Improved genome assembly of whale shark, the world's biggest fish: revealing intragenomic heterogeneity in molecular...

High-quality chromosome-level assemblies are essential for understanding genome evolution but remain difficult to obtain for complex genomes such as those of vertebrates. The whale shark (Rhincodon typus) is an endangered species whose ecology and evolutionary history remain poorly understood. Although genomic resources have been developed for this species, available assemblies have left key uncertainties in the chromosome structure.

We generated a near gap-free genome assembly of the whale shark using long-read sequencing and Hi-C scaffolding, markedly improving contiguity and completeness. In particular, the X chromosome was extended to nearly twice its previous length, and putative pseudoautosomal regions were identified. Moreover, we report the first Y-linked scaffolds for this species. Comparative analyses with the zebra shark revealed exceptionally low substitution rates across the genome. We further detected a negative correlation between chromosome length and synonymous substitution rate (dS), explained by a positional gradient, here referred to as "chromocline," in which substitution rates gradually decrease from chromosomal ends toward central regions. Notably, the X chromosome exhibited lower dS compared with autosomes of similar size, consistent with male-driven evolution.

This improved whale shark genome assembly overcomes major limitations of previous resources and enables refined analyses of sex chromosomes and genome-wide evolutionary dynamics. The enhanced sex chromosome resources provide a foundation for deeper investigations of reproductive biology in this species. Increased contiguity also reveals pronounced intragenomic heterogeneity in molecular evolutionary rates, indicating that positional effects and sex chromosome differences are key determinants of synonymous divergence. This resource will facilitate population genetic and conservation genomic studies in the whale shark.