Bony fish genomes: Status and gaps

Abstract

Bony fish constitute an exceptionally species-rich group of aquatic vertebrates, comprising more than 95% of all living fish. The adaptive processes on the diversity of environments they inhabit make them a highly diverse group from taxonomic, morphologic, and evolutionary standpoints. Furthermore, among their members we find species of high economic value for global aquaculture and fisheries. This has attracted the attention of multiple research fields, from ecology or evolutionary biology to comparative genomics. However, deep biological or evolutionary studies require suitable genomic resources, particularly high-quality reference genomes, across multiple species and taxonomic groups. Here, we revise the current status of open access bony fish genome assemblies, with special emphasis on existing gaps throughout their phylogeny. Recently, there has been a boom of information and up to 1,744 genomes are available, largely released in the last five years. They are distributed across 67 of the 72 recognized orders, where Cichliformes, Perciformes, Siluriformes, Cypriniformes and Cyprinodontiformes appear overrepresented, and across 268 families out of the 514 recognized. Overall, these figures cover around 5% of all described bony fish species. Despite five orders and 14 order-level incertae sedis families (mostly percomorphs) lacking genomic representation, high-throughput sequencing data for most gaps are available in the NCBI SRA repository. Future sequencing efforts aimed at improving assembly quality and filling the gaps in the fish phylogeny, in parallel to the evolution of sequencing and assembly technologies, will enhance our ability to answer open evolutionary questions in bony fish and provide genomic tools to boost fish production.