ArticlePloS one2014
An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 166 papers.
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Who cites it
166 citing papers in PubMed, 304 citations in OpenAlex.
- Impact of preanalytical factors on liquid biopsy in the canine cancer model.Communications medicine · 2026Article
- Genomic Landscape Analysis of Canine Pulmonary Adenocarcinoma Reveals Candidate Targetable Gene Fusions.Veterinary and comparative oncology · 2026Article
- Signatures of Radiation-Induced Stress and Putative Selection on Immune Targets in Chornobyl Wolves.Molecular ecology · 2026Article
- A Novel CFA3 Locus EncompassingGenes · 2026Article
- A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons.Mobile DNA · 2026Article
- Phenome-wide study connects behavioral genetics of odor detection dogs with temperament traits.Scientific reports · 2026Article
- Comparative Genomics and Phylogenomics of the Mustelinae Lineage (Mustelidae, Carnivora).Genome biology and evolution · 2026Article
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- Mitogenomic sequencing of the Brazilian Mastiff and Brazilian Terrier suggests a complex scenario of breed formation for two established Brazilian dog breeds.Genetics and molecular biology · 2026Article
- Adenovirus mediated gene therapy in cell lines derived from canine oral melanoma.Frontiers in immunology · 2026Article
- The role of epigenetic alterations in canine mammary cancer.The Journal of reproduction and development · 2026Review
- 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
- Article
- A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons.bioRxiv : the preprint server for biology · 2025Article
- Reapplication of the Type IV Hypersensitivity Quantitative Risk Assessment to Assess Ingredients Used on Canines.Veterinary medicine and science · 2025Review
- Horizontal transfer of nuclear DNA in transmissible cancer.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Performance Comparison of Genomic Best Linear Unbiased Prediction and Four Machine Learning Models for Estimating Genomic Breeding Values in Working Dogs.Animals : an open access journal from MDPI · 2025Article
- Strong correlation of gene counts and differentially expressed genes between a 3' RNA-Seq and an RNA hybridization platform in transcriptome analyses from canine archival tissues.Frontiers in veterinary science · 2025Article
- Fast and Accurate Enrichment of Canid Excrement for Species* and Other Analyses (FAECES*) Method for Noninvasive Genotyping of Field-Collected Canid Scat.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Transcriptomic profiling in canine B-cell lymphoma supports a synergistic effect of BTK and PI3K inhibitors.Frontiers in veterinary science · 2025Article
106 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
30 authors at 6 institutions in 3 countries.
Funding
Abstract
The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog ∼175,000 expressed loci. While about 90% of the coding genes previously annotated by EnsEMBL have measurable expression in at least one sample, the number of transcript isoforms detected by our data expands the EnsEMBL annotations by a factor of four. Syntenic comparison with the human genome revealed an additional ∼3,000 loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set. In addition to ∼20,700 high-confidence protein coding loci, we found ∼4,600 antisense transcripts overlapping exons of protein coding genes, ∼7,200 intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs (lincRNAs) and ∼11,000 transcripts were reported by two different library construction methods but did not fit any of the above categories. Of the lincRNAs, about 6,000 have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts.
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Registered trials
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.