If you’ve ever assembled a genome, you know what I daunting task it is. It’s quite literally like putting a huge extremely complex puzzle together, one where the pieces are extremely small, and doing this, of course, all with the use of a computer. The worse case scenario is the assembly of eukaryotic genomes where the puzzle is large in size with possibly millions of pieces to assemble, and some of these pieces look exactly like the other pieces. In this scenario, to develop an even remotely questionable assembly – one that may not be fully put together – it can take days to weeks of computational time on the fastest of multi-processor computers with plenty of memory (for keeping huge amounts of sequence data active).
In an attempt to ease the assembly of larger genomes – genomes larger than those your typical bacteria – a research group at the University of Oregon led by molecular biologist Eric Johnson has developed a technique, which they call restriction-site associated DNA markers, or ‘RAD’ for short, which aids in providing a clearer view of overlapping sequenced reads. A patent has been filed for this technology.
A new paper authored by Etter et al., entitled “Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads” and recently published in the journal PLoS One, provides proof of technology of the RAD technique by identifying genomic differences in numerous isolated populations, those from freshwater and saltwater habitats, of the threespine stickleback fish (see figure below).
The RAD markers act as placeholders that can be used to identify a space portion of the genome. By using these markers, the authors were able to piece together regions of close proximity. This quickly provided larger contigs than without using the RAD marker method. The authors stress that this technique is best used when applied to organisms that do not have a close reference genome. Two commentaries regarding this research are located here and here.