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BGI Says it Has Used the Illumina GA for De Novo Sequencing of Two Macaque Genomes


By Bernadette Toner

This article was originally published Nov. 12.

The Beijing Genomics Institute in Shenzhen and the Southern China Center for Innovative Pharmaceuticals said last week that they have sequenced and assembled the genomes of the Chinese rhesus macaque (Macaca mulatta) and the cynomolgus macaque (Macaca fascicularis).

BGI-Shenzhen said that it performed all the sequencing with the Illumina Genome Analyzer platform and used its SOAPdenovo program for assembly. The researchers used a whole-genome shotgun strategy that relied on paired-end libraries with a range of different insert sizes. Both genomes were sequenced to more than 60-fold coverage with more than 97 percent of each genome represented in the final assemblies, BGI said.

Further details of the project were not disclosed.

The institute noted in a statement that it has so far used the Illumina platform for the "rapid, accurate, and cost-effective completion of several large genome projects … including the giant panda genome."

BGI announced last year that it had completed the sequencing of the panda genome [see In Sequence 10/21/2008], but has not yet published a paper on the project.

Earlier this month, BGI published a paper in Nature Genetics on the sequence and de novo assembly of the cucumber genome. That effort used a combination of Sanger and Illumina sequencing technologies and was conducted in partnership with the Chinese Academy of Agricultural Sciences in Beijing [see In Sequence 11/3/2009].

In September, BGI researchers reported in Science that they had used the Illumina platform to resequence 40 silkworm genomes to about three-fold coverage each [see In Sequence 9/1/2009].

BGI said in a statement that comparisons of the two macaque genomes with that of the already sequenced Indian rhesus macaque "will provide valuable assessment of their different genetic basics," which will provide insight into human diseases, such as AIDS, Alzheimer’s, cancer, and malaria infection.

The institute conducted the project in partnership with the Southern China Center for Innovative Pharmaceuticals, a national drug research organization based in Guangzhou City that was opened last year. The governments of Guangdong Province and Guangzhou City have provided the center with around 700 million Chinese Yuan ($100 million) for its first three years of operation.