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 (+6 others)
2021 Communications Biology  
AbstractWe 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
more » ... s 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 fatcat:sme5phtnubgkzgwqrfooa6ncn4