DOI: 10.6078/d1dh7t
title: Data from: Evolution and dynamics of germline sex chromosome regulation in D. miranda

description: 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 lowly expressed,
 instead of suppression after sex linkage. For the young neo-X, DC is
 incomplete across all tissue and cell types and this dosage imbalance is
 rescued by contributions from Y-linked gametologs which produce
 transcripts that are translated to compensate both gene and protein
 dosage. We find an excess of previously autosomal testis genes becoming
 Y-specific, showing that the neo-Y and its masculinization likely resolve
 sexual antagonism. Multicopy neo-sex genes are predominantly expressed
 during meiotic stages of spermatogenesis, consistent with their
 amplification being driven to interfere with Mendelian segregation.
 Altogether, this study reveals germline regulation of evolving sex
 chromosomes and elucidates the consequences these unique regulatory
 mechanisms have on the evolution sex chromosome architecture.
description: # **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). MSL
 ChIP-seq: mir_MSE_peaks.narrowPeak: Output of MACS2 peak calling.
 mir_MSE_summits.bed: Output of MACS2 peak calling. Bulk tissue RNA-seq and
 ribo-seq: Dmir.STARpri.CDS.fc: Read counts from D. miranda tissue
 dissection. (Mapped by STAR and annotated with featurecounts)
 Dpse.STARpri.CDS.fc: Read counts from D. pseudoobscura tissue dissection.
 (Mapped by STAR and annotated with featurecounts) Dmir.ribo.Starpri.fc:
 Read counts from D. miranda ribosome profiling. (Mapped by STAR and
 annotated with featurecounts) Sequence homology: RB.pse2mir.RBH.new.txt:
 Reciprocal best hit calls between D.pseudoobscura and D.miranda
 transcripts. RB.pse2mir.RBH.noC.new.txt: Reciprocal best hit calls between
 D.pseudoobscura and D.miranda transcripts, but with neo-X linked genes
 removed in D. miranda. RB.pse2mir.RBH.noY.new.txt: Reciprocal best hit
 calls between D.pseudoobscura and D.miranda transcripts, but with neo-Y
 linked genes removed in D. miranda. usearch.clust.summary: results of
 homology based clustering to identify multicopy genes in D.miranda. ##
 Sharing/Access information Raw data for scRNA-seq can be found on the
 Sequenced Read Archive under BioProject: PRJNA907067 ## Code/Software n/a