Recent, full-length gene retrocopies are common in canids [RESOURCES]

Kevin Batcher1, Scarlett Varney1, Daniel York2, Matthew Blacksmith3, Jeffrey M. Kidd3,4, Robert Rebhun2, Peter Dickinson2 and Danika Bannasch1 1Department of Population Health and Reproduction, University of California, Davis, Davis, California 95616, USA; 2Department of Surgical and Radiological Sciences, University of California, Davis, Davis, California 95616, USA; 3Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA; 4Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA Corresponding author: dlbannaschucdavis.edu Abstract

Gene retrocopies arise from the reverse transcription and insertion into the genome of processed mRNA transcripts. Although many retrocopies have acquired mutations that render them functionally inactive, most mammals retain active LINE-1 sequences capable of producing new retrocopies. New retrocopies, referred to as retro copy number variants (retroCNVs), may not be identified by standard variant calling techniques in high-throughput sequencing data. Although multiple functional FGF4 retroCNVs have been associated with skeletal dysplasias in dogs, the full landscape of canid retroCNVs has not been characterized. Here, retroCNV discovery was performed on a whole-genome sequencing data set of 293 canids from 76 breeds. We identified retroCNV parent genes via the presence of mRNA-specific 30-mers, and then identified retroCNV insertion sites through discordant read analysis. In total, we resolved insertion sites for 1911 retroCNVs from 1179 parent genes, 1236 of which appeared identical to their parent genes. Dogs had on average 54.1 total retroCNVs and 1.4 private retroCNVs. We found evidence of expression in testes for 12% (14/113) of the retroCNVs identified in six Golden Retrievers, including four chimeric transcripts, and 97 retroCNVs also had significantly elevated FST across dog breeds, possibly indicating selection. We applied our approach to a subset of human genomes and detected an average of 4.2 retroCNVs per sample, highlighting a 13-fold relative increase of retroCNV frequency in dogs. Particularly in canids, retroCNVs are a largely unexplored source of genetic variation that can contribute to genome plasticity and that should be considered when investigating traits and diseases.

Received April 8, 2022. Accepted July 19, 2022.

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