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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
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
GigaScience, Volume 9, No. 4, Article giaa027, Year 2020
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Description
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. © 2020 The Author(s) 2020.
Authors & Co-Authors
Field, Matt A.
Australia, Townsville
James Cook University
Australia, Canberra
The Australian National University
Rosen, Benjamin D.
United States, Beltsville
Usda Ars Beltsville Agricultural Research Center
Dudchenko, Olga
United States, Houston
Baylor College of Medicine
United States, Houston
Rice University
Chan, Eva K.F.
Australia, Sydney
Garvan Institute of Medical Research
Australia, Kensington
Unsw Medicine
Edwards, Richard J.
Australia, Sydney
Unsw Sydney
Barton, Kirston M.
Australia, Sydney
Garvan Institute of Medical Research
Australia, Kensington
Unsw Medicine
Lyons, Ruth J.
Australia, Sydney
Garvan Institute of Medical Research
Hayes, Vanessa M.
Australia, Sydney
Garvan Institute of Medical Research
Australia, Kensington
Unsw Medicine
Australia, Sydney
The University of Sydney
Omer, Arina D.
United States, Houston
Baylor College of Medicine
United States, Houston
Rice University
Colaric, Zane L.
United States, Houston
Baylor College of Medicine
United States, Houston
Rice University
Keilwagen, Jens
Germany, Quedlinburg
Julius Kühn-institut - Federal Research Centre for Cultivated Plants
Smith, Martin A.
Australia, Sydney
Garvan Institute of Medical Research
Australia, Kensington
Unsw Medicine
Lieberman Aiden, Erez Lieberman
United States, Houston
Baylor College of Medicine
United States, Houston
Rice University
United States, Cambridge
Massachusetts Institute of Technology
China, Shanghai
Shanghaitech University
Smith, Timothy P.L.
United States, Washington, D.c.
Usda Agricultural Research Service
Statistics
Citations: 27
Authors: 14
Affiliations: 14
Identifiers
Doi:
10.1093/gigascience/giaa027
ISSN:
2047217X
Research Areas
Cancer
Disability
Genetics And Genomics
Participants Gender
Female