Chromosome‐Level Genome Assemblies of Two Softshell Turtles with ZZ/ZW Provide Insights into TE‐Driven Recombination Suppression in Sex Chromosomes

In this study, we present chromosome‐level genome assemblies for two softshell turtles, the spiny softshell ( Apalone spinifera ) and the wattle‑necked softshell ( Palea steindachneri ), and use population level resequencing to characterize their ZW sex chromosomes. Our results indicate that W‑chromosome degeneration in these species is associated primarily with a dramatic accumulation of transposable elements (TEs)—not with stepwise strata formation as seen in many birds and mammals—and that TE proliferation likely contributed to recombination suppression between Z and W. Specifically, the pseudoautosomal regions span 0–3.17 Mb in A. spinifera and 36.74–39.62 Mb in P. steindachneri , reflecting conserved synteny; protein‐coding W‐linked genes show a mean d N / d S ≈ 0.52, consistent with ongoing purifying selection; and TEs occupy 73.7%–83.3% of the W sequence, with LTRs (≈22.7%–23.3%) and LINEs (≈27.9%–34.7%) markedly enriched relative to the Z chromosome and autosomes. Molecular dating of LTR insertions places most activity within the past ∼40 million years, after species divergence and temporally consistent with the inferred onset of recombination suppression. Together, these findings support a model in which large‐scale TE accumulation drove rapid W‑chromosome differentiation in softshell turtles, offering a complementary pathway to strata‐based sex‑chromosome evolution and underscoring the potent role of mobile elements in shaping vertebrate sex chromosomes.