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

Wang, Chao and Wallerman, Ola and Arendt, Maja-Louise and Sundstrom, Elisabeth and Karlsson, Asa and Nordin, Jessika and Mäkeläinen, Suvi and Pielberg, Gerli Rosengren and Hanson, Jeanette and Ohlsson Andersson, Åsa and Saellström, Sara and Rönnberg, Henrik and Bersås Ljungvall, Ingrid and Häggström, Jens and Bergström, Tomas F. and Hedhammar, Åke and Meadows, Jennifer R. S. and Lindblad-Toh, Kerstin (2021). A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. Communications biology. 4 , 185
[Journal article]

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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. Here, the authors report an improved de novo reference genome for the domestic dog based on a female German Shepherd named Mischka. The new genome increases contiguity 55-fold over the previous dog assembly and uncovers functional elements that were not previously identifiable.

Authors/Creators:Wang, Chao and Wallerman, Ola and Arendt, Maja-Louise and Sundstrom, Elisabeth and Karlsson, Asa and Nordin, Jessika and Mäkeläinen, Suvi and Pielberg, Gerli Rosengren and Hanson, Jeanette and Ohlsson Andersson, Åsa and Saellström, Sara and Rönnberg, Henrik and Bersås Ljungvall, Ingrid and Häggström, Jens and Bergström, Tomas F. and Hedhammar, Åke and Meadows, Jennifer R. S. and Lindblad-Toh, Kerstin
Title:A novel canine reference genome resolves genomic architecture and uncovers transcript complexity
Series Name/Journal:Communications biology
Year of publishing :2021
Volume:4
Article number:185
Number of Pages:11
Publisher:NATURE RESEARCH
ISSN:2399-3642
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 403 Veterinary Science > Clinical Science
URN:NBN:urn:nbn:se:slu:epsilon-p-111013
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-111013
Additional ID:
Type of IDID
DOI10.1038/s42003-021-01698-x
Web of Science (WoS)000620119100001
ID Code:22751
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
(VH) > Dept. of Clinical Sciences
Deposited By: SLUpub Connector
Deposited On:12 Mar 2021 10:43
Metadata Last Modified:12 Mar 2021 10:51

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