Novel sequencing approach produces cucumber genome

Researchers based in China have used a combination of traditional and next generation sequencing technologies to produce a draft genome of the cucumber, Cucumis sativus L..

Typically the short read lengths of next generation technologies, such as Illumina's Genome Analyzer used in this study, precludes them from performing de novo sequencing. Normally assembly using next generation sequencing technologies is done by mapping their short reads on to a known reference genome.

For the genome of the cucumber, the researchers combined the long read and clone length of Sanger technology along with the high sequencing depth and low unit cost of the Illumina Genetic Analyzer platform.

The researchers compared the assemblies from the Sanger reads, the Illumina reads and Sanger plus Illumina reads and found the 'hybrid' approach to be significantly more efficient.

This suggests that next generation sequencing technologies can effectively be used to perform de novo sequencing at a dramatically lower cost and higher speed to traditional technologies.

The cucumber genome, which consists of 350 million base pairs, was published today in the journal Nature Genetics.