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

Chao Wang*, Ola Wallerman, Maja Louise Arendt, Elisabeth Sundström, Åsa Karlsson, Jessika Nordin, Suvi Mäkeläinen, Gerli Rosengren Pielberg, Jeanette Hanson, Åsa Ohlsson, Sara Saellström, Henrik Rönnberg, Ingrid Ljungvall, Jens Häggström, Tomas F. Bergström, Åke Hedhammar, Jennifer R.S. Meadows, Kerstin Lindblad-Toh

*Corresponding author for this work

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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.

Original languageEnglish
Article number185
JournalCommunications Biology
Volume4
ISSN2399-3642
DOIs
Publication statusPublished - 2021

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