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BGI Seeks Proposals to Sequence 1,000 Plant, Animal Genomes; Pledges $100M Toward Effort


By Julia Karow

This article, originally posted Jan. 11, has been updated with additional information from BGI.

China's BGI said last week that it plans to sequence the genomes of 1,000 important plant and animal reference species over the next two years as part of a new project that will solicit proposals from the scientific community.

BGI said that it will provide $100 million in funding for the project.

An international committee organized by BGI will select the species to be sequenced from proposals by researchers, based on the importance of the species, the applicant's financial resources, the project's scientific strength, and the experimental design.

Zhuo Li, vice president of international collaborations at BGI, told In Sequence that for now, the plan is to sequence 500 plants and 500 animals, although this ratio might shift depending on researchers' interests. The project's website will be updated monthly to show accepted proposals.

The committee, which Li said BGI is currently assembling, will also suggest a sequencing strategy and define standards for the reference genomes, depending on the funding available.

BGI will sequence and analyze the genomes on its in-house platform. According to Li, it will mainly use Illumina's sequencing technology, and "possibly, some long read lengths, too," though he did not specify that platform.

BGI plans to provide full funding for certain species that are of interest to the institute's research. For other species, it will match the funding provided by applicants or will help to coordinate funding from several applicants.

"Through many proof-of-concept studies, we have demonstrated that the technology is ready and the total cost is at a feasible scale," said Li in a statement.

BGI's $100 million will get the project off to "a very good start," Li said, but additional funding will be necessary to complete it.

He told In Sequence that the total project cost is difficult to predict because the genomes may differ in size and complexity, and final requirements for the assembled sequence quality may differ as well.

Li said that the project will provide a foundation for other studies in the species sequenced, such as epigenomics and transcriptomics studies. In addition, "scientists across many fields can also utilize these publicly available data for the development of better crop and livestock for the whole world."

Under a "Tree of Life" project to sequence economically and scientifically important animals and model organisms, which BGI started two years ago, the institute has already generated more than 20 reference genomes. Ongoing projects include the polar bear and the penguin genomes.

Last month, for example, BGI said that in collaboration with Qinghai University, it has completed sequencing the genome of the Tibetan antelope, although that study has not been published yet.

Also last month, BGI published a de novo assembly of the giant panda genome, sequenced entirely on Illumina's Genome Analyzer platform (see In Sequence 12/15/2009).

And earlier in the fall, BGI and collaborators published the sequence the cucumber genome, at a sequencing cost of approximately $3.3 million, using a mix of Sanger capillary and Illumina technologies (see In Sequence 11/3/2009).

BGI's project is one of several large-scale initiatives to generate reference genomes for eukaryotic species. Last year, for example, a group of scientists led by David Haussler at the University of California, Santa Cruz, and others launched the "Genome 10K" project, which aims to sequence and analyze the genomes of at least 10,000 vertebrate species using new sequencing technologies (see In Sequence 11/10/2009). Li said BGI will communicate and coordinate with the "Genome 10K" and other initiatives, and is seeking more collaborators worldwide.

According to its website, BGI currently has 28 Illumina Genome Analyzers, two Applied Biosystems SOLiD systems, and one Roche 454 GS FLX sequencer, as well as 100 Amersham MegaBACE 1000 and 11 Applied Biosystems 3730xl Sanger sequencers.