The Value of Reference Genomes in the Conservation of Threatened Species

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.

Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia

“…Of the 14,191 vascular plants that have been listed as threatened (Vulnerable, Endangered and Critically Endangered) on the IUCN Red List (version February 2019) 94 , 16 (~ 0.1%) have published genomes and only 64 have published transcriptomes as BioProjects on NCBI (~ 0.5%) 95 . Compared to about 1% of threatened animal species with published genomes on NCBI 96 , there are disproportionately few genome-wide resources in threatened plants.…”

The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda

“…While the Refseq-aligned dataset assigned more reads to both Metazoa (nt: Mean ± SD: 1,569 ± 2,843 sequences; Refseq: Mean ± SD: 3,810 ± 7,390 sequences; two-tailed p = 0.0022) and Viridiplantae (nt: Mean ± SD: 1,038 ± 1,669 sequences; Refseq: Mean ± SD: 1,187 ± 1,911 sequences; two-tailed p = 0.0041) than the nt-aligned dataset, the effect was larger for Metazoa (mean 2.43 × more assigned sequences) than Viridiplantae (mean 1.14 ×). In fact, the increase in Metazoa was greater than the increase in total Eukaryota (mean 1.46 ×), likely reflecting the disproportionate number of animal genomes in the Refseq database (e.g., Brandies et al, 2019).…”

“…This result could suggest that these important groups are particularly underrepresented in genomic surveys. The detection of vertebrates is moreover biased by species which have been genome sequenced -mostly large, charismatic taxa and model species (Brandies et al, 2019). Smaller and elusive animal species that constitute most of the diversity, such as shrews and frogs will be less likely detected.…”

Contemporary and historical selection in Tasmanian devils (Sarcophilus harrisii) support novel, polygenic response to transmissible cancer

“…We have a relatively short recorded history of infectious disease in wildlife, and therefore a limited ability to predict outcomes or intervene when warranted (7,8). High-throughput DNA-sequencing techniques and the generation of high-quality annotated reference genomes have revolutionized our ability to monitor and identify mechanisms of evolutionary responses to pathogens (8)(9)(10). Inter-specific comparisons of non-synonymous and synonymous variation (dN/dS) within protein-coding regions have long been used to identify positive selection at immune-related loci (11,12).…”