Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes

Dataset used to reproduce the analysis performed in "Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes" publication. The directory structure is the following:

• Gene_models - directory containing gene models (.gtf or .gff3 files) used for feature length comparisons across species
• intermediate_data - directory containing intermediate results from various scripts, the main purpose is to speed up the reproducibility of some longer running scripts
  • batch_adjusted_normalised_gene_expression_matrix.tsv - gene expression matrix used for evolutionary model fitting
  • fc.tsv - fold change matrix used for evolutionary model fitting
  • dated_species_tree.tre - species tree used throughout the model fitting step (newick format)
  • DGE_script_enviorment.RData - saved R environment from differential gene expression analysis
  • downregulated_IDs.RDS - gene IDs which undergo down-regulation throughout maternal-to-zygotic transition
  • maternal_IDs.RDS - gene IDs which meet the cut-off criteria for being considered as maternally expressed
  • N0_blasted.tsv - orthogroup annotations through blasting to a sequence database
  • N0.tsv - orthogroups inferred from OrthoFinder
  • OG_categories.tsv - classification of orthogroups based on them (I) having genes with maternal expression, but no significant down regulation, (II) having genes with maternal expression and significant down regulation throughout maternal-to-zygotic transition or (III) no maternal expression
  • OG_presence.tsv - binary matrix coding for which orthogroup which species have gene expression values
  • Paralog_variances.tsv - matrix containing variance metrics for paralogs in each species from before normalization across species
• Pannzer2_annotation - directory containing GO annotations for all species from the Pannzer2 tool, used for GO analyses
• quantification_files - directory containing all salmon quantification outputs
• transcriptomes - de novo assembled transcriptomes for non-model species