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- Creators: Tollis, Marc
- Creators: Broglio, Ronald
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).
The project intersects the environmental humanities, critical theory, and cultural studies with the Desert Southwest. It explores the fullness of desert places with regard to cultures, borders, and languages, as well as nonhuman forces and intensities like heat, light, and distance. Dispelling the dominant notion of desert as void or wasteland, it sets a stage to suit the polyvocality of desert place. My work is interdisciplinary because the desert demands it. It begins with Cormac McCarthy’s Blood Meridian in order to reorient readers towards the rupture of the US War With Mexico which helped set the national and cultural borders in effect today. I then explore Denis Villeneuve’s film Sicario to emphasize the correlation between political hierarchy and verticality; those who can experience the desert from above are exempt from the conditions below, where Urrea’s The Devil’s Highway and Gaspar de Alba’s Desert Blood take place. The novels expose the immanence and violence of being on the ground in the desert and at the lower end of said hierarchies. Analyzing Yuri Herrera’s Signs Preceding the End of the World and Mora’s Encantado enables what I term a desert hauntology to produce a desert full of memory, myth, ancestors, and enchantment. Finally, the project puts visual artists James Turrell and Rafa Esparza in conversation to discover a desert phenomenology. The result is an instigation of how far is too far when decentering the human, and what role does place-based art play in creating and empowering community.
John Ford was from Maine. Georgia O’Keeffe, from Wisconsin. Edward Abbey, Pennsylvania. As someone born and raised in the Desert Southwest, I’ve written the project I have yet to encounter.
