Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial

In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara. We developed a scat single-nucleotide polymorphism panel to inform conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity. Resequenced genomes revealed population crashes during global cooling events and differences in Ninu genes involved in anatomical and metabolic pathways. Despite captive history, Ninu have fewer long runs of homozygosity. We investigated Ninu biology using 12 tissue transcriptomes, revealing expression of conserved placentation genes, an XY, Y₂ sex chromosome system and olfactory receptor gene expansions. Genomics improved key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers.

Carolyn J. Hogg, Richard J. Edwards, Katherine A. Farquharson, Luke W. Silver, Parice Brandies, Emma Peel, Merly Escalona, Frederick R. Jaya, Rujiporn Thavornkanlapachai, Kimberley Batley, Tessa M. Bradford, J. King Chang, Zhiliang Chen, Nandan Deshpande, Martin Dziminski, Kyle M. Ewart, Oliver W. Griffith, Laia Marin Gual, Katherine L. Moon, Kenny J. Travouillon, Paul Waters, Camilla M. Whittington, Marc R. Wilkins, Kristofer M. Helgen, Nathan Lo, Simon Y. W. Ho, Aurora Ruiz Herrera, Rachel Paltridge, Jennifer A. Marshall Graves, Marilyn Renfree, Beth Shapiro, Kym Ottewell, Kiwirrkurra Rangers, Katherine Belov