ICCFGG 2022
#19 Evolutionary Insights enabled by assembly and annotation of the dog Y chromosome Jeffrey J. Schoenebeck 1 , Wengang Zhang 1 , Lel Eory 1 , Shelagh Boyle 2 , Jiaqi Yang 3 , Melany Jack- son 1 , Derya D. Ozdemir 1 , Andrew C. Kitchener 4 , Jacqueline Smith 1 , Emily Clark 1 , Sarah Emery 5 , Jennifer R. S. Meadows 6, Greger Larson 7 , Laurent Frantz 3,8, Jeffrey M. Kidd 5, Alan L. Archibald 1 jeff.schoenebeck@roslin.ed.ac.uk 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG UK, 2 MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK, 3 Department of Veterinary Sciences, Ludwig Maximilian University of Munich, Germany, 4 Department of Natural Sciences, National Museums Scot- land and School of Geosciences, University of Edinburgh, Edinburgh, UK, 5 Department of Human Genet- ics and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA, 6 Science for Life Laboratory and Uppsala University, Uppsala, Sweden 7 School of Archaeology, University of Oxford, UK, 8 Department of Organismal Biology, Queen Mary University of London, UK Background The Y chromosome plays an oversized role in biologists’ understanding of mammalian evolution, domestication, and reproduction. A major hindrance to studying Y chromosome functions is its complicated genomic structure which includes an overabundance of repetitive sequence, large multicopy gene families, and partial homology to the X chromosome. Here we describe an improved assembly of the dog Y chromosome (“RosY_1.0”) using long reads and scaffolding data generated for the Labrador retriever genome assembly, ROS_Cfam_1.0. Results RosY_1.0 is composed of three scaffolds totaling 6.8Mb, making it the longest canid Y chromosome assembly reported to date. Analysis of RosY_1.0 organization and gene content revealed features that are unique to canids. Within the pseudoautosomal boundary, we find two mutually exclusive genes, TETY2 (chrY) and CLDN34 (chrX). The testes-specific transcription of these genes appears to be regulated by a promoter that is used in common. Based on the synonymous substitution rates, studies of other mammals report three or more “degenerative strata” of Y gametologs. In contrast, our data indicate that dog Y gametolog degeneracy occurred in two strata. The transcriptional expression of Y chromosome genes appears to reflect the divergence of gametologs. Specifically, Y gametologs with testis-specific expression are more diverged than those whose expression is ubiquitous. Missense coding variants within BCORY1, KDM5D, OFD1Y, UBE1Y, and WWC3Y appear more frequently than predicted. These missense variants emerged during dog domestication and are distributed nonrandomly across phylogenetic dog clades. Conclusions RosY_1.0 reveals genomic features that distinguish the molecular and phylogenetic evolution of dogs.
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