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

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

  • Chao Wang
  • Ola Wallerman
  • Arendt, Maja Louise
  • 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

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.

TidsskriftCommunications Biology
StatusUdgivet - 2021

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