Next gen sequencing scores its first major success, the Giant Panda genome
The publication of a draft genome of the Giant Panda is reported in Nature today. This marks another significant milestone in the field of genomics as this is the first time that a Next Generation Sequencing (NGS) technique has been used to successfully piece together a mammalian genome from scratch.
Prior to this publication, NGS had been used to re-sequence the human genome, while making use of the previously published sequences generated by the older Sanger methods for their alignment.
The challenge with the Panda Genome was to correctly align the much shorter stretches of sequence (relative to the Sanger method) that the NGS technique produces without the benefit of a reference sequence to help with that alignment. To help achieve their goal, the authors generated an approximately 73-fold total coverage of the Panda genome, which is about 8 times more than the average coverage derived from a typical draft genome generated by Sanger methods.
As this is the first successful effort in this emerging area, it remains to be seen how accurate the sequence and alignment are, but this is an important first step for the field of genomics.
Of interest for the biologist, is the information it provides about the Panda’s digestive system. Although the Panda is taxonomically classed as a carnivore, its diet is primarily that of a herbivore. The sequencing effort suggests that this might be due to a loss of function mutation in one of the receptors for the umami component of taste (the others being sweetness, saltiness, sourness and bitterness), which is prevalent in high-protein foods such as meat. Alas, the data thus far only provide a hint at a potential reason for the Panda’s notoriously low fecundity rate.
If you wish to learn more about NGS, which is dramatically speeding up sequencing efforts while simultaneously cutting costs, you can read our article on the Wellcome Trust website, which features animations illustrating the methods behind each of the new techniques.