School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria 3052, Australia.
Department of Environment and Genetics, SABE, La Trobe University, Melbourne, Victoria 3086, Australia.
Gigascience. 2023 Mar 20;12. doi: 10.1093/gigascience/giad018. Epub 2023 Mar 28.
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.
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.
测试澳大利亚野犬是介于野生狼和家养犬种之间的功能性中间物种这一假设存在一个困难，那就是没有参考样本。在这里，我们将高质量的从头长读染色体组装与表观遗传足迹和形态学联系起来，描述了名为 Cooinda 的高山野犬雌性个体。建立高山野犬参考基因组至关重要，因为这种生态型存在于澳大利亚东海岸的沿海地区，而对该地区的第一批野犬的绘画和描述就是在这里完成的。
我们使用太平洋生物科学公司、牛津纳米孔技术公司、10X 基因组学公司、Bionano 公司和 Hi-C 技术的组合，生成了高质量的染色体水平参考基因组组装（Canfam_ADS）。与之前发表的沙漠野犬基因组组装相比，11、16、25 和 26 号染色体存在较大的结构重排。来自高山野犬 Cooinda 和之前发表的 9 个从头组装的犬类染色体数据的系统发育分析表明，野犬是单系的，并且在犬科动物中处于基础地位。网络分析表明，线粒体 DNA 基因组在预期的东南谱系内聚类，如高山野犬的情况所示。对调控区的比较鉴定出在胰高血糖素受体 GCGR 和组蛋白去乙酰化酶 HDAC4 基因内的 2 个差异甲基化区域，在高山野犬基因组中这些区域是非甲基化的，但在沙漠野犬中是高度甲基化的。形态学数据，包括颅形态的几何形态测量评估，将野犬 Cooinda 置于高山野犬种群水平变异范围内。脑组织的磁共振成像显示，她的颅腔容量比类似大小的家养犬大。
这些综合数据支持野犬 Cooinda 符合高山生态型典型的遗传和形态特征谱的假设。我们建议将她视为未来研究野犬进化历史、形态、生理和生态的原型样本。这只雌性个体已被制成标本，现陈列于悉尼的澳大利亚博物馆。
