ArticleGigaScience2020
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.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
40 citing papers in PubMed.
- Diploid dual assemblies reveal the telocentric structure and extensive allelic heterogeneity of canine genomes.NAR genomics and bioinformatics · 2026Article
- A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons.Mobile DNA · 2026Article
- Host adaptation and genome evolution of the broad host range fungal rust pathogen, Austropuccinia psidii.G3 (Bethesda, Md.) · 2026Article
- Fine-scale recombination rates inferred using the canFam4 assembly are strongly correlated with previous maps of dog recombination.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- A 120-y time series of genomes reveals the consequences of closed breeding in German Shepherd Dogs.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons.bioRxiv : the preprint server for biology · 2025Article
- Integrative Genotyping and Analysis of Canine Structural Variation Using Long-read and Short-read Data.Genome biology and evolution · 2025Article
- Chromosome-scale assembly with improved annotation provides insights into breed-wide genomic structure and diversity in domestic cats.Journal of advanced research · 2025Article
- DNA and Histone Modifications Identify a Putative Controlling Element (CE) on the X Chromosome ofCells · 2025Article
- Heterogeneous DNA methylation and gene expression patterns underly metabolic plasticity in canine astrocytoma-derived stem-like cells.Frontiers in oncology · 2025Article
- Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback.The plant genome · 2024Article
- Unraveling the DNA methylation landscape in dog blood across breeds.BMC genomics · 2024Article
- Chromosome-Level Genome Assembly of the Australian Rainforest Tree Rhodamnia argentea (Malletwood).Genome biology and evolution · 2024Article
- Article
- Large-scale genomic analysis of the domestic dog informs biological discovery.Genome research · 2024Review
- Duplications and Retrogenes Are Numerous and Widespread in Modern Canine Genomic Assemblies.Genome biology and evolution · 2024Article
- Review of Molecular Technologies for Investigating Canine Cancer.Animals : an open access journal from MDPI · 2024Review
- A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes.Communications biology · 2023Article
- Genome-wide methylation patterns from canine nanopore assemblies.G3 (Bethesda, Md.) · 2023Article
- Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.Genome biology · 2023Article
Corrections and comments
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Authors and funding
20 authors.
Funding
Abstract
backgroundThe 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.
findingsHere, 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.
conclusionsGSD 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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