Oct 29 2012

The CephSeq Consortium has a strategy


Table 1: Cephalopod species proposed for initial sequencing efforts.

H. maculosa 4.5 Gb 10× Indo-Pacific benthic toxicity
S. officinalis 4.5 Gb - East Atlantic- Mediterranean nectobenthic classic model for behavior and development, fisheries science
L. pealeii 2.7 Gb - Northwest Atlantic nectonic cellular neurobiology, fisheries science
E. scolopes 3.7 Gb - Hawaii nectobenthic animal-bacterial symbiosis, model for development
I. notoides - 50× Australia nectobenthic model for development, small genome size










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  1. 1

    Any word on the genome for Salt and Pepper Squid?

  2. 2

    Step 3: Profit!

  3. 3
    Jebus Is My Dog

    What about the Pacific Northwest Tree Octopus? Round 2 right?? Right?!??!

  4. 4


    Newb biology question: are there any species or families where this doesn’t hold? Are there any sorts of environments that would provide selective pressure not to have a sloppy genome? My intuition is that having a sloppy genome generally isn’t disadvantageous, and without anything working against it the tendency is to build up cruft.

  5. 5
    PZ Myers

    Prokaryotes tend to have fairly ‘clean’ genomes.

  6. 6
    A. R

    Most viruses have nice, neat genomes without junk. They can do some pretty weird transcriptional and post transcriptional modifications, and most will make fairly major post translational modifications to the product proteins. Polio, for example, has a genome that encodes a polyprotein that is cleaved into the functional proteins after translation. Ebola produces four proteins and a peptide from one gene by a combination of poly-A induced frameshifts during transcription, post transcriptional modification, and post translational cleavage and glycosylation. As another example of viral genomic weirdness, the Hepatitis B virus has a partially double stranded genome that is converted to a fully double stranded one by a reverse transcriptase during replication.

  7. 7

    Thank you both for the clarifications! I thought that was a possibility with non-eukaryotes, but didn’t consider it too much due to metazoan chauvinism. A.R., thanks for the details; I had no clue viruses worked that way. Very weird.

  8. 8
    Glen Davidson

    Know your potential rivals and masters.

    Always the best strategy.

    Glen Davidson

  9. 9


    DNA replication uses energy, so a sloppy genome would be disadvantageous if your energy budget is low, and if the time required to replicate the DNA is the rate limiting step to your reproduction.

    These two hold true in most prokaryotes, and as a result, prokaryotes tend to have a streamlined genome.

    But they don’t generally hold true for eukaryotes (a eukaryote can simply increase its number of mitochondria if it needs more energy, and their cell cycles are more complicated with DNA replication only being a small part of the whole), so eukaryotes have tended to accumulate sloppy genomes.

  10. 10

    It strikes me that getting good quality samples to sequence might be a bit more challenging with A. dux than with the other candidates on that list.

  11. 11
    A. R

    Selection pressure (almost) always wins in the end.

  12. 12
    A. R

    How, by the way, do we have 60X coverage on A. dux, and no coverage L. pealeii?!?!?

  13. 13

    Thanks for the great write up. It didn’t make it in but I advocated for

    CephSeq Phase 1: Random initial projects (what you see above)

    CephSeq Phase 2: Remainder of favorite species

    CephSeq Phase 3: CephSeq 1000 – community-based sequencing of all cephalopod species. Similar to the Vertebrate 10,000 and Arthropod 3,000.

    The relatively small size of the class makes its sequencing feasible, increasingly so as sequencing costs drop and sequencing quality improves. Comparisons of say octopus to human will be fascinating – but imagine full class comparisons of cephalopods to vertebrates, mapping traits in parallel across their trees at genomic and organismal levels. Fortunately, Phase 1 already captures much of the major diversity in cephalopods, so we’ll be able to start doing analyses such as this using the representative genomes in the not so distant future. But still, I like the idea of sequencing the entire class.

    And no, there aren’t a 1000 described species yet but the numbers are growing.

    And yes, many samples will be difficult to get – but start now and we’ll get there :)


  14. 14


    It’s amazing really. Just like many other South Australians I’d never previously cottoned on to the fact that Spencer Gulf had a seriously interesting giant cuttlefish population in a unique(ish) habitat. Once I knew about them, I couldn’t get enough.

    Lots and lots of people you’d never have thought had much scientific interest generally were deeply miffed that the Gulf’s Sepia amada animals missed out on threatened species status. Though everyone knew that one main driver of the application was a proposed industrial development slap bang in the middle of their breeding grounds, they still thought “our” giant cuttlefish were special. Of course, I might just be overlooking the boating and fishing enthusiasts who seem to have a lot of good knowledge if you can tolerate listening to them rattle on about some quite tedious stuff as well.

  15. 15
    Tigger_the_Wing, Back home =^_^=

    Since reading Pharyngula, I have a growing affection for cephalopods. I only own a few toy ones, though (none of them cuddly). I must remedy that with yarn.

    Oh, and an octopus finally moved into my Animal Crossing: Wild World town this week and was a huuuge disappointment, very badly mutated; I wonder what the genome sequence would look like on this?

  16. 16

    I can only say that this project is a perfect match for our long-read (we can do 10-20kb reads!) technology.

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