ASU Scholarship Showcase

Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.

Data Availability: All genomic and transcriptomic sequence files are available from the NIH-NCBI BioProject database (accession numbers PRJNA352725, PRJNA352726, and PRJNA281763). All genome assembly, transcriptome assembly, predicted protein, transcript, genome annotation, repeatmasker, phylogenetic trees, .vcf and GO enrichment files are available on Harvard Dataverse (doi:10.7910/DVN/EH2S9K).

Interdependent systems providing water and energy services are necessary for agriculture. Climate change and increased resource demands are expected to cause frequent and severe strains on these systems. Arizona is especially vulnerable to such strains due to its hot and arid climate. However, its climate enables year-round agricultural production, allowing Arizona to supply most of the country's winter lettuce and vegetables. In addition to Phoenix and Tucson, cities including El Paso, Las Vegas, Los Angeles, and San Diego rely on Arizona for several types of agricultural products such as animal feed and livestock, meaning that disruptions to Arizona's agriculture also disrupt food supply chains to at least six major cities.

Arizona's predominately irrigated agriculture relies on water imported through an energy intensive process from water-stressed regions. Most irrigation in Arizona is electricity powered, so failures in energy or water systems can cascade to the food system, creating a food-energy-water (FEW) nexus of vulnerability. We construct a dynamic simulation model of the FEW nexus in Arizona to assess the potential impacts of increasing temperatures and disruptions to energy and water supplies on crop irrigation requirements, on-farm energy use, and yield.

We use this model to identify critical points of intersection between energy, water, and agricultural systems and quantify expected increases in resource use and yield loss. Our model is based on threshold temperatures of crops, USDA and US Geological Survey data, Arizona crop budgets, and region-specific literature. We predict that temperature increase above the baseline could decrease yields by up to 12.2% per 1 °C for major Arizona crops and require increased irrigation of about 2.6% per 1 °C. Response to drought varies widely based on crop and phenophase, so we estimate irrigation interruption effects through scenario analysis. We provide an overview of potential adaptation measures farmers can take, and barriers to implementation.