The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology

J William O Ballard; Matt A Field; Richard J Edwards; Laura A B Wilson; Loukas G Koungoulos; Benjamin D Rosen; Barry Chernoff; Olga Dudchenko; Arina Omer; Jens Keilwagen; Ksenia Skvortsova; Ozren Bogdanovic; Eva Chan; Robert Zammit; Vanessa Hayes; Erez Lieberman Aiden

doi:10.1093/gigascience/giad018

The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology

Gigascience. 2023 Mar 20:12:giad018. doi: 10.1093/gigascience/giad018. Epub 2023 Mar 28.

Authors

J William O Ballard^{1

2}, Matt A Field^{3

4}, Richard J Edwards⁵, Laura A B Wilson^{6

7}, Loukas G Koungoulos⁸, Benjamin D Rosen⁹, Barry Chernoff¹⁰, Olga Dudchenko^{11

12}, Arina Omer¹², Jens Keilwagen¹³, Ksenia Skvortsova¹⁴, Ozren Bogdanovic¹⁴, Eva Chan^{14

15}, Robert Zammit¹⁶, Vanessa Hayes^{14

17}, Erez Lieberman Aiden^{11

12

18

19}

Affiliations

¹ School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria 3052, Australia.
² Department of Environment and Genetics, SABE, La Trobe University, Melbourne, Victoria 3086, Australia.
³ Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, Queensland 4870, Australia.
⁴ Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
⁵ School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
⁶ School of Archaeology and Anthropology, The Australian National University, Acton, ACT 2600, Australia.
⁷ School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
⁸ Department of Archaeology, School of Philosophical and Historical Inquiry, the University of Sydney, Sydney, NSW 2006, Australia.
⁹ Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705, USA.
¹⁰ College of the Environment, Departments of Biology, and Earth & Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA.
¹¹ The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
¹² Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA.
¹³ Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg 06484, Germany.
¹⁴ Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
¹⁵ Statewide Genomics, New South Wales Health Pathology, Newcastle, NSW 2300, Australia.
¹⁶ Vineyard Veterinary Hospital,Vineyard, NSW 2765, Australia.
¹⁷ Charles Perkins Centre, Faculty of Medical Sciences, University of Sydney, Camperdown, NSW 2006, Australia.
¹⁸ UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.
¹⁹ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

Abstract

Background: One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long-read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed.

Findings: We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on chromosomes 11, 16, 25, and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and 9 previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mitochondrial DNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified 2 differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphologic data, comprising geometric morphometric assessment of cranial morphology, place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue shows she had a larger cranial capacity than a similar-sized domestic dog.

Conclusions: These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphologic characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.

Keywords: de novo genome assembly; biogeography; cranium; long-read sequencing; type specimen.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Australia
Canidae* / genetics
Chromosomes
Dogs
Epigenome
Female
Genome, Mitochondrial*
Phylogeny
Wolves* / genetics

Abstract

Publication types

MeSH terms

Grants and funding