Evolution of ray-finned fish genomes: Status and directions with a primer on microRNA characterization

The rich biological and genetic diversity of ray-finned fishes (Actinopterygii) coupled with an increasing availability of genomic resources and tools makes this group of animals an attractive system for evolutionary studies of the genome. This chapter introduces recent advances and approaches relevant to such investigations, along with the current status and directions in the field. We outline the importance of whole genome duplication events and the subsequent rediploidization of the genome, the role played by transposable elements in fish evolution, and also introduce phylogenomics. We overview the main functional and regulatory elements encoded within fish genomes of interest in an evolutionary context and outline a step-by-step approach for the phylogenetic characterization of fish microRNAs, small molecules that regulate gene expression at the posttranscriptional level. This chapter introduces key themes in fish genome evolution and points the reader to both classic papers and recent cutting-edge studies for further exploration of this field.