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

Authors: FIELD, MATT - James Cook University; Rosen, Benjamin - Ben; DUDCHENKO, OLGA - Baylor College Of Medicine; CHAN, EVA - University Of New South Wales; MINOCHE, ANDRE - Garvan Institute Of Medical Research; EDWARDS, RICHARD - University Of New South Wales; BARTON, KIRSTON - Garvan Institute Of Medical Research; LYONS, RUTH - Garvan Institute Of Medical Research; ENOSI TUIPULOTU, DANIEL - University Of New South Wales; HAYES, VANESSA - University Of New South Wales; OMER, ARINA - Baylor College Of Medicine; COLARIC, ZANE - Baylor College Of Medicine; KEILWAGEN, JENS - Julius Kuhn Institute; SKVORTSOVA, KSENIA - Garvan Institute Of Medical Research; BOGDANOVIC, OZREN - Garvan Institute Of Medical Research; SMITH, MARTIN - University Of New South Wales; AIDEN, EREZ - Baylor College Of Medicine; Smith, Timothy - Tim; ZAMMIT, ROBERT - Collaborator; BALLARD, J. WILLIAM - University Of New South Wales

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/20/2020
Publication Date: 4/1/2020
Citation: Field, M.A., Rosen, B.D., Dudchenko, O., Chan, E.K.F., Minoche, A.E., Edwards, R.J., Barton, K., Lyons, R.J., Enosi Tuipulotu, D., Hayes, V.M., Omer, A.D., Colaric, Z., Keilwagen, J., Skvortsova, K., Bogdanovic, O., Smith, M.A., Aiden, E.L., Smith, T.P., Zammit, R.A., Ballard, J.O. 2020. Canfam_GSD: Denovochromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. GigaScience. 9(4):1-12. https://doi.org/10.1093/gigascience/giaa027.
DOI: https://doi.org/10.1093/gigascience/giaa027

Interpretive Summary: German Shepherd Dogs are one of the most common breeds on earth and have been bred for their utility and intelligence. They are often first choice for police and military work, as well as protection, disability assistance and search-and-rescue. Yet, GSD’s are well known to be afflicted with a range of genetic diseases that can interfere with their training. Such diseases are of particular concern when they occur later in life, and fully trained animals are not able to continue their duties. Here, we provide the draft genome sequence of a healthy German Shepherd female as a reference for future disease and evolutionary studies.

Technical Abstract: We generated an improved canid reference genome from a German Shepherd Dog (GSD) utilising a combination of Nanopore PromethION, PacBio SMRT, Chromium 10X, Bionano, and Hi-C technologies. The GSD assembly is approximately 80 times as contiguous as the current canid reference genome (20.9 Mb vs 0.267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer scaffolds (429 vs 3310) than the current canid reference genome CanFam v3.1. Two chromosomes (4 and 35) are assembled into single contigs with no gaps. Benchmarking Universal Single-Copy Orthologs analyses (BUSCO) results show 92.9% of the conserved single-copy genes are complete in the GSD assembly compared to 91.9% for CanFam v3.1. Detailed examination of the evolutionary important Alpha-amylase 2B (AMY2B) gene region reveals there are most likely seven copies of the gene indicative of a duplication of four copies of the gene with one copy disrupted. The GSD genome assembly has major improvement in continuity and quality over the existing canid reference. This genome sequence will enable further research related to canine diseases, the evolutionary relationships of canids, and other aspects of canid biology.