Transposable Elements and Sex Chromosome Evolution in Eulimnadia texana

Sex chromosomes often evolve through suppressed recombination and accumulation of transposable elements (TEs) on the sex-limited chromosome, leading to divergence and eventual degeneration. The clam shrimp Eulimnadia texana possesses proto-sex chromosomes (Z and W) at an early evolutionary stage, providing a unique opportunity to examine the initial genomic changes underlying sex chromosome differentiation. Additionally, both sex chromosomes are expressed in homogametic ZZ and WW shrimp, allowing a regular expression of both sex chromosomes in homozygotes.

We analyzed newly assembled ZZ (male) and previously published WW (hermaphrodite) genomes of E. texana. Sex-linked markers were mapped to identify the Z chromosome. TEs were annotated using a species-specific repeat library and RepeatMasker. The Z and W chromosomes were divided into bins and randomization tests compared TE accumulation between the sex chromosomes as well as between corresponding regions within these two chromosomes; the latter was focused on the putative sex-determining regions of both the Z and W. Kimura distance-based analyses were used to estimate TE age divergence.

The Z chromosome showed no significant TE enrichment relative to autosomes but was enriched for DNA transposons. The W chromosome exhibited significantly higher retrotransposon (LTR and LINE) accumulation. Only the sex-determining region of the W showed significantly elevated retrotransposon content compared to the Z. TE age landscapes indicated recent bursts of retrotransposon activity on the W.

These findings support theoretical predictions that retrotransposons accumulate in non-recombining regions, while DNA transposons are associated with recombining chromosomes. The W chromosome of E. texana shows early signs of differentiation, with localized retrotransposon buildup, while the Z remains autosome-like. This study highlights E. texana as a valuable model for understanding the genomic mechanisms of early sex chromosome evolution.