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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

Affiliation
Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield Road, Cairns, Australia
Field, Matt A.;
Affiliation
Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Baltimore Ave, Beltsville, United States
Rosen, Benjamin D.;
Affiliation
Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, United States
Dudchenko, Olga;
Affiliation
Garvan Institute of Medical Research, Victoria Street, Darlinghurst, Australia
Chan, Eva K. F.;
Affiliation
Garvan Institute of Medical Research, Victoria Street, Darlinghurst, Australia
Minoche, Andre E.;
Affiliation
St Vincent's Clinical School, University of New South Wales Sydney, Victoria Street, Darlinghurst, Australia
Edwards, Richard J.;
Affiliation
Garvan Institute of Medical Research, Victoria Street, Darlinghurst, Australia
Barton, Kirston;
Affiliation
Garvan Institute of Medical Research, Victoria Street, Darlinghurst, Australia
Lyons, Ruth J.;
Affiliation
St Vincent's Clinical School, University of New South Wales Sydney, Victoria Street, Darlinghurst, Australia
Tuipulotu, Daniel Enosi;
Affiliation
Garvan Institute of Medical Research, Victoria Street, Darlinghurst, Australia
Hayes, Vanessa M.;
Affiliation
Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, United States
Omer, Arina D.;
Affiliation
Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, United States
Colaric, Zane;
GND
1013858662
Affiliation
Julius Kühn-Institut, Erwin-Baur-Str. 27, Quedlinburg, Germany
Keilwagen, Jens;
Affiliation
Garvan Institute of Medical Research, Victoria Street, Darlinghurst, Australia
Skvortsova, Ksenia;
Affiliation
Garvan Institute of Medical Research, Victoria Street, Darlinghurst, Australia
Bogdanovic, Ozren;
Affiliation
Garvan Institute of Medical Research, Victoria Street, Darlinghurst, Australia
Smith, Martin A.;
Affiliation
Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, United States
Aiden, Erez Lieberman;
Affiliation
US Meat Animal Research Center, Agricultural Research Service USDA, Rd 313, Clay Center, United States
Smith, Timothy P. L.;
Affiliation
Vineyard Veterinary Hospital, Windsor Rd, Vineyard, Australia
Zammit, Robert A.;
Affiliation
St Vincent's Clinical School, University of New South Wales Sydney, Victoria Street, Darlinghurst, Australia
Ballard, J. William O.

Background: The German Shepherd Dog (GSD) is one of the most common breeds on earth and has been bred for its utility and intelligence. It is often first choice for police and military work, as well as protection, disability assistance, and search-and-rescue. Yet, GSDs are well known to be susceptible to 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. Findings: Here, we provide the draft genome sequence of a healthy German Shepherd female as a reference for future disease and evolutionary studies. We generated this improved canid reference genome (CanFam-GSD) utilizing a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. The GSD assembly is ∼80 times as contiguous as the current canid reference genome (20.9 vs 0.267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer scaffolds (429 vs 3,310) than the current canid reference genome CanFamv3.1. Two chromosomes (4 and 35) are assembled into single scaffolds with no gaps. BUSCO analyses of the genome assembly results show that 93.0% of the conserved single-copy genes are complete in the GSD assembly compared with 92.2% for CanFam v3.1. Homology-based gene annotation increases this value to ∼99%. Detailed examination of the evolutionarily important pancreatic amylase region reveals that there are most likely 7 copies of the gene, indicative of a duplication of 4 ancestral copies and the disruption of 1 copy. Conclusions: GSD genome assembly and annotation were produced with major improvement in completeness, continuity, and quality over the existing canid reference. This resource will enable further research related to canine diseases, the evolutionary relationships of canids, and other aspects of canid biology.

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License Holder: The Author(s) 2020.

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