code repo for the manuscript:

Gene transcriptional profiles in gonads of Bacillus taxa (Phasmida) with different cytological mechanisms of automictic parthenogenesis.

This repository contains the code used to study the molecular groundplan of automixis in Bacillus stick insects.

Experiment reads have been deposited under the NCBI BioProject PRJNA578804.

The manuscript is available here.

The scripts names are largely self-explanatory and the repo is organized in four folders:

• scripts_snakefiles

  • snakefile_orthology_inference
  • snakefile_transcriptome_annotation
  • snakefile_transcriptome_filter_aa
  • snakefile_transcriptome_goterms

• scripts_shell

  • assign_GOterms_to_orthogroups.sh
  • differential_expression.sh
  • gblocks.sh
  • msa_align.sh
  • omega_pos_sel_formatting.sh
  • orthogroups-differential-expression.sh
  • orthologs_assignment_exp_matrixes.sh
  • pep_2_cds_orthologs.sh
  • phylostratigraphy_BAT.sh
  • phylostratigraphy_BGM.sh
  • phylostratigraphy_BRO.sh
  • reformat_orthogroups.sh
  • taxonomy_assignement.sh

• scripts_R

  • gene_enrichment.R
  • normalized_counts_PCA.R
  • phylostratigraphy_and_sankyeys.R
  • phylostratigraphy_z-test.R

• intermediate_files

  • folder containing intermediate files necessary for paper figures, generated using the scripts in scripts_R.

NB: several abbreviations are used, including:

• BAT for Bacillus atticus
• BRO for Bacillus rossius
• BGM for Bacillus grandii
• BP for Biological Processes
• MF for Molecular Functions