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

dc.citation.articleNumbergiad018en_US
dc.citation.journalTitleGigaScienceen_US
dc.citation.volumeNumber12en_US
dc.contributor.authorBallard, J. William O.en_US
dc.contributor.authorField, Matt A.en_US
dc.contributor.authorEdwards, Richard J.en_US
dc.contributor.authorWilson, Laura A.B.en_US
dc.contributor.authorKoungoulos, Loukas G.en_US
dc.contributor.authorRosen, Benjamin D.en_US
dc.contributor.authorChernoff, Barryen_US
dc.contributor.authorDudchenko, Olgaen_US
dc.contributor.authorOmer, Arinaen_US
dc.contributor.authorKeilwagen, Jensen_US
dc.contributor.authorSkvortsova, Kseniaen_US
dc.contributor.authorBogdanovic, Ozrenen_US
dc.contributor.authorChan, Evaen_US
dc.contributor.authorZammit, Roberten_US
dc.contributor.authorHayes, Vanessaen_US
dc.contributor.authorAiden, Erez Liebermanen_US
dc.contributor.orgCenter for Theoretical and Biological Physicsen_US
dc.date.accessioned2023-04-25T14:48:10Zen_US
dc.date.available2023-04-25T14:48:10Zen_US
dc.date.issued2023en_US
dc.description.abstractOne 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.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.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.en_US
dc.identifier.citationBallard, J. William O., Field, Matt A., Edwards, Richard J., et al.. "The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology." <i>GigaScience,</i> 12, (2023) Oxford University Press: https://doi.org/10.1093/gigascience/giad018.en_US
dc.identifier.digitalgiad018en_US
dc.identifier.doihttps://doi.org/10.1093/gigascience/giad018en_US
dc.identifier.urihttps://hdl.handle.net/1911/114839en_US
dc.language.isoengen_US
dc.publisherOxford University Pressen_US
dc.rightsThis is an open access article distributed under the terms of the Creative Commons CC BY license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titleThe Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphologyen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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