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

Abstract The Ninu (Greater bilby, Macrotis lagotis) is a desert-dwelling, culturally and ecologically important marsupial. In collaboration with Indigenous rangers and conservation managers, we generated the first Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura) to understand their biology and guide Ninu conservation management. Resequenced genomes (temperate Ninu=6; semi-arid Ninu=6; Yallara=4) revealed two major population crashes during global cooling events. Despite their 45-year long captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom-bust life-history. We assessed the beneficial impact of targeted conservation actions, like translocations, in the contemporary metapopulation (N=363 Ninu) and designed a SNP panel used by Indigenous rangers in monitoring remote wild populations. We dig into the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus; an XY1Y2 sex chromosome system generated by fusion of the X with a large telocentric autosome; genes involved in anatomical and metabolic pathway adaptations to aridity; and expansions in olfactory receptor genes. Together, we demonstrate the holistic value of genomics in addressing key Indigenous and conservation management questions for ongoing conservation efforts.