Divergent selection, recombination variability, and noncoding introgression drive speciation and adaptation in threadfin Eleutheronema.

The fourfinger threadfin is traditionally considered to be the most precious fisheries resource in China, reflecting its cultural significance and high nutritional value, yet its genomic features and evolutionary history remain poorly understood. Here we assemble the first Eleutheronema rhadinum chromosome-level genome ( ~ 591 Mb) and conduct a comparative genomics analysis by juxtaposing it with its sister species, E. tetradactylum. We reveal significant gene family expansions associated with innate immunity, olfaction, and opsin. Analysis of over 7000 olfactory receptors across Eleutheronema and 47 other fish lineages highlights the influence of habitat-specific evolutionary pressures on olfactory system diversification. Genome resequencing reveals widespread and heterogeneous highly differentiated regions between species, emphasizing the role of natural selection, particularly long-term linked selection, in shaping genomic divergence. Noncoding variations might play a crucial role in promoting genomic divergence during Eleutheronema speciation. Additionally, we observe introgression footprints broadly distributed across the genome with considerable heterogeneity, occurring in noncoding regions and significantly associated with variation in recombination rates. Our results demonstrate that variation in recombination rates influences both genomic differentiation and introgression, helping maintain species boundaries despite ongoing gene flow. In sum, we provide genomic resources and insights into the evolutionary adaptation and conservation of Eleutheronema.