Supporting data for "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"

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, 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 We generated this improved canid reference genome (CanFam_GSD) utilising a combination of Pacific Bioscience, Oxford Nanopore,, 10X Genomics, 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 3,310) than the current canid reference genome CanFam v3.1. Two chromosomes (4 and 35) are assembled into single scaffolds with no gaps. Benchmarking Universal Single-Copy Orthologs analyses of the genome assembly results show 93.0% of the conserved single-copy genes are complete in the GSD assembly compared to 92.2% for CanFam v3.1. Homology-based gene annotation increases this value to about 99%. Detailed examination of the evolutionary important pancreatic amylase region reveals there are most likely seven copies of the gene indicative of a duplication of four ancestral copies and the disruption of one copy. 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:

• hi-c
• long read sequencing
• optical mapping
• de novo genome assembly
• canine hip dysplasia
• dna zoo

Read the peer-reviewed publication(s):

• Field, M. A., Rosen, B. D., Dudchenko, O., Chan, E. K. F., Minoche, A. E., Edwards, R. J., Barton, K., Lyons, R. J., Tuipulotu, D. E., Hayes, V. M., D. Omer, A., Colaric, Z., Keilwagen, J., Skvortsova, K., Bogdanovic, O., Smith, M. A., Aiden, E. L., Smith, T. P. L., Zammit, R. A., & Ballard, J. W. O. (2020). 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, 9(4). https://doi.org/10.1093/gigascience/giaa027 (PubMed:32236524)

Related datasets:

doi:10.5524/100712 IsCitedBy doi:10.5524/102356

Additional information:

https://www.dnazoo.org/assemblies/Canis_lupus_familiaris_German_Shepherd

Accessions (data included in GigaDB):

BioProject: PRJNA560310
Bioproject: PRJNA512907
GEO: GSE136348