Abstract
Conservation initiatives are now more crucial than ever—over a million plant and animal species are at risk of extinction over the coming decades. The genetic management of threatened species held in insurance programs is recommended; however, few are taking advantage of the full range of genomic technologies available today. Less than 1% of the 13505 species currently listed as threated by the International Union for Conservation of Nature (IUCN) have a published genome. While there has been much discussion in the literature about the importance of genomics for conservation, there are limited examples of how having a reference genome has changed conservation management practice. The Tasmanian devil (Sarcophilus harrisii), is an endangered Australian marsupial, threatened by an infectious clonal cancer devil facial tumor disease (DFTD). Populations have declined by 80% since the disease was first recorded in 1996. A reference genome for this species was published in 2012 and has been crucial for understanding DFTD and the management of the species in the wild. Here we use the Tasmanian devil as an example of how a reference genome has influenced management actions in the conservation of a species.
Highlights
We are currently in the midst of a global sixth mass extinction event, with biodiversity rapidly declining around the world [1], and extinction rates are accelerating [2]
Complex (MHC), toll-like receptors (TLR), natural killer (NK) receptors, cathelicidins, behavior, and reproductive genes which were all manually annotated [69,72,75,101,102]. Annotation of these genes was essential in facilitating species-specific downstream research and informing conservation management decisions in the Tasmanian devil, such as genetic variation analyses [69,70,72,75]; selection of individuals for release to the wild [63], individuals response to the immunotherapy [66]; changes of immune function with the onset of puberty [73]; and the influence of age and devil facial tumor disease (DFTD) on immune function [74] (Table 1)
The Tasmanian devil reference genome has enhanced our capacity to manage this species in the face of an infectious, clonal cancer
Summary
We are currently in the midst of a global sixth mass extinction event, with biodiversity rapidly declining around the world [1], and extinction rates are accelerating [2]. Recent reviews have highlighted the importance of implementing genomic data into conservation initiatives [13,15,16], the application of such powerful advances in sequencing technologies is lacking in the current literature This limited use in conservation may be due to a number of reasons including: costs, a lack of understanding of the potential of new genomics approaches, lack of expertise in developing and utilizing the data, and the absence of a reference genome for the species of interest (or a closely-related species) [13,15,17]. We show how the reference genome has allowed a range of conservation questions to be answered in a timely, cost-effective manner and enabled conservation researchers to adapt to the rapid advances in genomic technologies
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