Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C

Abstract

Background:The German Shepherd Dog (GSD) is one of the most common breeds on earth and has been bred for its utilityand intelligence. It is often first choice for police and military work, as well as protection, disability assistance, andsearch-and-rescue. Yet, GSDs are well known to be susceptible to a range of genetic diseases that can interfere with theirtraining. Such diseases are of particular concern when they occur later in life, and fully trained animals are not able tocontinue their duties.Findings:Here, we provide the draft genome sequence of a healthy German Shepherd female as areference for future disease and evolutionary studies. We generated this improved canid reference genome (CanFamGSD)utilizing a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. The GSDassembly is∼80 times as contiguous as the current canid reference genome (20.9 vs 0.267 Mb contig N50), containing farfewer gaps (306 vs 23,876) and fewer scaffolds (429 vs 3,310) than the current canid reference genome CanFamv3.1. Twochromosomes (4 and 35) are assembled into single scaffolds with no gaps. BUSCO analyses of the genome assembly resultsshow that 93.0% of the conserved single-copy genes are complete in the GSD assembly compared with 92.2% for CanFamv3.1. Homology-based gene annotation increases this value to∼99%. Detailed examination of the evolutionarily importantpancreatic amylase region reveals that there are most likely 7 copies of the gene, indicative of a duplication of 4 ancestralcopies and the disruption of 1 copy.Conclusions:GSD genome assembly and annotation were produced with majorimprovement in completeness, continuity, and quality over the existing canid reference. This resource will enable furtherresearch related to canine diseases, the evolutionary relationships of canids, and other aspects of canid biology Show more