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).

Frederik Ruysch, working in the Netherlands, introduced the term epithelia in the third volume of his Thesaurus Anatomicus in 1703. Ruysch created the term from the Greek epi, which means on top of, and thele, which means nipple, to describe the type of tissue he found when dissecting the lip of a cadaver. In the mid nineteenth century, anatomist Albrecht von Haller adopted the word epithelium, designating Ruysch's original terminology as the plural version. In modern science, epithelium is a type of animal tissue in which cells are packed into neatly arranged sheets. The epithelial cells lie proximate to each other and attach to a thin, fibrous sheet called a basement membrane. Epithelia line the surfaces of cavities and structures throughout the body, and also form glands. Although they lack blood vessels, epithelia contain nerves and can function to receive sensation, absorb, protect, and secrete, depending on which part of the body the epithelia line. During development, epithelia act in conjunction with another tissue type, mesenchyme, to form nearly every organ in the body, from hair and teeth to the digestive tract. Epithelia are an essential part of embryonic development and the maintenance and function of the body throughout life.

In nineteenth century Great Britain, Thomas Henry Huxley proposed connections between the development of organisms and their evolutionary histories, critiqued previously held concepts of homology, and promoted Charles Darwin's theory of evolution. Many called him Darwin's Bulldog. Huxley helped professionalize and redefine British science. He wrote about philosophy, religion, and social issues, and researched and theorized in many biological fields. Huxley made several methodological contributions to both invertebrate and vertebrate embryology and development, and he helped shape the extra-scientific discourse for these fields.

Hilde Proscholdt Mangold was a doctoral student at the Zoological Institute at the University of Freiburg in Freiburg, Germany, from 1920-1923. Mangold conducted research for her dissertation 'On the Induction of Embryonic Primordia by Implantation of Organizers from Different Species' ('Ueber Induktion von Embryonanlagen durch Implantation artfremder Organisatoren'), under the guidance of Hans Spemann, a professor of zoology at the University of Freiburg. The dissertation was the culmination of five experiments on three species of newt embryos, of the genus Triton (presently, Triturus), performed during the summers of 1921 and 1922, which resulted in a confirmation of Spemann's organizer concept. Spemann and Mangold published the dissertation in a 1924 edition of Roux's Archives for Microscopic Anatomy and Developmental Mechanics (Roux's Archiv fur Mikroskopische Anatomie und Entwicklungsmechanik)."

Between February 1969 and August 1970 Edward Kollar and Grace Baird, from the University of Chicago in Chicago, Illinois, published three papers that established the role of the mesenchyme in tooth induction. Drawing upon a history of using tissue interactions to understand differentiation, Kollar and Baird designed their experiments to understand how differentiated structures become specified. Their work overturned a widely accepted model that epithelium controls the identity of the structure, a phenomenon called structural specificity. Interactions between epithelium and mesenchyme control the development and differentiation of many parts during embryonic development, including structures like the gastrointestinal tract and hair. Thus, the realization that mesenchyme drives induction and differentiation during epithelio-mesenchymal interactions had far-reaching effects.