Genomic approaches have been greatly lacking in Antarctic species despite their tremendous potential for groundbreaking biological discovery. The research will characterize HOX clusters from two disparate lineages of notothenioid fishes, organisms whose evolutionary history and myriad anatomical and physiological adaptations provide a unique opportunity to study the genetics of adaptation to extreme environments. Hox gene complexes are known to be intimately involved in axial patterning and formation of structures that could have contributed, in part, to adaptive evolution of Antarctic fishes. Numerous metazoan HOX cluster datasets are readily available for comparison, and bacterial artificial chromosome (BAC) libraries have already been generated for the species to be examined: a nototheniid (Notothenia coriiceps, yellowbelly rockcod) and a channichthyid (Chaenocephalus aceratus, Scotia Sea "gapehead" icefish).
The resulting datasets will prove extremely useful for delineating those sequences having a role in adaptive evolution to the extreme environment. The data will allow identification of bona fide cis-regulatory (enhancer) sequences. In addition, we will carry out experiments to delineate presumptive tissue-specific enhancer elements within the HOX clusters that are involved in regulating hematopoietic lineage specification. The rationale behind these experiments hinges on the fact that the erythroid program in one of these fishes (icefish) has been completely abrogated. Thus, the comparative genomics approach should uncover those sequences that have been lost in the icefish lineage but retained in other lineages. The comparative experiments will be conducted in the zebrafish where a robust system for studying early lineage specification of blood progenitors has been developed.
The broader impacts of this work include generation of large, publicly available genomic datasets that will be accessible to evolutionary biologists, developmental biologists, and physiologists. Our previous HOX datasets from various primitive vertebrates (shark, bichir, pufferfish, zebrafish, coelacanth) have been used/analyzed repeatedly by the scientific community. The results will also have implications for an important biological phenomenon, the development of blood. Finally, the project will provide ample opportunities for graduate and undergraduate participation and training, and programs are already in place at the Benaroya Research Institute for research training of minority undergraduate students.
