03 08:28 pm (UTC)
holyschist: Image of a medieval crocodile from Herodotus, eating a person, with the caption "om nom nom" (Default)
From: [personal profile] holyschist
That's what it looked like to me, but I wasn't sure if they'd finished. And quality is always the question.

Date: 2009-09-07 02:06 am (UTC)
mrcreek: Rana palustris, the pickerel frog (Default)
From: [personal profile] mrcreek
Fortunately, we are basically already at the point where all major groups have a genome project in the works. Whatever species if your favorite, it probably has a (somewhat) close relative being sequenced. I'm more interested in the next step of sequencing multiple genomes from several individuals of the same species, to look at within-species diversity. The best species for such projects would show lots of variation in phenotypes: domestic dogs, stickleback fish, monkeyflowers, the cabbage-type vegetables, etc. All of these species are the targets of single-genome projects, but it's the prospect of poly-genome projects that gets me excited. Tiger salamanders are also a phenomenally diverse species, but that might be a while since salamanders have very large genomes.


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