Genome of the endangered eastern quoll (Dasyurus viverrinus) reveals signatures of historical decline and pelage color evolution

Abstract

The eastern quoll (Dasyurus viverrinus) is an endangered marsupial native to Australia. Since the extirpation of its mainland populations in the 20th century, wild eastern quolls have been restricted to two islands at the southern end of their historical range. Eastern quolls are the subject of captive breeding programs and attempts have been made to re-establish a population in mainland Australia. However, few resources currently exist to guide the genetic management of this species. Here, we generated a reference genome for the eastern quoll with gene annotations supported by multi-tissue transcriptomes. Our assembly is among the most complete marsupial genomes currently available. Using this assembly, we infer the species' demographic history, identifying potential evidence of a long-term decline beginning in the late Pleistocene. Finally, we identify a deletion at the ASIP locus that likely underpins pelage color differences between the eastern quoll and the closely related Tasmanian devil (Sarcophilus harrisii).

Fig. 1. Appearance and distribution of the eastern quoll.

a Photograph of an adult eastern quoll (photo credit Brett Vercoe). b Map of the state of Tasmania, showing 50 years of eastern quoll sightings across the Tasmanian main island and Bruny Island recorded in the Tasmanian Natural Values Atlas. Individual sightings are shown as blue dots.

Fig. 2. Assessment of genome integrity and completeness.

a Contact map of Omni-C data against chromosome-scale scaffolds in the eastern quoll assembly. The enrichment level of chromosomal contacts is shown as blue pixel intensity b Stacked bar plot comparing the recovery of mammalian BUSCO genes. Recovery in the eastern quoll is among the highest for sequenced marsupials, with low rates of duplicated or fragmented orthologs.

Fig. 3. Gene and repeat annotation.

a Heat map illustrating the density of annotated genes across eastern quoll chromosome-scale scaffolds. b Bar plot showing the distribution of annotated repeats by class.

Fig. 4. Demography and comparative genomics of pigmentation.

a Step plot illustrating inferred changes in eastern quoll effective population size (N_e) over time. Grey regions indicate periods in which Tasmania was separated from mainland Australia (~135–43 kya and ~14 kya to present). The blue region indicates the coldest period of the Last Glacial Maximum (~24–18 kya). The dashed red line represents the arrival of humans in Tasmania (~40 kya). Area between the black dashed lines at 2000 and 200,000 years represent the window within which MSMC analysis is expected to be accurate based on previous studies (1–100 thousand generations before present). b Photographs comparing pelage color of the Tasmanian devil and eastern quoll (photo credits Brett Vercoe). c Mapping coverage of Tasmanian devil long reads (in light purple) across the ASIP locus in the eastern quoll genome. Exons of the eastern quoll ASIP gene are shown as red blocks. The deletion region is indicated by the absence of mapped Tasmanian devil reads underlined by a purple bar and encompassing exon 1 (dashed box) of ASIP. The putative eastern quoll insertion is underlined by an orange bar, upstream of the Tasmanian devil deletion.