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).

George McDonald Church studied DNA from living and from extinct species in the US during the twentieth and twenty-first centuries. Church helped to develop and refine techniques with which to describe the complete sequence of all the DNA nucleotides in an organism's genome, techniques such as multiplex sequencing, polony sequencing, and nanopore sequencing. Church also contributed to the Human Genome Project, and in 2005 he helped start a company, the Personal Genome Project. Church proposed to use DNA from extinct species to clone and breed new organisms from those species.

Charles Robert Cantor helped sequence the human genome, and he developed methods to non-invasively determine the genes in human fetuses. Cantor worked in the US during the twentieth and twenty-first centuries. His early research focused on oligonucleotides, small molecules of DNA or RNA. That research enabled the development of a technique that Cantor subsequently used to describe nucleotide sequences of DNA, a process called sequencing, in humans. Cantor was the principal scientist for the Human Genome Project, for which scientists sequenced the entirety of the human genome in 2003. Afterwards, Cantor became the chief scientific officer for Sequenom Inc., a company that provided non-invasive prenatal genetic testing. Such tests use a pregnant woman's blood to identify genetic mutations in a fetus during the first trimester of pregnancy.

In 1969, Roy J. Britten and Eric H. Davidson published Gene Regulation for Higher Cells: A Theory, in Science. A Theory proposes a minimal model of gene regulation, in which various types of genes interact to control the differentiation of cells through differential gene expression. Britten worked at the Carnegie Institute of Washington in Washington, D.C., while Davidson worked at the California Institute of Technology in Pasadena, California. Their paper was an early theoretical and mechanistic description of gene regulation in higher organisms.

In 2002 Eric Davidson and his research team published 'A Genomic Regulatory Network for Development' in Science. The authors present the first experimental verification and systemic description of a gene regulatory network. This publication represents the culmination of greater than thirty years of work on gene regulation that began in 1969 with 'A Gene Regulatory Network for Development: A Theory' by Roy Britten and Davidson. The modeling of a large number of interactions in a gene network had not been achieved before. Furthermore, this model revealed behaviors of the gene networks that could only be observed at the levels of biological organization above that of the gene.