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Research article2021Peer reviewedOpen access

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

Wang, Chao; Wallerman, Ola; Arendt, Maja-Louise; Sundstrom, Elisabeth; Karlsson, Asa; Nordin, Jessika; Makelainen, Suvi; Pielberg, Gerli Rosengren; Hanson, Jeanette; Ohlsson, Asa; Saellstrom, Sara; Ronnberg, Henrik; Ljungvall, Ingrid; Haggstrom, Jens; Bergstrom, Tomas F.; Hedhammar, Ake; Meadows, Jennifer R. S.; Lindblad-Toh, Kerstin

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. Here, the authors report an improved de novo reference genome for the domestic dog based on a female German Shepherd named Mischka. The new genome increases contiguity 55-fold over the previous dog assembly and uncovers functional elements that were not previously identifiable.

Published in

Communications biology
2021, Volume: 4, number: 1, article number: 185Publisher: NATURE RESEARCH