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

Wang, C.; Wallerman, O.; Arendt, M.-L.; Sundstrom, E.; Karlsson, A.; Nordin, J.; Makelainen, S.; Pielberg, G. R.; Hanson, J.; Ohlsson, A.; Saellstrom, S.; Ronnberg, H.; Ljungvall, I.; Haggstrom, J.; Bergstrom, T. F.; Hedhammar, A.; Meadows, J. R. S.; Lindblad-Toh, K.

2020-07-02 genomics
10.1101/2020.07.02.185108 bioRxiv
Show 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.

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