Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem

Abstract

The dingo is Australia’s iconic top-order predator and arrived on the continent between 5,000-8,000 years ago. To provide an unbiased insight into its evolutionary affiliations and biological interactions, we coupled long-read DNA sequencing with a multiplatform scaffolding approach to produce an ab initio genome assembly of the desert dingo (85X coverage) we call CanLup_DDS. We compared this genome to the Boxer (CanFam3.1) and German Shepherd dog (CanFam_GSD) assemblies and characterized lineage-specific and shared genetic variation ranging from single– to megabase pair–sized variants. We identified 21,483 dingo-specific and 16,595 domestic dog-specific homozygous structural variants mediating genic and putative regulatory changes. Comparisons between the dingo and domestic dog builds detected unique inversions on Chromosome 16, structural variations in genes linked with starch metabolism, and seven differentially methylated genes. To experimentally assess genomic differences 17 dingoes and 15 German Shepherd dogs were fed parallel diets for 14 days. In dingoes, low AMY2B copy number and serum amylase levels are linked with high cholesterol and LDL levels. Gut microbiome analyses revealed enrichment of the family Clostridiaceae, which can utilize complex resistant starch, while scat metabolome studies identified high phenylethyl alcohol concentrations that we posit are linked with territory marking. Our study provides compelling genomic, microbiome, and metabolomic links showing the dingo has distinct physiology from domestic breed dogs with a unique role in the ecosystem.

Chromosome‐level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long‐reads, linked‐reads and Hi‐C

“…Accuracy was calculated as the estimated genome size, divided by the documented genome size. Additional benchmarking of the robustness of DepthSizer predictions was performed using ONT and PacBio sequence data for three high‐quality dog genomes: Basenji (Edwards et al, 2021), Dingo (Yadav et al, 2020) and German Shepherd Dog (Field et al, 2020). Raw reads from each technology were analysed independently using both the breed‐specific reference genome and the CanFam 3.1 dog reference (GCA_000002285.2; Lindblad‐Toh et al, 2005).…”

Chromosome-levelde novogenome assembly ofTelopea speciosissima(New South Wales waratah) using long-reads, linked-reads and Hi-C

“…Accuracy was calculated as the estimated genome size, divided by the documented genome size. Additional benchmarking of the robustness of DepthSizer predictions was performed using ONT and PacBio sequence data for three high-quality dog genomes: Basenji (Edwards et al, 2021), Dingo (Yadav et al, 2020), and German Shepherd 12 Dog (Field et al, 2020). Raw reads from each technology were analysed independently using both the breed-specific reference genome, and the CanFam 3.1 dog reference (GCA_000002285.2; .…”