{"entity": "publication", "iuid": "e5924e2e04a64152ac970d7f2353229e", "timestamp": "2026-07-12T17:36:04.180Z", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5924e2e04a64152ac970d7f2353229e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5924e2e04a64152ac970d7f2353229e"}}, "title": "A novel canine reference genome resolves genomic architecture and uncovers transcript complexity.", "authors": [{"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Arendt", "given": "Maja-Louise", "initials": "ML"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E", "orcid": "0000-0001-9526-8541", "researcher": {"href": "https://publications.scilifelab.se/researcher/20f87b64e71b4a00a9474ec4d898601d.json"}}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "M\u00e4kel\u00e4inen", "given": "Suvi", "initials": "S", "orcid": "0000-0001-7378-4991", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b1f91bf7dcd466a9814effddf67976e.json"}}, {"family": "Pielberg", "given": "Gerli Rosengren", "initials": "GR"}, {"family": "Hanson", "given": "Jeanette", "initials": "J"}, {"family": "Ohlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Saellstr\u00f6m", "given": "Sara", "initials": "S", "orcid": "0000-0001-5253-5830", "researcher": {"href": "https://publications.scilifelab.se/researcher/aac98530437d4d6890dffcbd31eabde0.json"}}, {"family": "R\u00f6nnberg", "given": "Henrik", "initials": "H", "orcid": "0000-0001-6098-5364", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f8783f23d664f4b98ef8f6ff03b6693.json"}}, {"family": "Ljungvall", "given": "Ingrid", "initials": "I"}, {"family": "H\u00e4ggstr\u00f6m", "given": "Jens", "initials": "J"}, {"family": "Bergstr\u00f6m", "given": "Tomas F", "initials": "TF", "orcid": "0000-0002-7480-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/b590797209ee4feab6302920621fc621.json"}}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "comparative study", "published": "2021-02-10", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "4", "issue": "1", "pages": "185"}, "abstract": "We present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine \"dark\" regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.", "doi": "10.1038/s42003-021-01698-x", "pmid": "33568770", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-01698-x"}, {"db": "pmc", "key": "PMC7875987"}], "notes": [], "created": "2021-02-17T19:15:39.689Z", "modified": "2024-01-16T13:48:40.742Z"}