Richard J Edwards1, Matt A Field2,3, James M Ferguson4, Olga Dudchenko5,6,7, Jens Keilwagen8, Benjamin D Rosen9, Gary S Johnson10, Edward S Rice11, La Deanna Hillier12, Jillian M Hammond4, Samuel G Towarnicki1, Arina Omer5,6, Ruqayya Khan5,6, Ksenia Skvortsova13,14, Ozren Bogdanovic1,13, Robert A Zammit15, Erez Lieberman Aiden16,17,18,19,20, Wesley C Warren21, J William O Ballard22,23. 1. School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia. 2. Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, 4878, Australia. 3. John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2600, Australia. 4. Kinghorn Center for Clinical Genomics, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW, 2010, Australia. 5. The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. 6. Department of Computer Science, Rice University, Houston, TX, USA. 7. Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA. 8. Julius Kühn-Institut, Erwin-Baur-Str, 27 06484, Quedlinburg, Germany. 9. Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD, 20705, USA. 10. Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, 65211, USA. 11. Department of Surgery, University of Missouri, Columbia, MO, 65211, USA. 12. Genome Sciences, University of Washington, Seattle, WA, 98195, USA. 13. Genomics and Epigenetics Division, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW, 2010, Australia. 14. St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2010, Australia. 15. Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW, 2765, Australia. 16. The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. erez@erez.com. 17. Department of Computer Science, Rice University, Houston, TX, USA. erez@erez.com. 18. Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA. erez@erez.com. 19. Faculty of Science, UWA School of Agriculture and Environment, University of Western Australia, Perth, WA, 6009, Australia. erez@erez.com. 20. Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China. erez@erez.com. 21. Department of Animal Sciences, University of Missouri, Columbia, MO, 65211, Australia. warrenwc@missouri.edu. 22. Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, 3086, Australia. jwoballard@gmail.com. 23. School of Biosciences, University of Melbourne, Parkville, Victoria, 3052, Australia. jwoballard@gmail.com.
Abstract
BACKGROUND: Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. RESULTS: Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. CONCLUSIONS: The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.
BACKGROUND: Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. RESULTS: Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. CONCLUSIONS: The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.
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