Evolution and dynamics of germline sex chromosome regulation in D. miranda

Although sex chromosomes have evolved from autosomes, they often have unusual regulatory regimes that are sex- and cell-type-specific such as dosage compensation (DC) and meiotic sex chromosome inactivation (MSCI). The molecular mechanisms and evolutionary forces driving these unique transcriptional programs are critical for genome evolution but have been, in the case of MSCI in Drosophila, subject to continuous debate. Here, we take advantage of the younger sex chromosomes in D. miranda (XR and the neo-X) to infer how former autosomes acquire sex-chromosome specific regulatory programs using single-cell and bulk RNA sequencing and ribosome profiling, in a comparative evolutionary context. We show that contrary to mammals and worms, the X’s are downregulated through germline progression most consistent with a loss of DC instead of MSCI, resulting in half gene dosage at the end of meiosis for all three X’s. Moreover, lowly expressed germline and meiotic genes on the neo-X are ancestrally..., , , # **Evolution and dynamics of germline sex chromosome regulation in D. miranda**

Although sex chromosomes have evolved from autosomes, they often have unusual regulatory regimes that are sex- and cell-type-specific such as dosage compensation (DC) and meiotic sex chromosome inactivation (MSCI). The molecular mechanisms and evolutionary forces driving these unique transcriptional programs are critical for genome evolution but have been, in the case of MSCI in Drosophila, subject to continuous debate. Here, we take advantage of the younger sex chromosomes in D. miranda (XR and the neo-X) to infer how former autosomes acquire sex-chromosome specific regulatory programs using single-cell and bulk RNA sequencing and ribosome profiling, in a comparative evolutionary context.

## Description of the data and file structure

scRNAseq:
miranda.testes.alevin.tar.gz: Alevin mapping of scRNA-seq data.
aggregate_countsxcelltype.txt: Aggregated read counts for genes (row) in each cell type (column).
...