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Simple Summary  Digital transcriptomics is rapidly emerging as a powerful new technology for modelling the environmental dynamics of the adaptive landscape in diverse lineages. This is particularly valuable in taxa such as turtles and tortoises (order Testudines) which contain a large fraction of endangered species at risk due to anthropogenic impacts on the environment, including pollution, overharvest, habitat degradation, and climate change. Sea turtles (family Cheloniidae) in particular invite a genomics-enabled approach to investigating their remarkable portfolio of adaptive evolution. Our de novo transcriptome assemblies and measurements of tissue- and temperature- specific global gene expression in the loggerhead sea turtle ( Caretta caretta ) reveal the genomic basis for potential resiliency in this endangered flagship species, and are crucial to future management and conservation strategies with attention to changing climates. We summarize the interactions among differentially expressed genes by producing network visualizations, and highlight the shared biological pathways related to development, migration, immunity, and longevity reported in the avian and reptilian literature. Our original results for loggerhead sea turtles provide a large, new comparative genomic resource for the investigation of genotype–phenotype relationships in amniotes.    Abstract   Background : Digital transcriptomics is rapidly emerging as a powerful new technology for modelling the environmental dynamics of the adaptive landscape in diverse lineages. This is particularly valuable in taxa such as turtles and tortoises (order Testudines) which contain a large fraction of endangered species at risk due to anthropogenic impacts on the environment, including pollution, overharvest, habitat degradation, and climate change. Sea turtles (family Cheloniidae) in particular invite a genomics-enabled approach to investigating their remarkable portfolio of adaptive evolution. The sex of the endangered loggerhead sea turtle ( Caretta caretta ) is subject to temperature-dependent sex determination (TSD), a mechanism by which exposure to temperatures during embryonic development irreversibly determines sex. Higher temperatures produce mainly female turtles and lower temperatures produce mainly male turtles. Incubation temperature can have long term effects on the immunity, migratory ability, and ultimately longevity of hatchlings. We perform RNA-seq differential expression analysis to investigate tissue- and temperature-specific gene expression within brain ( n  = 7) and gonadal ( n  = 4) tissue of male and female loggerhead hatchlings.  Results : We assemble tissue- and temperature-specific transcriptomes and identify differentially expressed genes relevant to sexual development and life history traits of broad adaptive interest to turtles and other amniotic species. We summarize interactions among differentially expressed genes by producing network visualizations, and highlight shared biological pathways related to migration, immunity, and longevity reported in the avian and reptile literature.  Conclusions : The measurement of tissue- and temperature-specific global gene expression of an endangered, flagship species such as the loggerhead sea turtle ( Caretta caretta ) reveals the genomic basis for potential resiliency and is crucial to future management and conservation strategies with attention to changing climates. Brain and gonadal tissue collected from experimentally reared loggerhead male and female hatchlings comprise an exceedingly rare dataset that permits the identification of genes enriched in functions related to sexual development, immunity, longevity, and migratory behavior and will serve as a large, new genomic resource for the investigation of genotype–phenotype relationships in amniotes.

Tissue and Temperature-Specific RNA-Seq Analysis Reveals Genomic Versatility and Adaptive Potential in Wild Sea Turtle Hatchlings (Caretta caretta)