The canine genome sequence is currently on its third build and is a near complete and well-annotated genome. However, there are still 223 unlocalized scaffolds for which the chromosome is known, but the position or orientation is not, and 15 completely unplaced scaffolds with no assigned chromosome. These scaffolds total 11.7 Mb and account for approximately 0.5% of the canine genome.

In a study investigating early-onset retinal degeneration (EORD) in the Miniature Long-Haired Dachshund (MLHD), the potential involvement of one particular scaffold, chrUn_AAEX03022082, was highlighted. To determine the chromosomal location of scaffold chrUn_AAEX03022082 we used a novel screening approach to identify BAC clones containing a scaffold specific probe sequence. A combination of next-generation sequencing of PCR and BAC sequencing libraries with de novo assembly was used to identify the exact genomic coordinate of chrUn_AAEX03022082, which was integrated into the canine genome.

The experimental approach used to determine the genomic coordinate of this scaffold and correct the canine genome sequence at this position will be discussed, as will further potential measures to improve the canine genome assembly in the future. Details of the mutation associated with EORD in MLHDs are documented in a separate abstract, submitted by Forman et al.