A team led by David Adams fromThe Wellcome Trust Sanger Instituteand colleagues at theMRC Mammalian Genetics UnitandCase Western Reserve Universitydemonstrate the application of next-generation sequencing to re-sequence whole mouse chromosomes for genetic studies in anarticlepublished today inGenome Biology.

Currently only a single mouse genome sequence is available – that of the mouse strain C57BL/6J. This sequence is rather different from the sequence of other mouse strains that are commonly used in genetic studies. In theGenome Biologyarticle, assemblies of chromosome 17 from the A/J and CAST/Ei strains were constructed from high-throughput sequence data at a depth of at least 22X. AJ is a classical laboratory strain, which is closely related to the ‘reference’ C57BL/6J strain, while the CAST/Ei strain is highly divergent from the reference as it was derived from a wild isolate. The authors identified single nucleotide polymorphisms (SNPs) and structural variants in the chromosome 17 assemblies and also demonstrate how these sequences can be used to profile quantitative trait loci genes. New algorithms for identifying copy number variations (CNVs) and for SNP filtering, as well as an assembly algorithm are also presented.

The new approaches demonstrated here open the way for a new era of rodent functional genomics.

Read thearticleby Adams and colleagues inGenome Biology.