A novel canine reference genome resolves genomic architecture and uncovers transcript complexity
Research output: Contribution to journal › Journal article › Research › peer-review
Documents
- A novel canine reference genome resolves genomic architecture and uncovers transcript complexity
Final published version, 3.41 MB, PDF document
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 language | English |
---|---|
Article number | 185 |
Journal | Communications Biology |
Volume | 4 |
ISSN | 2399-3642 |
DOIs | |
Publication status | Published - 2021 |
Number of downloads are based on statistics from Google Scholar and www.ku.dk
ID: 257969715