From genomes to functions in aquatic biology

In this paper we evaluate factors which should, in our opinion, be taken into account when genomic studies in aquatic organisms are extended to functions. Our first point is that genome-wide gene duplications characteristic of teleosts have enabled more rapid evolution in fish generally than usually in tetrapods. We further discuss factors that are pertinent when gene ontologies are used in animals with little earlier work combining genomic and functional data. We then review issues relating to transcription, especially transcription factor function and gene regulatory pathways. As the most important single factor affecting gene expression is translation, we emphasize the need to relate mRNA and protein level findings whenever functional inferences are made. We finish with considering the possible roles of functional genomics studies in aquatic environmental research. We have concentrated especially on fish, although many of the points made are common to all eukaryotes.