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).

Gavin de Beer was an English zoologist known for his contributions to evolution and embryology, in particular for showing the inadequacy of the germ layer theory as it was then proposed. He was born in London, England, on 1 November 1899, but was raised for his first thirteen years in France where his father worked for a telegraph company. He entered Magdalen College, Oxford, in 1917 but his studies were soon interrupted by World War I. After serving in the military, he returned to Oxford where he studied under Edwin Goodrich. He graduated in 1922 but stayed on as a fellow of Merton College and to teach in the Zoology Department. He was the Jenkinson Memorial Lecturer between 1926 and 1938.

Karl Wilhelm Theodor Richard von Hertwig is an important figure in the history of embryology for his contributions of artificial hybridization of sea urchin eggs and the formulation of his coelom theory. He was born 23 September 1850 in Friedelberg, Germany, to Elise Trapp and Carl Hertwig. Richard and his older brother Oscar began their studies at Jena under the direction of Ernst Haeckel from 1868 to 1871. In 1872 Hertwig became a lecturer in zoology at Jena while Oscar lectured in anatomy and embryology. As both brothers advanced in their respective fields, Hertwig left Jena to become a professor at Königsberg. In 1883 he was professor at Bonn and in 1885 in Munich, where he stayed until his retirement in 1925. Hertwig married Julia Braun in 1887 and had two sons and one daughter. He remained very active his entire life, outliving his brother Oscar by fifteen years.

Libbie Henrietta Hyman was born into a recently immigrated Jewish family on 6 December 1888 in Des Moines, Iowa. One of many siblings and daughter to parents Sabina Neumann and Joseph Hyman, who did not particularly support her interests in science, Hyman excelled in school and indulged her interests in biology in her free time. From a young age, Hyman collected and cataloged flora around her home. Despite being valedictorian of her high school class, Hyman's first job was labeling cereal boxes in a local factory. It was only when a former teacher became aware of Hyman's situation that Hyman was prompted to apply for college scholarships.

Isidore Geoffroy Saint-Hilaire studied anatomy and congenital abnormalities in humans and other animals in nineteenth century France. Under the tutelage of his father, Etienne Geoffroy Saint-Hilaire, Isidore compiled and built on his father's studies of individuals with developmental malformations, then called monstrosities. In 1832, Isidore published Histoire generale et particuliere des anomalies de l'organisation chez l'homme et les animaux (General and Particular History of Structural Monstrosities in Man and Animals), in which he defined the term teratology as the study of birth defects and deformities. Isidore Geoffroy Saint-Hilaire established teratology as a legitimate branch of scientific study.

Berthold Karl Hölldobler studied social insects like ants in Europe and the US during the twentieth and early twenty-first century. He focused on the social behavior of ants, the evolutionary origins of social insects, and the way ants use chemicals to communicate with each other. Hölldobler’s research reached popular audiences through his co-authored Pulitzer Prize winning book The Ants and through an award winning nature documentary called Ameisen: Die heimliche Weltmacht (Ants: Nature’s Secret Power). Hölldobler researched reproductive practices in specific ant species and helped explain how reproductive practices influence, and are influenced by, social behaviors.

Georges Cuvier, baptized Georges Jean-Leopold Nicolas-Frederic Cuvier, was a professor of anatomy at the National Museum of Natural History in Paris, France, through the late eighteenth and early nineteenth centuries. Scholars recognize Cuvier as a founder of modern comparative anatomy, and as an important contributor to vertebrate paleontology and geology. Cuvier studied the form and function of animal anatomy, writing four volumes on quadruped fossils and co-writing eleven volumes on the natural history of fish with Achille Valenciennes. Moreover, Cuvier constructed a system of classification based on specific and well-articulated principles to help anatomists classify animal taxa. Cuvier had public debate in 1830 with Etienne Geoffroy Saint-Hilaire, a dispute centered on whether form or function matters most for the study of anatomy and whether the transmutation of organic forms can occur over time. Cuvier's opinions influenced the development of biology in France, and his arguments against transmutation of types influenced the reception of Charles Darwin's theory of evolution by natural selection among many French naturalists.