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 sex of a reptile embryo partly results from the production of sex hormones during development, and one process to produce those hormones depends on the temperature of the embryo's environment. The production of sex hormones can result solely from genetics or from genetics in combination with the influence of environmental factors. In genotypic sex determination, also called genetic or chromosomal sex determination, an organism's genes determine which hormones are produced. Non-genetic sex determination occurs when the sex of an organism can be altered during a sensitive period of development due to external factors such as temperature, humidity, or social interactions. Temperature-dependent sex determination (TSD), where the temperature of the embryo's environment influences its sex development, is a widespread non-genetic process of sex determination among vertebrates, including reptiles. All crocodilians, most turtles, many fish, and some lizards exhibit TSD.

The General Embryological Information Service (GEIS) was an annual report published by the Hubrecht Laboratory in Utrecht, The Netherlands from 1949 to 1981 that disseminated contemporary research information to developmental biologists. The purpose of the annual report was to catalog the names, addresses, and associated research of every developmental biologist in the world. Pieter Nieuwkoop edited each issue from 1949 until 1964, when Job Faber began assisting Nieuwkoop. Bert Z. Salome joined the editing team in 1968 before Nieuwkoop ceased editing duties in 1971. Faber and Salome remained the editors from 1971 until the periodical's final year of circulation in 1981. The Hubrecht Laboratory, a national laboratory created to house a large collection of comparative embryological materials and loan them to interested researchers, sponsored the publication after World War II to facilitate international collaboration and prevent unnecessary duplication of work. The catalog of researchers and the scientific topics grew in number and variety as the field of developmental biology changed during the publication's thirty-two year history.

The Cell-Theory was written by Thomas Henry Huxley in Britain and published in 1853 by The British and Foreign Medico-Chirurgical Review. The twenty-two page article reviews twelve works on cell theory, including those in Germany by Caspar Friedrich Wolff in the eighteenth century and by Karl Ernst von Baer in the nineteenth century. Huxley spends much of The Cell-Theory on a cell theory proposed in the late 1830s by Matthias Schleiden and Theodor Schwann in Germany. Schleiden and Schwann maintained that the cell was the most fundamental unit of life and that the nucleus was the most significant cellular component. Huxley, instead, promoted an epigenetic theory of the cell, for which properties of life emerge from the outer cytoplasm, cell membrane, and wall (the periplast), as opposed to the inner contents of the cell, including the nucleus (the endoplast). Huxley's arguments in The Cell-Theory influenced future scientists about the role of epigenetic processes in embryology and development.

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.