Novel Sequencing Utilizing a Novel Two-Stage Sequence Capture Method

A new method to perform targeted sequencing in the highly complex maize genome promises to revolutionize genetic studies in agriculturally important species. Due to the large, highly repetitive nature of the genomes of many agriculturally important crops, developing a technology for unraveling them and capturing only the portions of interest is of critical importance. For instance, in the maize genome only 15% of the genome displays variation.

The new method, called the Two-Stage Sequence Capture Method, bypasses the need for blocking DNA, which prevents the repeats in the genome from inhibiting the capture process. Blocking DNA is a species-specific reagent that can be technically difficult to produce for each species in large quantities at high-quality. Without the blocking DNA, the new method employs two capture stages wherein the first uses an array to deplete repetitive sequences while the second captures the specific target regions. The scientists were able to demonstrate several thousand-fold enrichment and high coverage of target regions in the maize genome with this two-stage protocol.

 "Including its obvious uses in agricultural systems, this technology has immediate utility in other non-food crops like forest trees, biofuel grasses like sugarcane and miscanthus, and several non-model botanicals that are positioned to address interesting questions in genome architecture and gene/genome evolution. Many of these genomes are extremely large even when compared to maize, and the majority of the extra sequence is composed of repetitive DNA," said Brad Barbazuk, Assistant Professor of Biology at the University of Florida.

The article is available at http://www.nimblegen.com/news/press_rel/news_2010_03_18.html