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

Commun Biol. 2021 Feb 10;4(1):185. doi: 10.1038/s42003-021-01698-x.

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.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Dogs
  • Female
  • Gene Expression Profiling / standards*
  • Genetic Variation*
  • Genome*
  • Genomics / standards*
  • Genotype
  • INDEL Mutation
  • Phenotype
  • Polymorphism, Single Nucleotide
  • RNA-Seq / standards
  • Reference Values
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism
  • Transcriptome*

Substances

  • Transcription Factors