Teleost fishes are the most diverse clade of living vertebrates, representing over half of extant vertebrate species and occupying nearly all aquatic environments. Their evolutionary success has been shaped by whole-genome duplication, rapid lineage diversification, and extensive ecological adaptation over more than 250 million years. Despite their importance, a lack of comprehensive, phylogenetically representative genome-wide comparative resources has long limited the understanding of teleost genome evolution and macroevolutionary history.

Resently, in a study published in The Innovation, the research group led by Prof. HE Shunping from the Institute of Hydrobiology (IHB) of Chinese Academy of Sciences, together with multiple collaborators, presents the largest and most comprehensive comparative genomic resource for teleost fishes to date, enabling systematic investigation of genome evolution, phylogeny, and diversification patterns.

As part of Phase I of the Fish10K Project, the researchers newly sequenced and assembled 110 teleost genomes, including representatives from three previously unsequenced orders. By integrating these data with publicly available genomes, the researchers constructed a whole-genome alignment of 464 teleost species covering all extant orders. This dataset represents one of the largest vertebrate genome alignments and provides an unprecedented foundation for comparative and evolutionary analyses.

Comparative analyses revealed a pronounced trend of genome compaction in teleost evolution, driven primarily by intron shortening while exon lengths remained largely conserved. Teleost genomes also exhibit a distinctive transposable element composition dominated by DNA transposons rather than Long Interspersed Nuclear elements (LINEs). Freshwater species show significantly higher transposon content than marine species, suggesting a potential role of transposable elements in habitat-driven adaptive evolution.

Single-base-resolution analyses identified thousands of teleost-specific highly conserved genomic elements, many of which are associated with genes involved in neural development, fin morphogenesis, and locomotion. Functional validation demonstrated that some of these elements act as cis-regulatory modules, highlighting regulatory innovation following whole-genome duplication as a key driver of teleost diversification.

Whole-genome phylogenomic analyses resolved several long-standing controversies in teleost relationships, providing strong evidence against the monophyly of the proposed “Siluriphysi” clade. Integrating genomic and fossil evidence, the study refined the timing of teleost origin to before the Permian–Triassic mass extinction and revealed a multi-phase diversification history shaped by global extinction events.

Overall, this study establishes a foundational genomic framework for teleost fishes, offering critical insights into vertebrate genome evolution, phenotypic innovation, and adaptive radiation. The Fish10K genomic compendium will serve as a valuable long-term resource for evolutionary biology, biodiversity research, and aquatic genomics.

Comparative analysis of 464 genomes reveals the evolutionary history of teleosts (Image by IHB)

(Editor: MA Yun)