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

Matt A Field; Benjamin D Rosen; Olga Dudchenko; Eva K F Chan; Andre E Minoche; Richard J Edwards; Kirston Barton; Ruth J Lyons; Daniel Enosi Tuipulotu; Vanessa M Hayes; Arina D Omer; Zane Colaric; Jens Keilwagen; Ksenia Skvortsova; Ozren Bogdanovic; Martin A Smith; Erez Lieberman Aiden; Timothy P L Smith; Robert A Zammit; J William O Ballard

doi:10.1093/gigascience/giaa027

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. 2020 Apr 1;9(4):giaa027. doi: 10.1093/gigascience/giaa027.

Authors

Matt A Field^{1

2}, Benjamin D Rosen³, Olga Dudchenko^{4

5

6}, Eva K F Chan^{7

8}, Andre E Minoche, Richard J Edwards⁹, Kirston Barton^{7

10}, Ruth J Lyons⁷, Daniel Enosi Tuipulotu⁹, Vanessa M Hayes^{7

10

11}, Arina D Omer^{4

5}, Zane Colaric^{4

5}, Jens Keilwagen¹², Ksenia Skvortsova⁷, Ozren Bogdanovic^{7

9}, Martin A Smith^{7

10}, Erez Lieberman Aiden^{4

5

6

13

14}, Timothy P L Smith¹⁵, Robert A Zammit¹⁶, J William O Ballard⁹

Affiliations

¹ Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield Road, Cairns, QLD 4878, Australia.
² John Curtin School of Medical Research, Australian National University, Garran Rd, Canberra, ACT 2600, Australia.
³ Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Baltimore Ave, Beltsville, MD 20705, USA.
⁴ The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA.
⁵ Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA.
⁶ Center for Theoretical and Biological Physics, Rice University, Main St, Houston, TX 77005, USA.
⁷ Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia.
⁸ St Vincent's Clinical School, University of New South Wales Sydney, Victoria Street, Darlinghurst NSW 2010, Australia.
⁹ School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia.
¹⁰ Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia.
¹¹ Central Clinical School, University of Sydney, Parramatta Road, Camperdown, NSW 2050, Australia.
¹² Julius Kühn-Institut, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany.
¹³ Broad Institute of MIT and Harvard, Main St, Cambridge, MA 02142, USA.
¹⁴ Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, ShanghaiTech University, Huaxia Middle Rd, Pudong 201210, China.
¹⁵ US Meat Animal Research Center, Agricultural Research Service USDA, Rd 313, Clay Center, NE 68933, USA.
¹⁶ Vineyard Veterinary Hospital, Windsor Rd, Vineyard, NSW 2765, Australia.

Abstract

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.

Keywords: de novo genome assembly; DNA Zoo; Hi-C; canine hip dysplasia; long-read sequencing; optical mapping.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Chromosomes / genetics*
Dogs
Genome / genetics*
Genomics
Molecular Sequence Annotation
Sequence Analysis, DNA / methods*
Whole Genome Sequencing / methods*

Abstract

Publication types

MeSH terms

Grants and funding