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 status of Earth’s diversity is deteriorating quickly which will continue to impact humans’ way of life, as well as every other living creature, in all regions of the world. However, there are organizations taking action to protect biodiversity on our planet. The Convention on Biological Diversity (CBD) is one of those organizations and includes 196 signatories from around the world who are committed to strategies to preserve their biodiversity (Secretariat). Indeed, 98% of the parties which have participated in the Convention on Biological Diversity (CBD) have created national biodiversity strategies (NBS) and action plans (NBSAPs) (Secretariat). Yet, there are still countries that have yet to partake in these efforts. America continues to hold out against ratifying the CBD and remains the only developed country without a National Biodiversity Strategy. As an NBS for the U.S. is under consideration, my goal is to understand what works from previous plans. In particular, I focus on stakeholder engagement in Conservation Biodiversity Action Plans. Stakeholder engagement is important because, without it, there may be insufficient levels of integration of the action plans, which can lead to the failure of the CBDs conservation efforts. To address this question, I analyze the 193 strategies created for countries across the globe. My review describes the ways that stakeholders are engaged in National Biodiversity Strategies for CBD member countries. All plans mention some form of engagement. The most common types mentioned are ‘Education’, ‘Communication’, and ‘Training’. Examining the plans further reveals that most forms of engagement often are just mentioned and not completed. Close to 58% of the engagement forms are only completed about 50% of the time. Exceptions are surveys, interviews, and workshops, which are each completed in over 70% of plans that mention them. I then use this information to provide practical recommendations for creating an effective NBSAP for the United States.