I just returned from a NESCent Catalysis meeting on Cephalopod Genomics.
I was invited as a bioinformatics and genomics guy, and so I spent
four days in North Carolina talking about the opportunities and challenges
of sequencing cephalopods.
Cephalopods are a class of the molluscs, and include squid and
octopus, as well as Nautilus. As part of the molluscs, they're within
the broader Lophotrochozoa, a superphylum about which we know rather
little, genomically speaking.
The critters are pretty strange and interesting. They're suspected to
be quite intelligent, and are studied for their behavior. Octopus is
well known for camouflage and mimicry (see Roger Hanlon's video). Architeuthis, the
Giant Squid, is the
very definition of charismatic MEGAfauna. Loligo squid is widely
fished, and has a gigantic axon that is one of the classic models for
neurophysiology. My friend Erich Schwarz, who was also at the
meeting, said "this is as close as we're going to get to sequencing
The goal of the meeting was to chart a course forward to sequencing
cephalopod genomes. It was organized by Clifton Ragsdale, Laure
Bonnaud, and Leonid Moroz, and attended by about 30 people. 20 or
more of the attendees were members of the cephalopod community, while
the remaining people came from sequencing centers or bioinformatics
and genomics labs.
I had virtually no prior knowledge of cephs, and the first day -- on
the known biology, phylogeny, and genomes -- was an eye opener. The
smallest known ceph genomes, the pygmy squid Idiosepius, is around 2.1
Gb, and many of the genomes are 4-5 Gb, quite a bit larger than the
human genome (at ~3 Gb). Phylogenetically, the cephs are a deeply
diverged class and have about 700 species, separated by up to 300
million years or more -- as divergent as human and fish, roughly.
Unlike vertebrates, they may evolve rather quickly at a sequence
level, and to really use homology to connect sequences we may need to
sequence a bunch of cephs at various strategically-chosen distances
from each other.
The meeting concluded with a white paper writing session, and that will
presumably be made available soon. In the meantime, here are some of the
things that I found most interesting:
We ended up planning a sort of post-genomic consortium, as Eric
Edsinger-Gonzales pointed out to me. So many people are already
generating sequence (both genomic DNA and RNA) for cephs that the real
question is how to organize, collaborate, and advance as a field,
rather than how to start generating sequence.
The bioinformatics challenges for genomics on these critters are
really big. Large genomes, presumably full of repeats; unculturable
animals (meaning we can't inbreed quickly, and so are stuck with
whatever polymorphism rate we get for a critter); divergent genomes
and transcriptomes; and a really broad community scattered across 6
continents and studying between 4-10 species. I suspect that assembly
and annotation of these genomes is going to be really challenging.
We (the bioinformaticians, collectively) vehemently argued for a
liberal and explicit data-sharing policy. After a long morning
discussion about pre-publication data release, we reached a few
conclusions. First, so many people already have some sequence, and
sequencing capacity is distributed so widely, that things like the
Ft. Lauderdale agreement provide little
leverage in pressuring people to release their data. Second, there
has to be some positive incentive for people to release their data --
it's not enough to simply put in place protections for misuse of the
data. Third, many biologists do not yet subscribe to the idea that
data generation is relatively uninteresting compared to the analysis,
and (given the way pubs and grants reward people for being "first")
it's hard to blame them. Fourth, many biologists just don't see the
point of making the data available outside the community. In response
to all of these concerns, we put together a draft data sharing &
repository proposal (here);
if the community actually adopts it in the white paper, then it will
be the most explicitly liberal small-community data sharing policy
I've seen in biology. I have hopes.
Overall, I think it is increasingly hard to organize centralized or
community funding for genome projects and databases. In cases where
there isn't much funding or centralization, existing genomic resources
supported by big sites such as Ensembl and UCSC can serve as good
reference repositories. But I'm not sure what small communities
such as the cephalopod community are going to do for the next few
years. It looks like I'll be involved, so I'll let you know when
I find out...
p.s. While not directly part of the cephalopod meeting, I had an
interesting tweetstorm with Ewan Birney and Cameron Neylon this
morning, where we discussed the draft community data sharing proposal
that I'd posted. It ended with me typing up a section of the white
paper in Google Docs while they kibitzed on various aspects of the
writeup, live -- rather a unique experience for me :). Also of note, Casey
Bergman posted links to Michael Eisen's data sharing license, the
Batavia Open Genomic Data License, as well as his own
musings. Cameron also shared the
this page on
principles of data sharing and the responsibilities of data providers
and data users.
I came away from the discussion with Ewan and Cameron thinking that
the cultural gulf between organismal and molecular biologists on the
one side, and genomicists and bioinformaticians on the other side, was
still really wide and hence hard to bridge. At least some significant
part of this is driven by the culture of publication driven by the
federo-Elseverien funding/citation/impact factor complex prevalent in
Posted by Fabrizio Ghiselli on 2012-05-28 at 05:05.
I work on bivalve molluscs, and I understand 100% the challenge you're
going to face. I think you're taking the right way, and I wish the
same approach could be taken with bivalves one day... We need to know
much more about Lophotrocozoans! Best wishes, Fabrizio
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