Breaking News: The First Ant Genomes

Camponotus floridanus & Harpegnathos saltator

The journal Science has just reported the first ant genome study. Well, the first ant genomes. A pair of them, from the Florida Carpenter Ant Camponotus floridanus and the Indian jumping ant Harpegnathos saltator, both study animals in the lab of Arizona State University’s Juergen Liebig.

Abstract: The organized societies of ants include short-lived worker castes displaying specialized behavior and morphology and long-lived queens dedicated to reproduction. We sequenced and compared the genomes of two socially divergent ant species: Camponotus floridanus and Harpegnathos saltator. Both genomes contained high amounts of CpG, despite the presence of DNA methylation, which in non-Hymenoptera correlates with CpG depletion. Comparison of gene expression in different castes identified up-regulation of telomerase and sirtuin deacetylases in longer-lived H. saltator reproductives, caste-specific expression of microRNAs and SMYD histone methyltransferases, and differential regulation of genes implicated in neuronal function and chemical communication. Our findings provide clues on the molecular differences between castes in these two ants and establish a new experimental model to study epigenetics in aging and behavior.

Below is a schematic from the paper that on a crude level depicts the overall similarity of the new genomes to previously published insect genomes (click to enlarge):

These genomes could be a great resource for myrmecologists. And I mean that: they could be. But they probably won’t.

As this project was funded by a private source (the Howard Hughes Medical Institute), the original data are only available to the scientists directly involved. This not only means that outsiders cannot independently verify the results, but that the utility of these genomes to the larger research community is actually pretty small. These genomes- in the short term at least- will serve the careers of a few scientists. And of course some of the findings that emerge from this group’s papers will enter the broad sphere of human knowledge.

But to most working ant biologists, today’s announcement is not as momentous as it may sound. The public genomes coming out shortly (disclaimer: I’ve had a very minor role in one of them) will be of considerably broader impact.

*update: YAGS

13 thoughts on “Breaking News: The First Ant Genomes”

  1. Well, it’s still very exciting! It’s been too long, waiting for an ant genome. And hopefully John McCain won’t ruin my party mood after this.

    But the results won’t even be entered in GenBank?

  2. Anyway. Wikipedia says that silencing CpGs in tumor suppressor genes helps lead to cancer. I wonder if this study could also further our understanding of cancer development as well?

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  4. Raw sequencing data have been deposited
    in the National Center for Biotechnology Information
    as SRA020747 (C. floridanus genome), SRA020748
    (H. saltator genome), and GSE22680 (RNA-seq).
    Assemblies and annotations have been deposited
    at DNA Data Bank of Japan–European Molecular
    Biology Laboratory–GenBank under the accession
    AEAB00000000 and AEAC00000000. The versions
    described in this paper are the first deposited versions:
    AEAB01000000 and AEAC01000000.

    1. Thanks Jim. But there must be something I’m missing because searches on those accessions at both NCBI and EMBL come up blank.

      I’m wondering if it’s an institutional lag time between paper publication and the turning of the cogs at NCBI.

  5. Don’t overlook the gene expression experiments too! Those were really cool and give rise to future experiments in figuring out the molecular mechanisms behind caste determination, and aging!

    1. I agree. The genome paper is a really nice piece of work. I’ve got another blog post in the works about it.

      I do not mean to sound negative about the study itself. I’m just frustrated that I can’t access the data.

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  7. Alex, I am one of the senior corresponding authors on the recent Science paper – there are three of us who are collaborating on this large project, Danny Reinberg (NYU), Juergen Liebig (ASU) and my lab at University of Pennsylvania. I just want to say that the two ant genomes were immediately available as soon as they were published on Thursday.
    Sincerely, Shelley Berger

    1. Thanks for your comment, Shelley. I tried accessing the genomes through several channels-including the accessions listed in the paper- and the genomes did not go public until about a day after the online publication. Hence, my inability to find them.

      I issued a correction in a separate post once they were up on NCBI.

      I’ve got another post in the works that comments on the paper itself. It’s quite a nice piece of work, in my opinion.

  8. Alex gone wild (at least for a moment)?

    Alex, I just want to publicly state that we are not selling the genomes on the black market, nor do we have an auction where the highest bidders can get the genomes for their private genome collection. We do not have any undocumented amounts that recently entered our bank accounts.

    All this does not work, since the genomes are already publicly available as was stated in the paper. To my knowledge some people outside of our group are already working on them.

    It happens that publications of genome data get delayed. Ours was delayed by one day or so.

    I understand your excitement but some things just take a little bit of time.

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