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cephalopod genomic model

glowgoose

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Mar 4, 2007
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Hi folks,

Science needs a cephalopod laboratory model for comparative genomics!

with the new marine aquarium facility being constructed at where I work (University of Texas at Austin) I am contemplating the possibilities...

As far as I am aware, none of the ceph species are currently used as a genomics/genetics laboratory model. I would greatly appreciate your opinion on which species might become such a model. The requirements (in order of importance):

1. must propagate in aquarium
2. must be made to reproduce at a whim of experimenter (i.e. in any season, with any partner)
3. stages of development should be accessible (i.e., egg casing should be transparent and removable without killing the embryo)
3. have short generation time (from hatching to sexual maturity)
4. preferrably small (
 

Clem

Architeuthis
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:welcome:
Hello Misha,

I, personally can't answer your query, but you will get replies from those who can. Interesting work vis marine fluorescence you're doing at the Matz Lab, sir.

Cheers,
Clem
 

WhiteKiboko

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Granted, i'm a tad ignorant, but given the proper setup does anyone else get a squidish vibe? quick growth, large numbers, social, etc....

oh, also :welcome:
 

monty

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These folks used Euprymna scolopes

http://www.nature.com/nature/journal/v424/n6952/abs/nature01872.html

My dream "cephalopod genome project" would sequence an octopus, several squids, vampyroteuthis, spirula, argonauta, and nautilus, but that's at the "impractical" end of the spectrum, as opposed to your very pragmatic question...

I think cuttlefish might be worth considering, and perhaps large-egged dwarf octos.
 

monty

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Neogonodactylus;89228 said:
I was under the impression that O. bimaculoides is or already has been sequenced. It was chosen because it was a large egged species that can be reared.

Roy
That's great news! I hadn't heard anything about a "genome project" for any ceph...

I can't find any publication info on anything resembling a complete sequence, just some marker comparisons with other species and mitochondrial DNA:


http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7663761&dopt=Abstract
http://www.blackwell-synergy.com/do...0469.2004.00277.x?cookieSet=1&journalCode=jzs

but that could be consistent with "keeping it under wraps until publication," although I'd think that for a project like that that's unable to get "scooped" the lab would put it on their web page to give "we got a grant to do the octopus genome project" publicity... but I'm not always wise in the ways of strategic secrecy.

One last google search (for "octopus genome") did turn up this intriguing pair of sentences at http://www.oist.jp/faculty_brenner.html

We have also undertaken a study of the octopus genome. This organism has a large brain built on different principles from the vertebrate plan.
I can't find any publications related to this, though, so I don't know if it's bimacs...
 

monty

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I forgot to say :welcome: to TONMO, glowgoose, too... It sounds like you're up to some good stuff!
 

glowgoose

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monty;89230 said:
That's great news! I hadn't heard anything about a "genome project" for any ceph...

I can't find any publication info on anything resembling a complete sequence, just some marker comparisons with other species and mitochondrial DNA:


http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7663761&dopt=Abstract
http://www.blackwell-synergy.com/do...0469.2004.00277.x?cookieSet=1&journalCode=jzs

but that could be consistent with "keeping it under wraps until publication," although I'd think that for a project like that that's unable to get "scooped" the lab would put it on their web page to give "we got a grant to do the octopus genome project" publicity... but I'm not always wise in the ways of strategic secrecy.

One last google search (for "octopus genome") did turn up this intriguing pair of sentences at http://www.oist.jp/faculty_brenner.html



I can't find any publications related to this, though, so I don't know if it's bimacs...
OK, here is what is on the surface:

1. The only two species on which some genomics have been attempted (in both cases, random sequencing of expressed genes, called EST - expression sequence tags) are Euprymna scolopes (bobtail) and Idiosepius (tiny chaps attaching themselves to Zostera grass). That's what in Genbank (http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi). There is just a few octopus sequences suggesting that nobody yet approached the genome.

2. Despite Brenner's claim that Monty cites (btw Brenner is the guy who introduced the nematode Caenorhabditis elegans as a model) there is no mention of octopus sequencing on the Joint Genome Institute website (http://www.jgi.doe.gov/sequencing/allinoneseqplans.php) and no sequences in Genbank. JGI, being a federal institution, has to keep everythig open, so if it is not showing than it is not happening. There is no cephalopod sequencing project at JGI at all, in fact. So if it is going on, it is kept quiet - which woudl be extremely unusual, only pharmacologists do that.

please let me know if you find something else!
 

robyn

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Jan 19, 2007
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Hi Misha,

Welcome.

Re: accession numbers. I'm not sure if this is at all what you're looking for, but here's some citations that include accession numbers for cephalopod taxa:

Lindgren et al, 2004. Cladisitics 20. 60 ceph species, sequences of 18S, 28S, H3 and COI.

Passamaneck et al, 2004. Mol Phylogenetics and Evolution 32. 7 ceph species. Sequences of LSU and SSU

Strugnell et al, 2005. Mol Phylo and Ev. 37. 35 coleoid species. Genes ODH, pax-6, Rhodopsin, COI, 12S and 16S

Piertney et al, 2003, Mol Phylo and Ev. 27. 11 cirrate species. Gene 16S

Pernice et al, 2006. Mol Phylo and Ev. 40. 3 ceph species, Genes Hox

I hope this is vaguely useful. If its not what you need, apologies! Cool stuff and nice website, BTW.

I have pdfs that I can forward if you would like.

Robyn.
 

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