Illumina (NASDAQ: ILMN) today announced that researchers at the Beijing Genomics Institute (BGI), Shenzhen are the first to complete de novo sequencing of the giant panda genome. Exclusively using Illumina’s Genome Analyzer, a small team of scientists—in one month—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. These data will help researchers better understand the genetic underpinnings of disease, molecular mechanisms of evolution, and impact of captive breeding in giant pandas. Additional information on the giant panda genome will be presented next week at the Plant and Animal XVII Genome (PAG) Conference in San Diego, California.

Ruiqiang Li, Ph.D., Director of Bioinformatics Division of BGI, Shenzhen commented about the project. “The giant panda has a unique, evolutionary status in China and is considered a national treasure. Using solely Illumina’s next-generation sequencing technology, we completed de novo sequencing of the giant panda genome, dramatically accelerating the process of decoding genetic information for this endangered species. Now, researchers around the globe can access new data that will help protect and monitor the giant panda.”

The research team sequenced 80% of the giant panda genome, obtaining greater than 95% coverage in gene regions, and N50 contig size of approximately 300kb. 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. 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,” continued Ruiqiang Li. “Compiling the genome was also very easy. Using our Short Oligonucleotide Alignment Program (SOAP), we finished the assembly in only two days.”

According to Oliver Ryder of San Diego Zoo’s Conservation Research, the existence of a giant panda genome sequence will enable more detailed studies of giant panda populations in the wild. “Findings from this study will play a critical role in how scientists shape future studies on the giant panda. The sequencing of the giant panda genome is the first project of this magnitude dedicated to applying scientific information to conserve an endangered species. China, and specifically the BGI, Shenzhen team deserve recognition for being the first group to undertake such a project. Their efforts will directly contribute to conservation efforts that preserve giant pandas in their natural habitat.”

In early 2008, BGI, Shenzhen purchased 11 Genome Analyzers, increasing the organization’s total number of Illumina next-generation sequencing systems to 17. As evidenced by recent whole-genome sequencing achievements in human, plant, and animal studies, researchers at BGI, Shenzhen continue to accelerate the rate of discovery and expand the scientific community’s understanding of genetic variation and diversity across complex genomes.

“We are excited that the BGI, Shenzhen has had this level of success with the Genome Analyzer. From the Asian genome, to the cucumber genome, now to the giant panda genome, they are pushing the limits of the sequencing technology and spanning a broad range of complex genomes,” said Tristan Orpin, Senior Vice President of Commercial Operations at Illumina. “We will continue to support them as they scale their research facility and look forward to celebrating future milestones with them.”

About the Giant Panda Genome Project

The giant panda project was sponsored and carried out by BGI-Shenzhen in collaboration with the Kunming Institute of Zoology at the Chinese Academy of Sciences; the Institute of Zoology at the Chinese Academy of Sciences in Beijing; the Chengdu Giant Panda Breeding Research Base; the China Giant Panda Research Center, and many other Chinese and foreign scientists. Additionally, the solid support of local governments and enterprises made this project possible.

About BGI Shenzhen

BGI Shenzhen is among the world’s leading scientific organizations, and aims to advance the understanding of biology and medicine through the use of large-scale sequencing and bioinformatics analysis. The headquarters of BGI recently moved to Shenzhen from Beijing. The institute also has spun-off a sequencing service branch that offers sequencing services to the international community. BGI promotes the use of genome-scale scientific approaches and strongly supports collaborative efforts in order to achieve this goal.