The folder contains the following datasets (fasta files, and text files): 

Dataset S1: Genome assemblies: P. cognata male high quality final genome assembly, P. cognata genome assembly before scaffolding with Hi-C data.

Dataset S2: Transcriptome assembly and transcripts genomic location: P. cognata final transcriptome assembly, transcript location on the first 25 
super-scaffolds, transcript location on all scaffolds.

Dataset S3: Identification of X-linked scaffolds: male and female coverage for P. cognata for all scaffolds in windows of 10000 bp (Male.soapfinal, 
Female.soapfinal), median coverage per scaffold and X vs Autosomal assignments for all scaffolds (assign_cov.txt) and median coverage per scaffold and X 
vs Autosomal assignments for the 25 super-scaffolds (data25_cov.txt).

Dataset S4 : Gene expression and dosage compensation: .txt files containing Non-normalised and normalised gene expression datasets for tissue-specific 
gene expression and sex-biased gene expression analyses, as well as for dosage compensation analysis in all tissues, for expression analysis of POF gene. 
.txt files containing differentially expressed genes between males and females for sex-biased gene expression analysis.

Dataset S5: GC content and nucleotide diversity: txt file containing GC content for windows of 10000 bp; txt file containing pi diversity for windows of 
28000 bp and males and females.

Dataset S6: Repeat content: txt file with the location and classification of repeats across the genome, a fasta file of the masked genome, and the 
consensus repeat library used for masking.

Dataset S7: Homology: Files for the “Homology of the P. cognata and C. homonivorax X chromosomes'' analysis, including the set of Panorpa protein file 
generated (Panorpa_prots.fa), the set of orthologs (Panorpa_Chominivorax_1to1.txt and Panorpa_Dmel_1to1 1.txt) and the gene names with their location in 
the dipteran species (gene_names_true, cds_loc.txt, and Dmel_longestCDS_chromosome.joinable). For the “Conservation of X-linked gene content between P. 
cognata and other insects” analyses: set of orthologs in each of the other species (CDS_vs_genome.sortedbyDB.nonredundant). For the analysis with B. 
germanica, txt files containing our coverage results for different individuals. 

Dataset S8: Genespace input (gff and peptides): .fa and .gff files for the genome synteny analysis.

Table S2: List of genomic samples generated, and the parts of the analysis they were used for. 

Please note that the pipelines used to generate these files can be found here: https://github.com/ClemLasne/PanorpaX.