ArticleProceedings of the National Academy of Sciences of the United States of America2021
Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 62 citations in OpenAlex.
- 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
- A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons.Mobile DNA · 2026Article
- Unraveling IGK locus in dog breeds: IMGTNAR genomics and bioinformatics · 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 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
- The RSPO2 gene is associated with bilateral anterior amelia in Chihuahuas.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Identification of a minimal Alu domain required for retrotransposition.Nucleic acids research · 2025Article
- Canine genome-wide association study identifiesScience (New York, N.Y.) · 2025Article
- MicroRNAs implicated in canine diffuse large B-cell lymphoma prognosis.FEBS open bio · 2024Article
- The DoGA consortium expression atlas of promoters and genes in 100 canine tissues.Nature communications · 2024Article
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- Novel crossover and recombination hotspots massively spread across primate genomes.Biology direct · 2024Article
- Review
- Large-scale genomic analysis of the domestic dog informs biological discovery.Genome research · 2024Review
- Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes.Nucleic acids research · 2024Article
- 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
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Authors and funding
13 authors at 4 institutions in 2 countries.
Funding
Abstract
Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3' end of LINE-1_Cfs (i.e., LINE-1_Cf 3'-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.