Teleost fishes are the most diverse clade of living vertebrates. Their evolutionary success has been shaped by whole-genome duplication, rapid lineage diversification, and extensive ecological adaptation over more than 250 million years. However, the understanding of teleost genome evolution and macroevolutionary history has been limited by a lack of comprehensive, phylogenetically representative genome-wide comparative resources.

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

The researchers sequenced and assembled 110 teleost genomes including representatives from three previously unsequenced orders, as part of Phase I of the Fish10K Project. By integrating these data with publicly available genomes, they 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 a 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 exhibited a distinctive transposable element composition dominated by DNA transposons rather than Long Interspersed Nuclear elements. Freshwater species showed significantly higher transposon content than marine species, suggesting the 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 were associated with genes involved in neural development, fin morphogenesis, and locomotion. Functional validation demonstrated that some of these elements acted as cis-regulatory modules, highlighting regulatory innovation following whole-genome duplication as a key driver of teleost diversification.

Whole-genome phylogenomic analyses resolve several long-standing controversies in teleost relationships, providing strong evidence against the monophyly of the proposed “Siluriphysi” clade. This study, integrating genomic and fossil evidence, refines the evolutionary timeline of teleosts to before the Permian-Triassic extinction, and reveals a multi-phase diversification history shaped by global extinction events.

This study offers 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.