# Telomere-to-Telomere Genome Assembly of Two Hemiculter Species Provide Insights into the Genomic and Morphometric Bases of Adaptation to Flow Velocity

## TL;DR

This study uses high-quality genome assemblies to explore how two fish species adapted to different water flow conditions through genetic and morphological changes.

## Contribution

The paper provides chromosome-level T2T genomes and identifies genetic mechanisms underlying adaptation to flow velocity in two Hemiculter species.

## Key findings

- H. bleekeri evolved a streamlined body and pelagic eggs, supported by expansions in body shape-related genes.
- H. leucisculus uses adhesive eggs, linked to expansions in adhesion-related gene families.
- High-quality T2T genomes enable insights into adaptive strategies in response to hydrodynamic environments.

## Abstract

Flow velocity is a key environmental factor that exerts multifaceted effects on fish growth and adaptation. Through long-term natural selection, fish have evolved adaptability to specific flow conditions, which not only relate to oxygen supply and food acquisition but also play a decisive role in reproduction, development, and population maintenance. To investigate the genomic mechanisms through which hydrodynamic environments drive divergence in closely related species, we focused on two sister species, Hemiculter bleekeri and Hemiculter leucisculus, which are adapted to contrasting flow regimes. We generated high-quality, chromosome level telomere-to-telomere (T2T) genomes and integrated comparative genomic analyses, we investigated the genetic basis underlying body shape regulation and reproductive strategies, aiming to decipher the adaptive evolutionary patterns of these species in response to differing hydrodynamic conditions from an integrated genotype phenotype perspective. We integrated PacBio HiFi, Hi-C, and Oxford Nanopore Technologies (ONT) ultra-long read sequencing data to construct high-quality T2T reference genomes for both species. The final genome assemblies are 0.998 Gb for H. bleekeri and 1.05 Gb for H. leucisculus, with each species possessing 24 chromosomes and all chromosomal sequences assembled into single contigs. Contig N50 values reached 40.45 Mb and 40.66 Mb, respectively, and both assemblies are gap-free. BUSCO assessments yielded completeness scores of 99.34% for both genomes, confirming their high continuity and accuracy. Integrated morphometric and genomic analyses revealed distinct adaptive strategies in two Hemiculter Species. H. bleekeri has evolved a streamlined body, underpinned by expansions in body shape related genes, and a pelagic egg strategy. In contrast, the adhesive egg strategy of H. leucisculus is supported by expansions in adhesion-related gene families. This divergence reflects adaptation to distinct flow velocity. By combining high-quality chromosome-level T2T genomes with morphometric and comparative genomic approaches, this study establishes a comprehensive framework for understanding the molecular mechanisms underlying adaptive evolution in freshwater fishes inhabiting contrasting flow velocity.