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Pandamonium

Last month saw the publication of the Giant Panda genome (Nature 463, 311-317 (21 January 2010) | doi:10.1038/nature08696). This is a remarkable achievement for a couple of reasons. First, well, it’s a Panda Genome! There is no question that pandas have captured the imagination of the majority of us. I had the chance to see some pandas up close a few years ago at the San Diego Zoo, and they certainly live up to their billing as big and cuddly. One of the things that strike you when you see a panda is that they are rather slow and that they always seem to be eating (at least when I saw them).Pandas are bona fide bears but unlike their cousins, prefer a diet of almost exclusively bamboo. So, it’s much safer to keep a panda in your back yard than a grizzly. In order to optimally feed on the bamboo stalks, giant pandas have evolved a sixth ‘digit’. This appendage serves as a thumb to help them grip the bamboo during mealtime. This remarkable adaptation was famously discussed in Stephen J. Gould’s essay The Panda’s Thumb (which you can read in the book of the same name that collects some of his essays on evolution that he regularly published in Natural History or you can find it on the net pretty easily). In the essay, Gould shows how the famous thumb is actually an evolved wrist bone that has come in handy.

The genome sequence reveals that the panda has fewer functional taste receptors that sense unami, which is linked to meat and other protein-rich foods (the other receptors sense sweet, sour, salty, and bitter tastes). This might be a contributor to the unique vegetarian diet of the panda, and suggests a great plot line for horror movie where genetically enhanced unami receptors in the panda could turn a cute child’s favorite into a man-eating maniac; but I digress.

Another cool thing about this paper is that the whole sequence was done on an Illumina platform. These next generation sequencers provide short reads (for the panda genome these were 52 bp) and therefore provide some significant technical and informatics challenges during genome assembly. Nevertheless, the group was able to cover the 21 panda chromosomes with 56x coverage. This is a remarkable achievement and points to the future of genome sequencing and analysis.

But in my mind, the most amazing aspect of the panda genome is what’s missing. The panda genome lacks the genes that could be predicted to encode enzymes to help in the digestion of the bamboo.This means that it is the panda microbiome that is the unsung hero of the panda dietary regime. To really understand these unique creatures then, we also need to sequence the microbes that are essential to its lifestyle. No doubt this is ongoing, but again it points the remarkable role that microbes have in evolution and behavior.