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Panda genome completed using short-read sequencing
The giant panda has become the first mammal to see its genome completed using a next-generation sequencing technology, which trades short reads for high volume. Overall, the panda looks like a carnivore, despite its bamboo-chewing ways.
Over the weekend, Nature released a paper that describes the genome of the giant panda. The results do tell us something about the animal itself—it's a vegetarian that looks like a carnivore—but is probably more notable for how it was obtained. It's the first genome to be completed using sequence from the relatively new Illumina platform, which typically reads less than 100 bases from each piece of DNA, but can read massive amounts of DNA in parallel.
Illumina isn't one of the technologies I've covered yet in our DNA sequencing series, but it's similar to some of the other ones, like Complete Genomics, in that the read length is very short (an average of 52 bases for the panda). But Illumina machines produce staggering amounts of these short reads in each run, and provided the authors with enough sequence to read each base, on average, 73 times. Figuring out how all these tiny pieces (all 3.3 billion of them) overlap is a serious computational problem, but the authors used a software package called SOAP that's specifically designed to handle these short reads.
The genome that resulted looks a lot like the one from the only other carnivore sequenced, the dog. Despite some remaining gaps, the authors were able to find 99 percent of the dog genes in the panda genome, including enzymes typically involved in digesting meat. In contrast, they were unable to find any gene that looks like it would allow the panda to digest foliage, and they suggest we need to look to its gut bacteria to understand how it does that. So, although the panda is an exclusive herbivore behaviorally, its genome doesn't appear to have committed it to that lifestyle.
Nature, 2009. DOI: 10.1038/nature08696
The giant panda has become the first mammal to see its genome completed using a next-generation sequencing technology, which trades short reads for high volume. Overall, the panda looks like a carnivore, despite its bamboo-chewing ways.
Over the weekend, Nature released a paper that describes the genome of the giant panda. The results do tell us something about the animal itself—it's a vegetarian that looks like a carnivore—but is probably more notable for how it was obtained. It's the first genome to be completed using sequence from the relatively new Illumina platform, which typically reads less than 100 bases from each piece of DNA, but can read massive amounts of DNA in parallel.
Illumina isn't one of the technologies I've covered yet in our DNA sequencing series, but it's similar to some of the other ones, like Complete Genomics, in that the read length is very short (an average of 52 bases for the panda). But Illumina machines produce staggering amounts of these short reads in each run, and provided the authors with enough sequence to read each base, on average, 73 times. Figuring out how all these tiny pieces (all 3.3 billion of them) overlap is a serious computational problem, but the authors used a software package called SOAP that's specifically designed to handle these short reads.
The genome that resulted looks a lot like the one from the only other carnivore sequenced, the dog. Despite some remaining gaps, the authors were able to find 99 percent of the dog genes in the panda genome, including enzymes typically involved in digesting meat. In contrast, they were unable to find any gene that looks like it would allow the panda to digest foliage, and they suggest we need to look to its gut bacteria to understand how it does that. So, although the panda is an exclusive herbivore behaviorally, its genome doesn't appear to have committed it to that lifestyle.
Nature, 2009. DOI: 10.1038/nature08696
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