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BGI Says Nearly 50 Reference Species Genomes Complete or Nearing Completion

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By Julia Karow

China's BGI said last week that almost half of approximately 100 genome sequencing projects launched so far under its 1,000 Plant and Animal Reference Genomes project have already been completed or are nearing completion.

The project, first announced in January, seeks to sequence the genomes of 1,000 important plant and animal reference species over the next two years (IS 1/12/2010).

Finished projects include the genomes of cucumber, watermelon, cabbage, Chinese cabbage, panda, Tibetan antelope, penguin, and polar bear, while ongoing projects include the genomes of plum blossom, orchid, tobacco, tea, cotton, yak, grouper, flounder, oyster, diamondback moth, earthworm, giant salamander, and symbiont genomes.

According to Bicheng Yang, a BGI spokesperson, BGI researchers are pursuing a de novo sequencing strategy in which they combine gradient insert libraries with paired-end reads generated on the Illumina platform. For plant genomes with highly repetitive sequences, they also generate BAC and fosmid end sequences by Sanger sequencing in order to improve the assembly results.

About half of the projects launched so far are collaborations, involving teams from China, Japan, Australia, US, and Europe, Yang said, though all sequencing is performed at BGI. While collaborators generally contribute part of the funding and BGI covers the remainder, some projects are fully funded by BGI, for example a symbiont genome project in collaboration with US scientists.

The cost for each project differs, depending on characteristics of each genome, such as genome size, repeat sequences, GC-content, polyploidy and heterozygosity, as well as the desired assembly quality and data analysis, Yang said.

So far, BGI has published the giant panda genome and the cucumber genome, and has submitted the sequence data for these to GenBank. "The rest will also be publicly available after we are happy with the quality," Yang said. Papers on several more genomes are currently under review or in preparation, he added. "The idea is to publish all of the projects and eventually make the data available for the community."

BGI is currently looking for additional proposals for the project.

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