We propose to develop a comparative transcriptomic database that will facilitate analysis of nucleotide sequence divergence and tissue-specific expression patterns of genes involved in adaptive and innate immune response across three species of cyprinid fishes. The study species are evolutionarily related to zebrafish and fathead minnow, which are both important models for study of evolution, development, immunology, and toxicology of teleost fishes. Specifically, we will generate an RNA-seq database for three cyprinid species that reflect phylogenetic breadth of the family in North America, but that inhabit identical dryland river habitats where they are exposed to a similar pathogens and thermal and oxygen stress. Additional linkages of immune response, pathogen loads, and stress response will be facilitated by comparison of these particular species because they have been shown to vary in response to physiological stress imposed by these harsh physiological conditions. Our project will examine tissue-specific expression patterns (skin, gut, gill, and lymphoid [kidney & spleen combined]) among organs that mount different kinds of immunological response to pathogens. Using this comparative transcriptomic dataset, we will test hypotheses related to divergence of nucleotide sequences and abundances of host transcripts, and transcripts of commensal and pathogenic organisms across species and tissues type using a phylogenomics approach. Our project relies heavily on CETI-sponsored infrastructure and expertise, directly addresses the CETI theme and the interests of its faculty, and will facilitate development of collaborative proposals that link immunology, ecology, and conservation biology of aquatic organisms in harsh aquatic environments.