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Researchers sequence dark matter of life
Date:9/18/2011

uencing.

Researchers sequenced a single cell of E. coli with this method to verify the accuracy of the algorithm and recovered 91 percent of its genes, doing nearly as well as conventional sequencing from cultured cells. This provides enough data to answer many important biological questions, such as what antibiotics a species of bacteria produces. It also, for the first time, enables researchers to perform in-depth studies to figure out which proteins and peptides the bacteria living in human beings use to communicate with each other and with their host.

The scientists then turned to a species of marine bacteria that had never been sequenced before part of the dark matter of life. They not only sequenced its genome, but also analyzed it and were able to get information about how it lives and moves. The fairly complete and annotated genome they obtained was the first genome obtained via MDA to be deposited in GenBank, the genetic sequence database at the National Institutes of Health. With the help of the new algorithm developed by Pevzner and colleagues, thousands more are set to follow.

Pevzner's team is at work on a second-generation version of the algorithm. Lasken and his team plan to continue their work on improving MDA as well.

Lasken keeps a few hundred tubes filled with unsequenced bacteria in his laboratory at the Venter Institute in La Jolla, Calif. Each represents a bacterial terra incognita that scientists soon will explore using the method developed through the combined efforts of researchers at the UC San Diego Jacobs School of Engineering, the Venter Institute and Illumina.

"It's a very big step forward," Lasken said.


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Contact: Ioana Patringenaru
ipatrin@ucsd.edu
858-822-0899
University of California - San Diego
Source:Eurekalert  

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