A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference

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

doi:10.1101/2020.07.02.185108

GenomicsbioRxivJul 2, 2020

Preprint

A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference

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

Abstract

Here we present a new high-quality canine reference genome with gap number reduced 41-fold, from 23,836 to 585. Analysis of existing and novel data, RNA-seq, miRNA-seq and ATAC-seq, revealed a large proportion of these harboured previously hidden elements, including genes, promoters and miRNAs. Short-read dark regions were detected, and genomic regions completed, including the DLA, TCR and 366 cancer genes. 10x sequencing of 27 dogs uncovered a total of 22.1 million SNPs, Indels and larger structural variants (SVs). 1.4% overlap with protein coding genes and could provide a source of normal or aberrant phenotypic modifications.

PDF DOI