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- All Subjects: Developmental Biology
- Creators: Kusumi, Kenro
- Creators: Navis, Adam R.
- Creators: Tollis, Marc
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).
Research in chemical induction seeks to identify the compound or compounds responsible for differentiation in a developing embryo. Soren Lovtrup compared the search for these compounds to the search for the philosopher's stone. It was based on the assumption that the differentiating agents have to be chemical substances either within cells or in the extracellular matrix. However, despite numerous efforts to understand them, the nature of these substances remained largely a mystery from the 1930s until the 1980s, when the new era of molecular induction based on molecular genetics provided a new perspective. During the period of emphasis on chemical induction, a variety of different experiments were conducted aimed at discovering the chemical nature of the inducer. In some experiments, the organizer region was killed by heat to assess the inducing ability of a dead organizer. Other experiments used natural and synthetic compounds to attempt. Although none of these experiments identified a chemical inducer with any certainty, they did discover many related properties of the developing embryo.
"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.