Researchers at the Beijing Genomics Institute (BGI) have completed de novo sequencing of the giant panda genome. Over one month, using Illumina's Genome Analyzer, they produced 150 gigabases of sequence that was used to assemble the three gigabase genome belonging to Jingiing, the giant panda that was the 2008 Olympic mascot.
The research team sequenced 80% of the giant panda genome, obtaining greater than 95% coverage in gene regions, and N50 contig size of approximately 300 kb. Using paired reads averaging 75 base pairs each per run, 50X coverage of the genome was generated.
“The combination of long-paired reads and high data quality enabled us to complete de novo sequencing of a complex organism,” points out Ruiqiang Li, Ph.D., director of bioinformatics division of BGI. “This achievement marks a significant milestone: it demonstrates that mammalian-sized genomes can be assembled using de novo sequencing on the Illumina Genome Analyzer at a fraction of the cost and time it would have previously taken to complete a project of this magnitude. Compiling the genome was also very easy. Using our Short Oligonucleotide Alignment Program, we finished the assembly in only two days.”