cephalopod genomic model

glowgoose

Larval Mass
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#1
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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#2
: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

Colossal Squid
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#3
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

Colossal Squid
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#4
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.
 

Neogonodactylus

Haliphron Atlanticus
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#5
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
 

monty

Colossal Squid
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#6
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

Colossal Squid
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#8
I forgot to say :welcome: to TONMO, glowgoose, too... It sounds like you're up to some good stuff!
 

glowgoose

Larval Mass
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#9
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

Vampyroteuthis
Supporter
#10
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.
 

monty

Colossal Squid
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#11
that Strugnell et al paper is great; I haven't looked at the others yet... in the non-coleoid domain, there's also a chapter in Saunders & Landman 1987 Nautilus: The Biology and Paleobiology of a Living Fossil that covers a bit of living nautilus info. The chapter authors are Woodruff, Carpenter, Saunders, and Ward, and refer to more details in "Woodruff, D.S. and Carpenter, M.P., 1987, Biochemical genetics of Nautilus (in prep.)" which I can't find.

Unfortunately, while I'm good at looking up papers, I don't know enough of the terminology to read them without looking up several words per paragraph, so I apologize in advance if I contribute any foolishness to this discussion... I'm trying to pick up molecular palaeontology "on the street." In particular, I don't know the terms to know if the Nautilus paper's 1987 MolBio techniques are so outdated that they're not relevant to the discussion, but I wonder if they kept the samples such that they could compare the Nautilus to the results Robyn just mentioned...

p.s. it's pretty easy to find Brenner's email at the Salk with google. If Roy doesn't have more details on that, perhaps sending him an inquiry would get us a bit more info. I've never emailed a Nobel Laureate before...
 

robyn

Vampyroteuthis
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#12
I drew a blank on the Woodruff and Carpenter paper as well. From what I can tell from the book, they used allozyme data and built a tree on a distance-based method. Obviously genetic sequence data gives better resolution than this, and distance-based methods are not so hot anymore, although I imagine their approach was pretty good for 1987.

I agree the Strugnell et al paper is excellent - MrBayes is an easy program to abuse, from what little I understand of it, but these authors do a really nice job of explaining their methods, and the bias of AIC toward over-fitted models is nicely shown. The combined-methods paper from Cladistics is quite good too, despite the rapidly-disintegrating reputation of cladistics as a science...

Several of those papers have sequences from nautiluses in their lists.
 

main_board

Vampyroteuthis
Supporter
#13
At the last CIAC conference there were a few presentations regarding cephalopod genetics. From the CIAC website, there a link to past conferences, and in the 2006 section there's a link for a PDF with the abstracts (among other information).

So none of these entail entire sequencing, so I'm not sure if these apply at all, but I thought I would post them anyways as a FYI:

Conservation of Hox genes among molluscs: the cephalopod exception
Mathieu Pernice, Jean S. Deutsch, Aude Andouche, Renata Boucher-Rodoni, Laure Bonnaud

Issues in oegopsid phylogenetics: can molecular data help to further resolve relationships within Oegopsida?
Annie Lindgren

Phylogeny and population genetics of Alloteuthis (Loliginidae) and discovery of a cryptic species
F.E. Anderson, V. Laptikhovsky, A. Pilsits, G. Bello

Genetic diversity of isolated populations of Nautilus pompilius in the Coral Sea
Billy Sinclair

Genetic and morphological identification of Onykia paralarvae from Northern Hawaiian and western Pacific waters
Wakabayashi Toshie, Tsunemi Kubodera, Taro Ichii, Mitsuo Sakai, Seinen Chow

Squids of the family Gonatidae – genetic relationships and life cycle strategies
O.N. Katugin, A.R. Lindgren, E. Amezquita, M.K. Nishiguchi

The papers haven't been published yet, so all you get is an abstract, but it also gives some contact details if you want to get ahold of any of the researchers.

I know that CIAC was also in support of a Cephalopod Barcode of Life project, and there appear to be some already in the system. Of course, these aren't entire sequences either.

From your list of requirements, I'm thinking Sepia bandensis. They're resonably small (9-14 cm), I guess as easy to keep as any ceph is, kind of social, and have short generation times (less than a year). The eggs are usually black from ink, but eventually clear up (I have no idea if the black can be removed prematurely). People on the boards are in the process of working out the kinks in aquaria breeding. Its been done and can be done, but controlling the details you request is not possible yet (at least I don't think).

Disclaimer: None of this is my own experience, just what I've picked up/remembered from previous threads and info from Thales' excellent article I linked to above. So in conclusion, I guess I don't have a whole lot to contribute. But this thread sounds interesting!


Cheers!
 

main_board

Vampyroteuthis
Supporter
#14
I meant to include this as well. Though none deal with entire sequences, there is a fairly broad selection of sections that are sequenced between all the papers (maybe you can piece together an entire sequence 8) ).

Sorry for the extra post. I tried to just add this in by editting my last post but it wouldn't save.

Cheers!
 

monty

Colossal Squid
Staff member
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#15
main_board;89256 said:
Sorry for the extra post. I tried to just add this in by editting my last post but it wouldn't save.
that's weird. I did an edit to add the p.s. in my post, but I do have super-staff-powers... how did it fail? Did it get an error message, or did it do that "spin the spinner forever when you click the submit button" thing?

Thanks for the post, in any case... lots of fun stuff to read...

- M
 

main_board

Vampyroteuthis
Supporter
#16
monty;89257 said:
"spin the spinner forever when you click the submit button" thing?
That's what it did, aye! Funny indeed. I went and editted my second quick post no problem (when I posted them). Then went back and tried to edit the first (and save you all of the second) but it wouldn't have it. This same thing happened earlier too.

Cheers!
 

monty

Colossal Squid
Staff member
Supporter
#17
main_board;89260 said:
That's what it did, aye! Funny indeed. I went and editted my second quick post no problem (when I posted them). Then went back and tried to edit the first (and save you all of the second) but it wouldn't have it. This same thing happened earlier too.

Cheers!
I sometimes find that if I use the "go advanced" I can submit from the "advanced" page even when the "quick reply" doesn't work... but it'd be nice to track this pesky bug down. What browser and OS are you using?
 

Nancy

Titanites
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Moderator
#18
I was contacted last year by an editor of a newsletter wanting to report on a group doing sequencing of O.bimaculoides.
At that time he wanted to use my photos. Then he decided to wait until the project was completed.

I've contacted him again for more information, since I've heard nothing for about a year.

Nancy
 

Neogonodactylus

Haliphron Atlanticus
Staff member
Moderator
#19
This is consistent with what I know. We were asked last year to recommend a species that would be suitable for sequencing. We recommended O. bimaculoides and helped locate and animal. A colleague dissected out various tissues for them and these will also be used in the analysis. Unless they give me permission, I do not feel free to name the lab doing this.

Roy
 

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