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.