Data and code supporting the publication 'Emergence and stabilisation of a neo-Y chromosome in nematode species with rare males'

The data tables mostly concern the four focal Mesorhabditis nematode species studied in the paper and referred to by their strain codes: JU2817 is M. belari, JU2855 is M. monhystera, DF5017 is M. longespiculosa and AF72 is M. spiculigera. Code: sex_chrom_evo_repo_git_archive.tar.gz Data: annotation_files.tar.gz: The GFF3 files in `genome_annotation_files` contain the gene predictions for the four focal Mesorhabditis species of the study. `all_gene_assignments_with_male_female_counts_and_functional_annotations.tsv.gz`: table containing each gene, its assignment (autosome, X, Y), its location on the assembled genome, its male and female normalised DNA-Seq counts (columns 'female_est_counts_normalised' and 'male_est_counts_normalised') and RNA-Seq counts (columns starting with 'RNA'), eggNOG-based annotations for the gene (columns 'Description', 'Preferred_name', 'PFAMs', the latter being PFAM domains found if any) and C. elegans orthologs if any (notably 'celegans_wormbase' can be searched in [WormBase](https://wormbase.org)) `all_Y_genes_with_male_female_counts_and_functional_annotations.tsv.gz` the same information as above but for Y-assigned genes `hhblits_annotations_genes_in_families_specific_to_Y_chromosomes.tsv`: table containing domain-level annotations for genes in families occurring specifically on Y chromosomes, obtained using hh-suite. orthology_files.tar.gz: `orthofinder_phylogenetic_orthogroups_n0_mesorhabditis_plus_celegans.tsv.gz`: table containing orthogroups (HOGs; =gene families) for the four focal Mesorhabditis species plus C. elegans `meso_orthogroups_with_all_nonfocal_genes_min_count_10.tsv.gz`: table containing HOGs with the assignment of member genes (autosome, X, Y), with a focus on specific assignments ('focal_genes' column) and strains and whether the other genes are also in the same assignment class or not. This allows finding all gene families that are specific of the Y chromosome, notably. Y_gene_families_of_interest.tar.gz: `hen_1_like_family_all_proteins.msa`: Multiple-Sequence Alignment (MSA) of all *hen-1*-like genes - present on the Y chromosomes of both M. belari and M. monhystera `tra_1_like_family_all_proteins.msa`: MSA of all *tra-1*-like genes - present on the Y chromosomes of both M. belari and M. monhystera The other MSAs are for gene families with terms of interest, that occur only in one of M. belari or M. monhystera all_busco_hits_with_nigon_assignments.tsv.gz: table containing the BUSCO genes (from nematoda_odb10) found in the four focal Mesorhabditis species of the study and their corresponding Nigon assignment. computationally_assigned_chroms_after_manual_inspection.tsv.gz: table containing the assignment (autosome, X, Y, unclear) of each assembled scaffold for each of the four focal Mesorhabditis species of the study. The median normalised female and male DNA-Seq coverages are provided, the relative frequency of autosomal, X, Y and unclear-assigned component genes is also provided, and assignment based on the coverages, the gene assignments, and manual inspection (in cases of disagreements or ambiguity) are provided. The latter was the final classification used in the paper. X_autosome_counters.tar.gz: `X_autosome_counters_hits_with_scaffold_and_nigon_assignments.tsv.gz`: Hits of known X:autosome ratio counting genes from C. elegans to the genomes of the four focal Mesorhabditis species, with the hit scaffold's assignment (last column) orthology_CDS: one alignment file (.msa) and one table of dN distances (.csv) each for the X:autosome ratio counting genes fox-1, sex-1 and sea-2 X_and_Y_enriched_satellites.tsv.gz: satellites detected using our two approaches (kseek and trf), with the strain it was identified in, which type of chromosome it was identified in (column `scaffold_type`; X or Y), the fraction of occurrences of the satellite in this chromosome type compared to the rest of the genome (column `frac_occs_in_target_genome`) and the fraction of all bases of the chromosome type covered by occurrences of the satellite (column `fraction_of_target_genome_occupied_by_feature`). Contact: brice.letcher[at]ens-lyon.fr; marie.delattre[at]ens-lyon.fr