A novel canine reference genome resolves genomic architecture and uncovers transcript complexity.

Autor: Wang C; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden. chao.wang@imbim.uu.se., Wallerman O; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden., Arendt ML; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.; Department of Veterinary Clinical Sciences, University of Copenhagen, Frederiksberg D, Denmark., Sundström E; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden., Karlsson Å; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden., Nordin J; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden., Mäkeläinen S; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden., Pielberg GR; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden., Hanson J; Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden., Ohlsson Å; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden., Saellström S; Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden., Rönnberg H; Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden., Ljungvall I; Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden., Häggström J; Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden., Bergström TF; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden., Hedhammar Å; Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden., Meadows JRS; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden., Lindblad-Toh K; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden. kersli@broadinstitute.org.; Broad Institute of MIT and Harvard, Cambridge, MA, USA. kersli@broadinstitute.org.
Jazyk: angličtina
Zdroj: Communications biology [Commun Biol] 2021 Feb 10; Vol. 4 (1), pp. 185. Date of Electronic Publication: 2021 Feb 10.
DOI: 10.1038/s42003-021-01698-x
Abstrakt: 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.
Databáze: MEDLINE
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