{"entity": "publication", "iuid": "d9f5e881314d420490e3e1add0fe0a18", "timestamp": "2026-09-28T12:22:59.027Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d9f5e881314d420490e3e1add0fe0a18.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d9f5e881314d420490e3e1add0fe0a18"}}, "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-affiliated.scilifelab.se/researcher/cfac9dfcdfc04a88b002ffe4ee8a5bb4.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-affiliated.scilifelab.se/researcher/b7ba04d84aa2401da56c1b438d7ee741.json"}}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a285875862f24b6fa0b378550da371fa.json"}}, {"family": "M\u00e4kel\u00e4inen", "given": "Suvi", "initials": "S", "orcid": "0000-0001-7378-4991", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f7781ef7a4f4e9daa8621c0f9910180.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-affiliated.scilifelab.se/researcher/85a961c79c6541a99bd227f3846fc56b.json"}}, {"family": "R\u00f6nnberg", "given": "Henrik", "initials": "H", "orcid": "0000-0001-6098-5364", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/46c497dfc2b3477b95906859a654cf41.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-affiliated.scilifelab.se/researcher/f503392d65ac4ab1a4b1d459ea0f37bb.json"}}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f363e8d74594ffeb0d68aa6d774b242.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}], "type": "comparative study", "published": "2021-02-10", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "185", "issn-l": "2399-3642"}, "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": [], "xrefs": [{"db": "pmc", "key": "PMC7875987"}, {"db": "pii", "key": "10.1038/s42003-021-01698-x"}], "notes": [], "created": "2026-09-23T06:48:39.909Z", "modified": "2026-09-23T06:48:40.061Z"}