Abstract
Previous assembly gaps that are now resolved in the Great Dane genome are enriched for sequences with an extreme GC content and are located near transcription start sites and recombination hot spots. The identified gene models include 2151 genes whose start positions map to a gap in the CanFam3.1 assembly. Due to their sequence composition, many of these sequences are recalcitrant to analysis using Illumina short-read sequencing. Several additional canine assemblies are now available that have improved continuity and gene annotations.
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