Saving Our Endangered Species One Genome At A Time

Revive & Restore (R&R) and Dovetail Genomics (DTG) co-sponsored their inaugural Conservation Genomics Summit on October 27, 2021.  This virtual event brought six prominent conservation biologists together with an audience of more than 350 to discuss the application of genomics tools to the preservation of biodiversity.

The invited speakers and the attendees engaged with one another and had their questions answered by speakers through live Q&A, chats, and a networking breaks in between sessions. In this blog, I will provide a brief synopsis and cover the highlights from each of our speakers. If you missed the summit, we still have you covered. You can catch the on-demand recordings by registering HERE

What are R&R and DTG working together to achieve?

R&R is the leading wildlife conservation organization incorporating biotechnologies into standard conservation practice. DTG provides R&R with high-quality reference genomes that are a critical first step to fully understanding the biology of endangered species. This partnership will accelerate R&R’s Wild Genomes program by making high quality reference genomes more accessible to R&R funded researchers.

Figure 1. R&R and DTG have formed a partnership to expand the use of genomics tools in conservation biology. A high-quality reference genome is the first step in understanding the genetic diversity of a species and is needed to manage and conserve at-risk populations. The usability of genomic features, like SNPs, structural variants and runs of homozygosity depends on the contiguity and accuracy of the reference assembly. These genomic features can then be used to develop genomic tools (e.g., SNP arrays) or drive population-scale resequencing efforts. In turn, the data generated from these tools can then be applied to understand conservation features, such as genetic diversity and admixture, that will provide the conservation biologist with valuable data for the population under study. Now, armed with a wide range of accurate genomic data, the conservation biologist can focus on rescuing at-risk species by using a variety of conservation applications, such as introducing greater genetic diversity into an inbred population by way of wildlife or plant translocation.

Ryan Phelan, co-founder and Executive Director of R&R, highlighted recent success stories during her engaging talk, such as the cloning of America’s most endangered mammal, the Black-footed ferret (Mustela nigripes), and exciting advances in gene-editing that will help restore the American chestnut tree (Castanea dentata) to its historical abundance. Ryan also provided insight into intended consequences and how action must be taken now to preserve biodiversity before it is lost forever.

Bernardi, Giacomo -- Headshot_round

Giacomo Bernardi initiated the scientific panel talks with an exciting update on his work with the critically endangered Bangaii cardinalfish (Pterapogon kauderni). This species has a very limited range in the Bangaii Archipelago of Indonesia and has seen drastic decline due to overfishing for the aquarium trade. While local populations are genetically very well adapted to their environment, they are also particularly vulnerable to collection and local extinction.

A high-quality DTG genome assembly is underway, enabled by a unique crowd-funding program, AG4 (“A Genome for”). As part of the program, DTG makes donations on behalf of their customers until enough funds are raised to pay for the reference genome. Dr. Bernardi will use the reference assembly to genetically profile fish prior to reintroduction into their historical geographic locations.

The second talk was a dual presentation by Jeremy Yoder (California State University, Northridge) and Moises Exposito-Alonso (Carnegie Institution for Science) on their work inventorying genomic diversity of the Joshua tree (Yucca brevifolia). The Joshua tree is under severe threat from climate change and habitat destruction. “We are conducting whole-genome resequencing of 300 Joshua trees sampled across the species’ range to produce the first large-scale sequencing of a keystone desert species” stated Dr. Yoder. “This will likely enable discovery of new genes related to the evolution of extremophile plants, allow us to map genetic variants for climate adaptation, and predict climate change resilience of extant Joshua tree populations to better target conservation efforts.”

Extending these efforts, Dr. Exposito-Alonso presented recent work developing a mathematical model for the estimation and prediction of genetic diversity loss within a species. Using the Joshua tree as an example, Dr. Exposito-Alonso discussed the need to better quantify diversity loss. “Given pre-21st century values of ecosystem transformations, we estimate that over 10% of genetic diversity may be extinct, already surpassing the United Nations targets for genetic preservation,” he stated. “These estimated losses could rapidly increase with advancing climate change and habitat destruction, highlighting the need for new forecasting tools that assist in the rapid implementation of policies to protect genetic resources.”

Lauren Schiebelhut (University of California, Merced) discussed how sea star wasting disease has decimated most of the Sunflower sea star’s (Pycnopodia helianthoides) population across the West coast of North America. The species is now critically endangered. Dr. Schiebelhut stated “these dramatic declines and their community consequences have spurred the need for quick concerted actions to conserve the species and collect the information necessary to inform potential conservation interventions. With Revive & Restore, we are working to discover genomic variants associated with vulnerability to wasting and temperature stress.” A high-quality genome assembly was a crucial first step in this effort and was provided by DTG through the R&R Wild Genomes Program. The assembly will be used to generate the genomic insights needed to help inform conservation decisions and increase success along two conservation trajectories: (1) captive breeding for potential out-planting and (2) assessing wild populations for potential translocation and other conservation actions.

Charles Yakov Feigin_round

Charles Feigin (Princeton University) recently received a DTG-R&R genome assembly for Eastern quoll (Dasyurus viverrinus). While this species once occupied much of Australia, it has experienced severe declines and is now restricted to the island of Tasmania. The Tasmanian population is now suffering from inbreeding depression due to the localized geography. Dr. Feigin will use the reference genome and historical mainland specimens to find extinct alleles, that, when genetically engineered into Tasmanian individuals, will give them the fitness traits to survive when introduced to mainland Australia.

The Eastern quoll genome is one of the first haplotype-resolved (i.e., true diploid) assemblies that DTG is now providing customers. Stated Dr. Feigin: “What I think Revive & Restore has been very far-sighted about is focusing the (Wild Genomes) program on high-quality, future-proofed reference genomes – assemblies that are as close to a perfect representation of the underlying genome as possible.” The haplotype-resolved Eastern quoll assembly is just that – a highly accurate and complete set of two sub-assemblies, built independently and faithfully representing the true diploid genome of the species.

Ellie Armstrong (Washington State University) rounded out the invited speaker session with an update on her research genomically profiling the U.S. captive tiger (Panthera tigris) population. Sadly, the number of captive tigers worldwide greatly outnumbers the wild population. It is therefore important and relevant to understand the genetic diversity and history of the captive tiger population. Dr. Armstrong compared 148 captive tiger whole genomes with 115 wild tiger genomes across six subspecies. While the genomes of the wild individuals were pure, and showed no signs of recent admixture, the genomes of the captive tigers were a mosaic of the six subspecies due to indiscriminate and irresponsible crossbreeding by private captive tiger facilities. The captive tigers also showed a broader range of heterozygosity and ROH than the wild animals, again, an indicator of inter-breeding and in-breeding, respectively.

Dr. Armstrong is now the second recipient of an AG4 award for assembling the wolverine (Gulo gulo) genome. The genome assembly will be a first step to understanding the population demographics and genetic diversity of this mysterious, and possibly threatened, species.

Genome assemblies are typically haploid and as such, genome assemblers are forced to choose randomly between maternal or paternal alleles at heterozygous positions. This results in an assembly that is a mosaic of the two haplotypes and not a true representation of the genome.

With a solution to this problem, Mark Daly from DTG closed the summit announcing the launch of the newest DTG service, haplotype-resolved (true diploid) genome assembly.

Using a unique combination of PacBio HiFi long reads (for high SNP call accuracy) and Dovetail® Omni-C® data (for even, whole genome SNP coverage) + HiRise scaffolding, DTG is now providing true diploid assemblies to its customers. Foundational to this both de novo and scaffolding projects, the customer will receive two independent assemblies – one for each haplotype, each built independently from the original HiFi contigs. Diploid assemblies represent the true genome providing a huge step forward in understanding the genetics of at-risk species.

Pseudo-haploid True Diploid
  • Only represent half the genome
  • Mosaic of maternally and paternally derived haplotypes
Provides accurate understanding of:

  • Runs of homozygosity
  • Hybridization
  • Cis versus trans mutations
  • Allele-specific expression
  • Local-ancestry inference
  • Structural variation
  • Genotype imputation
  • LD patterns
  • Haplotype frequency differences
  • Segmental duplications
  • Complex gene families
  • Designing mating schemes