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Potoroos in truffle

The critically endangered Gilbert's potoroo or Ngilkat (Potorous gilbertii) is believed to be Australia's rarest mammal and the world’s rarest marsupial.

Gilbert's potoroo is a small kangaroo-like marsupial in the family Potoroidae. It was first recorded for science in 1840 by the collector John Gilbert (hence the name). The few known historical records of the potoroo are all from the southwestern coast of Southwest Australia in 1843, 1866, 1869, and 1875, and the uncertain date of 1890s to the west. The species was believed to be extinct for over 100 years before it was rediscovered in 1994 in Two Peoples Bay Nature Reserve.

Photo Description – Gilbert's Potoroo or Ngilkat (Potorous gilbertii) Photo Courtesy – Dick Walker and GPAG

As soon as the species was rediscovered, it was recognised that the population was extremely vulnerable as it occurred in very long unburnt vegetation (60+ years) with high fuel loads and given its restricted distribution could be lost in a single fire.

For the past 25 years the Department of Biodiversity, Conservation and Attractions (DBCA) has undertaken a range of recovery actions including attempts at captive breeding and various types of assisted reproduction to establish a sufficiently large population of captive animals to use to create insurance populations in case the Two Peoples Bay population was lost. Unfortunately, due to Gilbert’s potoroo’s extremely specialist diet (over 90% hypogeal fungi, e.g. truffles, which makes it one of the most fungi-dependent mammals in the world) and possibly other genetic and behavioural characteristics, neither captive breeding nor any other assisted reproduction techniques were successful.

In 2005, DBCA and the Gilbert’s potoroo Recovery Team decided to abandon attempts at captive breeding and to focus instead on creating insurance populations at locations outside Two Peoples Bay. Ten animals were introduced to Bald Island east of Two Peoples Bay between 2005 and 2007 and into a 380-ha fenced enclosure at Waychinicup from 2010. In 2015 the long-predicted fire at Two Peoples Bay, ignited by a severe lightning storm, destroyed over 95% of Gilbert’s potoroo habitat leaving only about 5 survivors. A third safe haven population on Middle Island was created in 2018 to provide additional security for the species.

Gilbert’s potoroo is listed as Critically Endangered under the IUCN Red List, the Australian EPBC Act (1999) and the Western Australian Biodiversity Conservation Act (2016). The current population is estimated at about 100-120 individuals: Two Peoples Bay (about 3-5 animals), Bald Island (est. 70 animals), the Waychinicup enclosure (25 known animals) and Middle Island (10 translocated animals).

The long-term goal of the recovery program for Gilbert’s potoroo is to improve its conservation status by increasing both the size of existing populations and the number of populations. In order to do this, it is critical to understand the distribution of genetic diversity across the four sub-populations (wild and translocated) to inform population management strategies (including genetic augmentation or assisted gene flow) aimed at maximizing the retention of genetic diversity at the species level.

Today, we share the chromosome-length genome assembly for the Gilbert's potoroo. The assembly was generated using a sample from 2009 provided by Dr Tony Friend from DBCA. This is a $1K genome assembly, with contig N50 of 46kb and scaffold N50 of 558Mb. See our Methods page for more detail on the procedure.

The interactive contact map of the Gilbert's potoroo's chromosomes is included below, alongside the whole-genome alignment to another closely related marsupial from our collection, the tammar wallaby. Despite the close chromosome count, the whole-genome alignment suggests substantial interchromosomal rearrangements since the last common ancestor of the two species (estimated to have existed ~24 MYA). This is the first version of the genome assembly for the species ever. Since our first tackle at this, we've generated more data and hope to generate even more, so stay tuned!

The work was enabled by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Illumina Inc., Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia. The work was provided as an in-kind contribution to a Western Australian State Natural Resource Management Community Stewardship Grant awarded to the Gilbert's Potoroo Action Group, a volunteer community group seeking to help save Gilbert's potoroo.

Whole-genome alignment plot between the Gilbert's potoroo chromosome-length genome assembly (Potorous_gilbertii_HiC, 2n=12,13) and a closely related marsupial from our collection, the tammar wallaby (me-1k, 2n=16). Both genome assemblies are $1K genome assemblies.

We hope that this chromosome-length assembly will provide the genomics resource to assist in estimating the genome-wide genetic diversity present in the existing population as well as management of the species. We also hope that this data will enable research on genes involved in adaptation and disease, further increasing our ability to improve species resilience in the population management strategy. Working with the Gilbert's potoroo recovery team this resource will facilitate the integration of genetic information into conservation management for the species. We believe that creation of this genomic resource will have lasting benefits for the genetic management and long-term survival of this critically endangered species.

Join Gilbert’s Potoroo Action Group (GPAG), DNA Zoo Australia/University of Western Australia & Department of Biodiversity, Conservation & Attractions for an afternoon event Saturday September 4, 2021, 1:00pm - 4:00pm to unveil the genome puzzle for the world's rarest marsupial, Gilbert’s Potoroo, & learn about the importance of genetics for endangered species conservation. The genome will be launched by former WA Chief Scientist Prof Lyn Beazley & followed by a truffle-themed afternoon tea & time for discussion, socialising & participation in puzzles & activities.

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