Biology subjects

Zammit, R. A.

Publications and source records attributed to Zammit, R. A..

3 recordsLinked to original sources

bioRxiv2020

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

The dingo is Australias 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.

genomics↗

bioRxiv2020

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

BackgroundBasenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. ResultsHere, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. ConclusionsThe growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.

genomics↗

bioRxiv2020

Metabolomics shows the Australian dingo has a unique plasma profile

Dingoes have not been artificially selected in the past 3,500 years. They occupy a wide range of the Australian mainland and play a crucial role as an apex predator with a generalist omnivorous feeding behaviour. In contrast, humans have selected breed dogs for novel and desirable traits. First, we explore whether the distinct evolutionary histories of dingoes and domestic dogs can lead to plasma metabolomic differences. We study metabolite composition differences between dingoes (n=15) and two domestic dog breeds (Basenji n= 9 and German Shepherd Dog: GSD n=10). After accounting for within group variation, 62 significant metabolite differences were detected between dingoes and domestic dogs, with a greater number of differences in protein (n= 14) and lipid metabolites (n= 12). Most differences were observed between dingoes and domestic dogs and fewest between the domestic dog breeds. Second, we investigate variation between pure dingoes (n=10) and dingo-dog hybrids (n=10) as hybridisation is common. We detected no significant differences in metabolite levels between dingoes and dingo-dog hybrids after Bonferroni correction. However, power analyses reported that increasing the sample size to 15 could result in differences in uridine 5-diphosphogalactose (UDPgal) levels related to galactose metabolism. We suggest this may be related to an increase in Amylase 2B copy number in hybrids. Our study illustrates that the dingo metabolome is significantly different from domestic dog breeds and hybridisation is likely to influence carbohydrate metabolism.

ecology↗