In the course of assembling an insect genetics lecture for the “Insects & People” class I needed, but could not find, a graph showing the number of insect genomes sequenced by year. So I made one myself:
Data are adapted from Wikipedia. The 2007 spike is a spate of Drosophila genomes intended for comparison with the genetics model workhorse D. melanogaster, while the 2011 peak is due, in part, to all the new ant genomes.
I do apologize for the extra slow blogging of late. I’ve been positively slammed.
*update: and this will look positively pathetic once the i5K genomes start rolling in.
In case you were wondering about the ant genomes that have been, are currently being, and are proposed be sequenced, Phil Ward and Juergen Gadau have curated a list. I found the database format difficult to navigate, so I’ve distilled the ant roster into a single table:
The completed and in-progress genomes reflect economically important or laboratory model ants. As these tend to be clustered in Myrmicinae, the proposed genomes are a phylogeneticist’s wish list representative of the broader spectrum of ant diversity.
The bullet ant, Paraponera clavata
An army ant raid passes peacefully through a trail of Atta cephalotes leafcutters.
We interrupt Army Ant Week to announce that a paper describing the Atta cephalotes leafcutter ant genome has just been published. I’ll report more on this research next week, once we take leave of the army ants.
Suen G, Teiling C, Li L, Holt C, Abouheif E, et al. (2011) The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle. PLoS Genet 7(2): e1002007. doi:10.1371/journal.pgen.1002007
A big day for ant science! Four new genomes are public.
These genomes complement two already-released projects, bringing the total to six. Yes, six. A year ago we didn’t have one, and now the floodgates are open.
Although these latest efforts are not the first ant genomes out, today’s announcement is in some respects more significant than the earlier one. Those of us who work in a comparative context- learning by contrasting traits among disparate taxa- now have enough data to start weighing the genomes against each other in a meaningful way.
I should note that I am a co-author on one of the papers (I played a minor role annotating an odorant-binding gene array in Linepithema), so my commentary here is not exactly dispassionate. Nonetheless, I will be posting my impressions of the research this week as time permits.
Until then, here’s a bestiary of the newly-sequenced species:
The Argentine ant is one of the world’s most pernicious pest ants, spreading from its native South America to warmer regions around the world. It frequently displaces native species, altering the local ecology, and it also invades homes and greenhouses. This species has become a model social insect for studies of nestmate recognition and for studies of ecological invasions. Click for the genome.
The red harvester ant is an iconic desert insect of the American southwest, its enormous nests visible even from satellite photos. This granivorous species has been a model for studying ant social behavior and the genetics of speciation. Click for the genome.
Atta cephalotes is one of several giant leafcutter species native to Central and South America. These ants are true farmers, tending to underground fungus gardens fed with cut vegetation. They are of interest for their highly modified caste structure and for the complexity of their agricultural interactions. Click for the genome.
The red imported fire ant- another South American insect- is the most studied ant species of all time. Since its arrival in the southern United States from Brazil in the 1930′s, the fire ant and its memorable sting have achieved a sort of infamy. The new genome will complement an extensive scientific literature. Click for the genome.
[note: at the time of this post, not all genomes have yet been released on genbank, though they should have been. grrrr....]
***update*** the genomes are blastable here
[correction: When the genome paper first emerged I stated that the genomes would not be made public. This impression- due to a lag time between online publication and data release- was erroneous, and I hope the authors accept my apology.]
A few days have passed since the publication by Bonasio et al of the first ant genomes, those of the Florida Carpenter ant Camponotus floridanus and the Indian jumping ant Harpegnathos saltator. After reading over the paper and the supplemental information, here are my thoughts. Continue reading →
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.
Acyrthociphon pisum, the Pea Aphid
The genome sequence of the pea aphid Acyrthosiphon pisum was published today in PLoS. Concurrently, a set of supporting papers has come out in Insect Molecular Biology. This genome is significant for a number of reasons- it’s the first Hemipteran genome to be sequenced, aphids have an unusual reproductive cycle, and this particular species is a serious agricultural pest.
I’ve not had time to fully digest the paper, but it seems the salient features of this genome are:
- extensive gene duplications
- a higher gene count than most other known genomes (including our own!), perhaps related to all the duplications
- a surprising loss of immune genes
source: The International Aphid Genomics Consortium 2010 Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biol 8(2): e1000313. doi:10.1371/journal.pbio.1000313
A few months ago we learned via an unintentionally leaked press release that a team of researchers lead by Nicole Gerardo and Cameron Currie had won a Roche Applied Sciences grant competition. The team will be sequencing the complete genome of 14 players from the ant/fungus/microbe co-evolutionary system, including three attine ants from different genera.
The announcement is now official.
An Acromyrmex queen, with brood, in the fungus garden
Atta cephalotes, in the fungus garden
Big ant news today! Roche Applied Sciences is apparently funding the sequencing of a series of genomes- three ant and an array of fungal and microbial genomes- in an ambitious project to better understand the relationships among the players in the celebrated ant-fungus relationship. The sequencing project is headed by Nicole Gerardo of Emory University and Cameron Currie of the University of Wisconsin.
This trend in genomics away from sequencing isolated organisms in favor of comparative projects is a welcome one. With multiple attine species- in addition to several existing ant projects- we’ll have considerable power to determine the genes most involved in the ants’ switch from a predatory to an agrarian life style.
This weekend, Arizona State University is hosting a slate of myrmecologists to brainstorm on ant genomes. I’d link to the meeting information, but apparently the gathering is so informal that they’ve not given the event a web page. In any case, the topic is this: in the age of (relatively) cheap genomes, which ants should we sequence? And, what should we do with the assembled data?
I originally planned to attend, but life intervenes and I’m frozen to the tundra of central Illinois. Instead, I will register here a few suggestions about which species should considered, in addition to the already-funded projects (Harpegnathos, Camponotus, Solenopsis and Pheidole). My criteria are twofold. First, the ant must occupy a phylogenetic position that will maximise insight when considered with the exisiting genomes. Second, the ant should have some additional property whose study will benefit from genomic information. Here’s the list:
Continue reading →