An international consortium, headed by the Beijing Genomics Institute (BGI), published its first report on the sequencing and analysis of the giant panda genome. Researchers at BGI sequenced a draft of the Ailuropoda melanoleura genome in Oct. 2008, but the new report is the first publication of their sequencing efforts and initial analyses. The panda is the first bear to have been sequenced.
Using the Illumina Genome Analyzer and a whole genome shotgun approach, the team examined the 2.4 billion kb of a three-year-old female panda, Jingjing, from the Chengdu breeding center. To verify sequence assembly, the researchers used Sanger sequencing of nine artificial bacterial chromosomes. To date, the team has analyzed 2.25 billion base pairs, representing 94% of the bear’s entire genome. The observed sequence gaps are likely a result of the tandem repeats and transposable elements.
The panda genome had more than 2500 species-specific genes, and according to the report, 36% of the genome is composed of transposable elements similar to the dog genome. The researchers said that the giant panda genome consists of 21,001 genes, including 18,643 orthologous to those in dogs, mice, and humans. The team discovered 26 of the 27 giant panda genes catalogued in the National Institutes of Health (NIH) GenBank. The gene they did not detect is present only on the Y chromosome and was expectedly absent in the female panda.
The team’s initial analysis of the giant panda genome has provided insights in the giant panda’s diet preferences and genetic diversity. The researchers hope their study may aid in conservation efforts of the giant panda.
The paper titled, “The sequence and de novo assembly of the giant panda genome,” was published online on Dec. 13 at Nature.