Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

BMC Genomics

Benjamin D. Rosen¹  Matt A. Field²  Wesley C. Warren³  J. William O. Ballard⁴  Edward S. Rice⁵  Gary S. Johnson⁶  La Deanna Hillier⁷  Ksenia Skvortsova⁸  Jens Keilwagen⁹  Jillian M. Hammond^1,10  James M. Ferguson^1,10  Richard J. Edwards^1,11  Samuel G. Towarnicki^1,11  Ozren Bogdanovic^1,12  Ruqayya Khan^1,13  Arina Omer^1,13  Olga Dudchenko^1,14  Erez Lieberman Aiden^1,15  Robert A. Zammit^1,16 

[1] Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, 20705, Beltsville, MD, USA;Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, 4878, Cairns, QLD, Australia;John Curtin School of Medical Research, Australian National University, 2600, Canberra, ACT, Australia;Department of Animal Sciences, University of Missouri, 65211, Columbia, MO, Australia;Department of Ecology, Environment and Evolution, La Trobe University, 3086, Melbourne, Victoria, Australia;School of Biosciences, University of Melbourne, 3052, Parkville, Victoria, Australia;Department of Surgery, University of Missouri, 65211, Columbia, MO, USA;Department of Veterinary Pathobiology, University of Missouri, 65211, Columbia, MO, USA;Genome Sciences, University of Washington, 98195, Seattle, WA, USA;Genomics and Epigenetics Division, Garvan Institute of Medical Research, Victoria Street, 2010, Darlinghurst, NSW, Australia;St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, 2010, Sydney, NSW, Australia;Julius Kühn-Institut, Erwin-Baur-Str, 27 06484, Quedlinburg, Germany;Kinghorn Center for Clinical Genomics, Garvan Institute of Medical Research, Victoria Street, 2010, Darlinghurst, NSW, Australia;School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052, Sydney, NSW, Australia;School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052, Sydney, NSW, Australia;Genomics and Epigenetics Division, Garvan Institute of Medical Research, Victoria Street, 2010, Darlinghurst, NSW, Australia;The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA;Department of Computer Science, Rice University, Houston, TX, USA;The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA;Department of Computer Science, Rice University, Houston, TX, USA;Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA;The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA;Department of Computer Science, Rice University, Houston, TX, USA;Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA;Faculty of Science, UWA School of Agriculture and Environment, University of Western Australia, 6009, Perth, WA, Australia;Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China;Vineyard Veterinary Hospital, 703 Windsor Rd, 2765, Vineyard, NSW, Australia;

关键词: Canine genome;    Domestication;    Comparative genomics;    Artificial selection;   

DOI  :  10.1186/s12864-021-07493-6

来源: Springer

【 摘 要 】

BackgroundBasenjis 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.ResultsHere, 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.ConclusionsThe 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.

【 授权许可】

CC BY