Supporting data for "A reference genome for the critically endangered woylie, Bettongia penicillata ogilbyi"

Biodiversity is declining globally, and Australia has one of the worst extinction records for mammals. Development of sequencing technologies has opened genomics to wildlife, which is an important tool for conservation and management. Despite this, only 5% of threatened Australian species currently have a genome available through NCBI. Here we report the first reference genome for the woylie (<i>Bettongia penicillata ogilbyi</i>), a critically endangered marsupial from Western Australia, and the first genome within the Potoroidae family. The woylie reference genome was generated using PacBio HiFi long-reads, resulting in a 3.39Gb assembly with a scaffold N50 of 6.49Mb and 86.5% complete mammalian BUSCOs. Assembly of a global transcriptome from pouch skin, tongue, heart and blood RNAseq reads was used to guide annotation with Fgenesh++, resulting in the annotation of 24,655 genes. The woylie reference genome is a valuable resource for conservation, management and investigations into disease-induced decline of this critically endangered marsupial.