Sunday, 13 December 2009

Panda genome!

As if out of nowhere, a long list of Chinese scientists and a handful of collaborators elsewhere have managed to sequence the entire genome of the giant panda.

Genome sequencing projects usually use a combination of sequencing technologies to build up to the complete genome. The more traditional sequencing methods are expensive and time consuming but generate longer stretches of sequence, which are easier to arrange into the correct order. The newer or “next-generation sequencing” technologies are quick and relatively cheap but churn out short sequences from which it’s a much tougher task to assemble big genomes. But these researchers have arrived at a draft genome of the giant panda using next-generation sequencing technology alone, they report in Nature today.

It’s a remarkable achievement, though I have to confess the paper is a bit dull. It is a sequencing paper after all. But there are several things that are worthy of note.
  1. The panda genome is estimated at 2.40 Gb, which is kind of comparable to the only other carnivore – the dog – that has received the genome treatment.
  2. The panda genome appears to have a low divergence rate compared to the dog or humans. Basically, things have been ticking along pretty slowly along the panda branch.
  3. With the genome in the bag, the researchers have attempted a commendable bit of functional genomics. Pandas, they discover, have all the genes encoding meat-digesting enzymes. So from a genetic perspective, they look totally carnivorous even though they don’t eat meat.
  4. Conversely, they have none of the genes typical of herbivores that are needed to digest plant matter. This is not particularly surprising, but it does lead them to the rather interesting conclusion that “the bamboo diet of the panda is unlikely to be dictated by its own genetic composition, and may instead be more dependent on its gut microbiome.” This brings to mind the winners of the 2009 IgNobel Biology Prize – Japanese scientists who managed to harness the digestive power of panda gut microbes. Here’s the link to their original 2001 article.
  5. But why did the panda switch from a carnivorous diet – which their ancestors once presumably had – to near total herbivory? Intriguingly, the panda genome reveals a messed up gene that means perhaps pandas suddenly lost the taste for meat. It’s hard to imagine a single genetic change leading to a complete ecological shift, but it’s very interesting nonetheless.
This achievement, of which a lot of people should be rightfully proud, will surely be useful for panda conservation. We wait and see...

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