Delineating the W sex chromosome in the clam shrimp, Eulimnadia texana.

Introduction: Sex chromosomes have evolved independently across various lineages, often showing convergent degradation of the sex-limited chromosome. While extensively studied in model organisms with ancient sex chromosomal systems, the evolution of early-stage sex chromosomes remains poorly understood. Eulimnadia texana, a freshwater crustacean with a unique androdioecious breeding system (ZZ, ZW, and viable WW genotypes), provides a rare opportunity to study early sex chromosome evolution. This study examines E. texana's W chromosome for evidence of a small localized non-recombining region, characterized by a transposable element (TE) "hotspot", low gene density, and low GC content.

Methods: Sex-linked markers were mapped onto the W chromosome (Scaffold 1). TEs in the WW genome were identified using RepeatModeler and RepeatMasker. Statistical analyses compared TE distribution between the genome and Scaffold 1, which was then divided into 20 equal-sized "bins" for finer-scale statistical analyses. Gene density and GC content were analyzed across these bins.

Results: While no significant TE accumulation was found across the entire W chromosome compared to the remaining genome, a specific region (6.6-8.8 Mb, fourth bin) showed significantly higher TE accumulation. This region also exhibited low gene density and low GC content, indicative of reduced recombination.

Conclusion: Our findings suggest that E. texana's W chromosome contains a smaller region of crossover suppression, supporting the hypothesis that it is in a proto-sex chromosome in early evolutionary development. This study provides valuable insights into early sex chromosome evolution and establishes E. texana as an ideal model for further investigation of evolutionary processes driving proto-sex chromosome differentiation.