Wednesday, 10 February 2010

The sequence and de novo assembly of the giant panda genome

The sequence and de novo assembly of the giant panda genome

 Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.


SOAPdenovo uses the de Bruijn graph algorithm7 and applies a stepwise strategy to make it feasible to assemble the panda genome using a supercomputer (32 cores and 512Gb random access memory (RAM))


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