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 Cell in Development and Inheritance, by Edmund Beecher Wilson, provided a textbook introduction to cell biology for generations of biologists in the twentieth century. In his book, Wilson integrated information about development, inheritance, chromosomes, organelles, and the structure and functions of cells. First published in 1896, the book started with 371 pages, grew to 483 pages in the second edition that appeared in 1900, and expanded to 1,231 pages by the third and final edition in 1925. Wilson dedicated the book to the cell biologist Theodor Boveri, whose work established the roles of chromosomes in cell division. With its explanations and many illustrations and diagrams, The Cell in Development and Inheritance enabled embryologists to better understand development in terms of cell structure and function.

"In vitro Experiments on the Effects of Mouse Sarcomas 180 and 37 on the Spinal and Sympathetic Ganglia of the Chick Embryo" were experiments conducted by Rita Levi-Montalcini in conjunction with Viktor Hamburger and Hertha Meyer and published in Cancer Research in 1954. In this series of experiments, conducted at the University of Brazil, Levi-Montalcini demonstrated increased nerve growth by introducing specific tumors (sarcomas) to chick ganglia. Ganglia are clusters of nerve cells, from which nerve fibers emerge. This work led to the discovery of nerve growth factor (NGF) and later the Nobel Prize in Physiology or Medicine in 1986.

Epidermal growth factor is a signaling molecule that stimulates the growth of epidermal tissues during development and throughout life. Stanley Cohen discovered epidermal growth factor (EGF) during studies of nerve growth factor as a side effect of other experiments. EGF stimulates tissue growth by initiating a variety of cellular mechanisms. This work led to the 1986 Nobel Prize in Physiology or Medicine awarded to Cohen and Rita Levi-Montalcini. At the Nobel Award ceremony Levi-Montalcini focused her acceptance speech on nerve growth factor, while Cohen focused his on epidermal growth factor. Although they presented different topics, they were close collaborators and their combined effort led to the discovery of nerve growth factor. They had worked together in Viktor Hamburger's laboratory at Washington University in St. Louis.