Bony fish genomes: Status and gaps

Area of Science:

• Ichthyology
• Genomics
• Evolutionary Biology

Background:

• Bony fish (Osteichthyes) represent over 95% of fish species and are crucial for aquaculture and fisheries.
• Their adaptive radiation has led to immense taxonomic, morphological, and evolutionary diversity.
• Genomic resources, especially high-quality reference genomes, are vital for deep biological and evolutionary research.

Purpose of the Study:

• To review the current status of open-access bony fish genome assemblies.
• To identify existing gaps in genomic representation across bony fish phylogeny.
• To highlight the potential for future research and applications in aquaculture.

Main Methods:

• Literature review and database mining of publicly available bony fish genome assemblies.
• Phylogenetic analysis to assess coverage across recognized fish orders and families.
• Examination of Sequence Read Archive data for underrepresented groups.

Main Results:

• A significant increase in bony fish genome assemblies, with 1744 available, primarily in the last five years.
• Genomic data covers 67 of 72 recognized orders and 268 of 514 families, representing approximately 5% of all described species.
• Overrepresentation of genomes from orders like Cichliformes and Perciformes; gaps exist in five orders and 14 families, though sequencing data is often available.

Conclusions:

• While bony fish genomic resources have expanded, substantial gaps remain in phylogenetic coverage.
• Available high-throughput sequencing data offers opportunities to fill these gaps.
• Future sequencing and assembly advancements will enhance evolutionary insights and support sustainable aquaculture.