Panda Genome Sequenced!

Last week in Nature, a large group of scientists announced that they had, for the first time, successfully sequenced the entire genome of the Giant Panda. Their paper describes the extraordinary amount of work required to sequence an entire genome. The researchers extracted the DNA of a 3 year old female living in the Chengdu breeding center. The task: to sequence all of the panda's 20 pairs of autosomes and 1 pair of sex chromosomes. And to do so without breaking the researchers collective banks. The method: create many, many short read sequences of DNA using parallel sequencing technology and piece them together to construct the full sequence. Using parallel sequencing (in particular the llumina Genome Analyser sequencing technology) allowed the researchers to avoid the "prohibitive costs associated with sequencing and assembling large eukaryotic genomes". To that end, the researchers constructed 37 paired-end sequencing libraries, containing a total of 176 gigabases of usable sequence, made up of sequences with an average read length of 52 base pairs. They fed this mass amount of data into a 32 core, 512 GB RAM supercomputer, piecing together a total genome 2.40 gigabases long.

Following the construction of their genome sequence, the researchers went on a meta-analysis spree, comparing the panda genome to both dogs and humans. The group reports that humans, dogs, and pandas all possess approximately 1.4 gigabases of non-repetitive sequence within their genome. Of that 1.4 gigabases, all three species have 846 megabases (~60.4%) in common. Dogs and pandas share ~83% of their non-repetitive sequence, with pandas and humans sharing ~72% and dogs and humans sharing ~64.5%.

The researchersand also searching for several genes of interest to panda aficionados, including the genes encoding for taste receptors. Interestingly, an analysis of the sequence for the T1R1 gene, which encodes the taste receptor for umami, shows a loss-of-function mutation. The authors speculate that this mutation may explain pandas' exclusively herbivorous diet, despite their taxonomic classification of carnivores.

Pandas from the Wolong Natural Nature Reserve

For a gloriously detailed description of the sequencing process, and for more hints at the wonders waiting to be uncovered withinin the panda genome, the original article should be viewed in all its splendor. The Sequence and De Novo Assembly of the Giant Panda Genome. Li R, et al. Nature 463: 311-317 (2010).

A side note: the home of the 3 year old female Panda, the Chengdu breeding center, is a facility working alongside the Wolong Panda Breeding Center to conserve the Giant Panda through extensive breeding programs. The Chengdu center boasts a population of 83 pandas that have been bred from an original population of 6 wild pandas. Pictures of the Chendgu pandas, as well as video of the most recent group born at the Wolong Center are guaranteed to lighten any day with a hearty does of adorable.


Astra Bryant

Astra Bryant is a graduate of the Stanford Neuroscience PhD program in the labs of Drs. Eric Knudsen and John Huguenard. She used in vitro slice electrophysiology to study the cellular and synaptic mechanisms linking cholinergic signaling and gamma oscillations – two processes critical for the control of gaze and attention, which are disrupted in many psychiatric disorders. She is a senior editor and the webmaster of the NeuWrite West Neuroblog