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

Authors: BALLARD, J. WILLIAM - La Trobe University; FIELD, MATT - James Cook University; EDWARDS, RICHARD - University Of New South Wales; WILSON, LAURA - University Of New South Wales; KOUNGOULOS, LOUKAS - University Of Sydney; Rosen, Benjamin - Ben; CHERNOFF, BARRY - Wesleyan University; DUDCHENKO, OLGA - Baylor College Of Medicine; OMER, ARINA - Baylor College Of Medicine; KEILWAGEN, JENS - Julius Kuhn Institute; SKVORTSOVA, KSENIA - Garvan Institute Of Medical Research; BOGDANOVIC, OZREN - University Of New South Wales; CHAN, EVA - Garvan Institute Of Medical Research; ZAMMIT, ROBERT - Collaborator; HAYES, VANESSA - Garvan Institute Of Medical Research; AIDEN, EREZ - Baylor College Of Medicine

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/28/2023
Publication Date: 3/28/2023
Citation: Ballard, J.O., Field, M.A., Edwards, R.J., Wilson, L.A., Koungoulos, L.G., Rosen, B.D., Chernoff, B., Dudchenko, O., Omer, A., Keilwagen, J., Skvortsova, K., Bogdanovic, O., Chan, E.K., Zammit, R.A., Hayes, V., Aiden, E.L. 2023. The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology. GigaScience. https://doi.org/10.1093/gigascience/giad018.
DOI: https://doi.org/10.1093/gigascience/giad018

Interpretive Summary: Each species is described by a binomial with a single specimen expressly designated as the name-bearing type by the original author. Unfortunately, type specimens can be damaged, and obtaining long-read DNA data from many types is difficult. Such is the case with the Australian dingo: the type being represented by a 19th-century fragment of maxilla with insitu teeth from a cave deposit. Here we propose the Alpine dingo archetype Cooinda to represent the type specimen representing the regional morphotype. We link morphological descriptions of head shape and magnetic resonance imaging of brain tissue, long read de novo chromosomal and mitochondrial DNA assemblies with the epigenome to facilitate ongoing research and taxonomic discussions.

Technical Abstract: The Zoological Code of nomenclature ensures that every animal has a unique and universally accepted scientific name. However, problems can arise where there is no surviving type specimen, and the scientific description is rudimentary. Further, there can be nomenclatural disjunction if collection and specimen information is not linked with DNA sequence data. Both these issues occur in the Australian dingo. The passing of Cooinda the Alpine dingo has enabled us to connect her morphology with her chromosomal DNA, mitochondrial DNA and epigenetic footprints that would otherwise have been impossible. Morphological data, comprising geometric morphometric assessment of cranial morphology and magnetic resonance imaging of brain tissue, situate this female within population-level cranial variation for Alpine dingoes and suggest a larger cranial capacity than a similar-sized domestic dog. The generated assembly uses a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies to assemble a high-quality chromosome-level reference genome (Canfam_ADS). Compared to the previously published Desert dingo assembly, there are structurally important rearrangements on Chromosomes 11, 16, 25 and 26. Phylogenetic analyses of chromosomal data from the Alpine dingo and nine previously published de novo canine assemblies show dingoes are monophyletic relative to domestic dogs. Network analyses show that the mtDNA of Cooinda clusters within the southeastern lineage, as expected for an Alpine dingo. Epigenome profiling unravelled thousands of putative gene regulatory regions in the Alpine dingo genome. Comparison of regulatory regions identified two regions that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. These were regulatory regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes. These morphological and genomic data will enable further research into dingo functional morphology ecology and population genomics. It will facilitate the determination of the arrival of dingoes into Australia and, most generally allow accurate determination of the evolutionary relationships of canids, including their domestication.