ArticleBMC genomics2021
Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- On the ancestry and evolution of the extinct dire wolf.Cell genomics · 2026Article
- Diploid dual assemblies reveal the telocentric structure and extensive allelic heterogeneity of canine genomes.NAR genomics and bioinformatics · 2026Article
- Influence of homozygosity on genomic structural variation analyses for predicting ACL rupture risk in the Labrador Retriever and Rottweiler.Frontiers in genetics · 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
- Non-seasonal breeding appears dominant with incomplete penetrance in Australian Basenji dogs.Scientific reports · 2025Article
- Genetic testing predicts appearance but not behavior in dogs.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Integrative Genotyping and Analysis of Canine Structural Variation Using Long-read and Short-read Data.Genome biology and evolution · 2025Article
- Mitochondrial Impostors: Prevalence and Impacts of NUMTs on Genetic and Evolutionary Studies in Carnivora.Genome biology and evolution · 2025Article
- Complete mitochondrial genome of Houttuynia cordata sheds light on the evolution of complex structural features in early angiosperms.BMC plant biology · 2025Article
- Small but Mitey: A Gapless Telomere-to-Telomere Assembly of an Unidentified Mite With a Streamlined Genome.Genome biology and evolution · 2025Article
- Pangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics.Genomics, proteomics & bioinformatics · 2025Article
- Delayed postoperative hemorrhage (DEPOH) in an Irish Wolfhound with theFrontiers in veterinary science · 2025Article
- Repeat-Rich Regions Cause False-Positive Detection of NUMTs: A Case Study in Amphibians Using an Improved Cane Toad Reference Genome.Genome biology and evolution · 2024Article
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- 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
- Whole-mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory.Ecology and evolution · 2024Article
- Review of Molecular Technologies for Investigating Canine Cancer.Animals : an open access journal from MDPI · 2024Review
- Genome-wide methylation patterns from canine nanopore assemblies.G3 (Bethesda, Md.) · 2023Article
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Authors and funding
19 authors.
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Abstract
backgroundBasenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness.
resultsHere, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection.
conclusionsThe growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.
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