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Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem

View ORCID ProfileSonu Yadav, View ORCID ProfileOlga Dudchenko, View ORCID ProfileMeera Esvaran, View ORCID ProfileBenjamin D. Rosen, View ORCID ProfileMatt A. Field, View ORCID ProfileKsenia Skvortsova, View ORCID ProfileRichard J. Edwards, View ORCID ProfileShyam Gopalakrishnan, View ORCID ProfileJens Keilwagen, View ORCID ProfileBlake J. Cochran, Bikash Manandhar, View ORCID ProfileMartin Bucknall, View ORCID ProfileSonia Bustamante, View ORCID ProfileJacob Agerbo Rasmussen, View ORCID ProfileRichard G. Melvin, Arina Omer, Zane Colaric, View ORCID ProfileEva K. F. Chan, View ORCID ProfileAndre E. Minoche, Timothy P.L. Smith, M. Thomas P. Gilbert, View ORCID ProfileOzren Bogdanovic, View ORCID ProfileRobert A. Zammit, View ORCID ProfileTorsten Thomas, View ORCID ProfileErez L. Aiden, View ORCID ProfileJ. William O. Ballard
doi: https://doi.org/10.1101/2020.11.15.384057
Sonu Yadav
1School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, High St, Kensington, NSW 2052, Australia
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Olga Dudchenko
2The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
3Department of Computer Science, Rice University, Houston, TX, USA
4Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA
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Meera Esvaran
5School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney NSW 2052, Australia
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Benjamin D. Rosen
6Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705
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Matt A. Field
7Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
8John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
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Ksenia Skvortsova
10Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
11St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2010, Australia
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Richard J. Edwards
1School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, High St, Kensington, NSW 2052, Australia
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Shyam Gopalakrishnan
12Center for Evolutionary Hologenomics, Faculty of Health and Medical Sciences, The GLOBE Institute University of Copenhagen, Copenhagen, Denmark
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Jens Keilwagen
13Julius Kühn-Institut, Erwin-Baur-Str. 27 06484 Quedlinburg, Germany
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Blake J. Cochran
14School of Medical Sciences, University of New South Wales, Sydney NSW 2052, Australia
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Bikash Manandhar
14School of Medical Sciences, University of New South Wales, Sydney NSW 2052, Australia
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Martin Bucknall
15Mark Wainwright Analytical Center, University of New South Wales, Sydney NSW 2052
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Sonia Bustamante
15Mark Wainwright Analytical Center, University of New South Wales, Sydney NSW 2052
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Jacob Agerbo Rasmussen
12Center for Evolutionary Hologenomics, Faculty of Health and Medical Sciences, The GLOBE Institute University of Copenhagen, Copenhagen, Denmark
16Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
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Richard G. Melvin
17Department of Biomedical Sciences, 1035 University Drive Duluth, University of Minnesota, MN 55812 USA
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Arina Omer
2The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Zane Colaric
2The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Eva K. F. Chan
9NSW Health Pathology, Newcastle NSW 2300
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Andre E. Minoche
10Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
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Timothy P.L. Smith
18US Meat Animal Research Center, Agricultural Research Service USDA, Rd 313, Clay Center, NE 68933, USA
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M. Thomas P. Gilbert
12Center for Evolutionary Hologenomics, Faculty of Health and Medical Sciences, The GLOBE Institute University of Copenhagen, Copenhagen, Denmark
19NTNU University Museum, Trondheim, Norway
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Ozren Bogdanovic
1School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, High St, Kensington, NSW 2052, Australia
10Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
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Robert A. Zammit
20Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW, 2765
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Torsten Thomas
5School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney NSW 2052, Australia
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Erez L. Aiden
2The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
3Department of Computer Science, Rice University, Houston, TX, USA
4Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA
21Faculty of Science, UWA School of Agriculture and Environment, University of Western Australia, Perth WA
22Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech University, Shanghai, China
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J. William O. Ballard
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  • For correspondence: jwoballard@gmail.com
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Abstract

The dingo is Australia’s iconic top-order predator and arrived on the continent between 5,000-8,000 years ago. To provide an unbiased insight into its evolutionary affiliations and biological interactions, we coupled long-read DNA sequencing with a multiplatform scaffolding approach to produce an ab initio genome assembly of the desert dingo (85X coverage) we call CanLup_DDS. We compared this genome to the Boxer (CanFam3.1) and German Shepherd dog (CanFam_GSD) assemblies and characterized lineage-specific and shared genetic variation ranging from single– to megabase pair–sized variants. We identified 21,483 dingo-specific and 16,595 domestic dog-specific homozygous structural variants mediating genic and putative regulatory changes. Comparisons between the dingo and domestic dog builds detected unique inversions on Chromosome 16, structural variations in genes linked with starch metabolism, and seven differentially methylated genes. To experimentally assess genomic differences 17 dingoes and 15 German Shepherd dogs were fed parallel diets for 14 days. In dingoes, low AMY2B copy number and serum amylase levels are linked with high cholesterol and LDL levels. Gut microbiome analyses revealed enrichment of the family Clostridiaceae, which can utilize complex resistant starch, while scat metabolome studies identified high phenylethyl alcohol concentrations that we posit are linked with territory marking. Our study provides compelling genomic, microbiome, and metabolomic links showing the dingo has distinct physiology from domestic breed dogs with a unique role in the ecosystem.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem
Sonu Yadav, Olga Dudchenko, Meera Esvaran, Benjamin D. Rosen, Matt A. Field, Ksenia Skvortsova, Richard J. Edwards, Shyam Gopalakrishnan, Jens Keilwagen, Blake J. Cochran, Bikash Manandhar, Martin Bucknall, Sonia Bustamante, Jacob Agerbo Rasmussen, Richard G. Melvin, Arina Omer, Zane Colaric, Eva K. F. Chan, Andre E. Minoche, Timothy P.L. Smith, M. Thomas P. Gilbert, Ozren Bogdanovic, Robert A. Zammit, Torsten Thomas, Erez L. Aiden, J. William O. Ballard
bioRxiv 2020.11.15.384057; doi: https://doi.org/10.1101/2020.11.15.384057
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Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem
Sonu Yadav, Olga Dudchenko, Meera Esvaran, Benjamin D. Rosen, Matt A. Field, Ksenia Skvortsova, Richard J. Edwards, Shyam Gopalakrishnan, Jens Keilwagen, Blake J. Cochran, Bikash Manandhar, Martin Bucknall, Sonia Bustamante, Jacob Agerbo Rasmussen, Richard G. Melvin, Arina Omer, Zane Colaric, Eva K. F. Chan, Andre E. Minoche, Timothy P.L. Smith, M. Thomas P. Gilbert, Ozren Bogdanovic, Robert A. Zammit, Torsten Thomas, Erez L. Aiden, J. William O. Ballard
bioRxiv 2020.11.15.384057; doi: https://doi.org/10.1101/2020.11.15.384057

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