Chapter 3: Fishomics: Genetics, Genomics, and Transcriptomics of Fishes
S. Elizabeth Alter
Since the first edition of Methods for Fish Biology was published in 1990, the field of fish genetics has been dramatically transformed by rapid advances in genomic sequencing and editing technologies. This tranformation has resulted in breakthroughs in our understanding of the evolution and ecology of fishes and a deeper knowledge of the relationship between the genome and phenome. Braasch et al. (2015) have characterized the ongoing revolution as a “genomic tsunami,” and others have referred to a data avalanche, firehose, or deluge; no matter the preferred metaphor, it is clear that we are now able to tackle questions in fish biology that would have been well out of reach in 1990. Over the last decade alone, improvements in massively parallel sequencing (MPS; also called high-throughput sequencing or next-generation sequencing) and other technologies have led to discoveries in teleost functional genomics, molecular evolution, systematics and phylogenetics, and genomic architecture. For example, using new methods in genomics, transcriptomics, and gene editing, fish biologists can interrogate genomes to determine the genetic basis of traits (e.g., McGaugh et al. 2014; Varshney et al. 2016); assess the effects of environmental stressors on genome-wide gene expression (Ao et al. 2015; Reid et al. 2016); retrieve information about entire fish communities from water samples (Hänfling et al. 2016; Port et al. 2016); study the effects of large-scale genomic architecture on fish evolution (Chalopin et al. 2015; Cortesi et al. 2015; Tørresen et al. 2018); improve understanding of species loss and effects of habitat alteration (e.g., ocean acidification; Taranger et al. 2015; Arthington et al. 2016; Ottinger et al. 2016); and much more. As fishes represent the most speciose group of vertebrates, fish genomes can yield incredible insights into the evolutionary history of vertebrate genomes (Posthlethwait et al. 2000; Jaillon et al. 2004; Kasahara et al. 2007; Chalopin et al. 2015). In addition, because up to 70% of genes involved in human disease have homologues in teleost fishes (Howe et al. 2013), fish genomes have proven highly valuable as models for human health and translational genetics. For example, advanced genomic knowledge in fishes such as the Zebrafish Danio rerio has been used to identify cancer genes (e.g., Ceol et al. 2011).