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

作者：J. William O. Ballard, Matthew A. Field, Richard J. Edwards, Laura A. B. Wilson, Loukas Koungoulos, Benjamin D. Rosen, Barry Chernoff, Olga Dudchenko, Arina D. Omer, Jens Keilwagen, Ksenia Skvortsova, Ozren Bogdanović, Eva K.F. Chan, Robert A. Zammit, Vanessa M. Hayes, Erez Lieberman Aiden · 发表于：GigaScience · 年份：2023 · DOI：10.1093/gigascience/giad018 · 被引用次数：12 · 研究领域：Human-Animal Interaction Studies、Genomic variations and chromosomal abnormalities、Veterinary Oncology Research

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 mor...