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Posts Tagged ‘genomics’

The Pea Aphid Genome

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

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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

An Acromyrmex queen, with brood, in the fungus garden

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Atta cephalotes, 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.

Source: PhysOrg

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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:

(more…)

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