Monday, January 19, 2009

You could call it symbiomics (but please do not)... but whatever name you use, this is $^@#&* so cool.

Once again, Nancy Moran's lab has knocked the scientific wind out of me with a cool paper. This seems to happen every 6 months or so (and I hope my paper with her lab a few years ago knocked the wind out of some others). And this new one, even though it is in a non OA journal which I usually avoid writing about here, is so cool, I just had to say something. So, if you are interested in a brilliant study of "The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria" see the recent Science paper by Moran, Heather McLaughlin and Rotem Sorek. Here are some key lines that summarize some of what they did:
We documented the dynamics of symbiont genome evolution by sequencing seven strains of Buchnera aphidicola from pea aphid hosts....
....A. pisum is native to Eurasia, but has been introduced worldwide. It was first detected in North America in the 1870s (11). We sequenced the genomes of seven Buchnera-Ap strains descended from two colonizers of North America (and hence diverging up to 135 years ago), including two strains diverging in the laboratory for 7.5 years. Solexa sequencing was combined with verification by Sanger sequencing (12), to determine genomic sequences of these seven strains (Table 1)....
...Our estimated mutation rate for base changes was unexpectedly high: more than 10 times the previous estimates of mutation rate calculated on the basis of silent site divergences in both Buchnera and free-living bacteria...
...Our model predicts that the initial step leading to genome reduction is a shift in nucleotide composition toward higher A+T content....

Alas, I am really busy right now finishing some grants and papers or I would try to write more, especially since some may not be able to get this paper.  Note for you conflict of interest aficionados -  much of the sequencing for this project was done at the Joint Genome Institute where I have an Adjunct appointment.

1 comment:

  1. They don't really speculate on it, but what do you think is the reason for the dramatic mutation rate? It was much higher than previously observed, but why? Is the reality of homoplasmy skewing our estimates of divergence rates?

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