Timema_Sex_Biased_Gene_Exp

This is the repository for the collected scripts used in the study:

Parker, D. J., Bast, J., Jalvingh, K., Dumas, Z., Robinson-Rechavi, M., Schwander, T. (2019). Sex-biased gene expression is repeatedly masculinized in asexual females. Nature Communications. 10: 4638.

The version of scripts used in the paper are archived at http://dx.doi.org/10.5281/zenodo.3451445

Components

DATA

• Contains read counts, GO terms, and dN/dS estimates for input to the scripts below.

SCRIPTS

Differential expression analyses

Main analyses using orthologs between sexual and asexual sister species

• Get Sex-biased genes:

  • Sex_bias_edgeR.R

• Get Sex-limited genes:

  • Sex_bias_edgeR_Sex_limited_expression.R

• bring expression data together:

mkdir Output/DE_joined	
for sp in Tbi Tce Tcm Tpa Tps; do
	for tiss in WB RT LG; do
	
	python3 sex_bias_asex_edgeR_tidier.py \
		-i Output/DE -s \
		"TTT_lrt_"$sp"_sex_bias_"$tiss".csv" -a sex_asex -o "Output/DE_joined/"$sp"_"$tiss"_RBBH_disp_allsepar" \
		 -x $sp"_"$tiss"_F_FPKM_RBBH_1.csv"
	done
done

• plot

  • Sex_bias_plotsetc.R

• Test for a relationship between the shift in sex-biased gene expression in asexual females and sexual-asexual divergence time

  • divergence_and_change_in_SB.R

Using female virgin whole-body samples to independently verify sex-biased genes

• Use virgin female whole-body samples to call sex-biased genes

  • Sex_bias_edgeR_withVIfemales.R

  • bring expression data together:

   mkdir Output/DE_joined_Virgin	
   for sp in Tbi Tce Tcm Tpa Tps; do
   	for tiss in WB; do
  
   	python3 sex_bias_asex_edgeR_tidier.py \
   		-i Output/DE_Virgin -s \
   		"TTT_lrt_"$sp"_sex_bias_"$tiss"_Vi.csv" -a sex_asex -o "Output/DE_joined_Virgin/"$sp"_"$tiss"_RBBH_disp_allsepar_Vi" 
   	done
   done
  

  • Plot it out
    • Sex_bias_plotsetc_withSB_from_Vi_and_Md_females.R

Analyses using orthologs between all sexual and asexual species

• Get Sex-biased genes

  • Sex_bias_edgeR_10sp_orths.R

• bring expression data together

mkdir Output/DE_joined_10sp
python3 sex_bias_asex_edgeR_tidier.py -i Output/DE_10sp/ -s \
    TTT_lrt_Tbi_sex_bias_WB.csv,TTT_lrt_Tce_sex_bias_WB.csv,TTT_lrt_Tcm_sex_bias_WB.csv,TTT_lrt_Tpa_sex_bias_WB.csv,TTT_lrt_Tps_sex_bias_WB.csv \
	-a sex_asex -o Output/DE_joined_10sp/ALL_WB_10sp_disp_allsepar_wCPM -c cpm_df_WB_10sp_ALL.csv

python3 sex_bias_asex_edgeR_tidier.py -i Output/DE_10sp/ -s \
    TTT_lrt_Tbi_sex_bias_RT.csv,TTT_lrt_Tce_sex_bias_RT.csv,TTT_lrt_Tcm_sex_bias_RT.csv,TTT_lrt_Tpa_sex_bias_RT.csv,TTT_lrt_Tps_sex_bias_RT.csv \
	-a sex_asex -o Output/DE_joined_10sp/ALL_RT_10sp_disp_allsepar_wCPM -c cpm_df_RT_10sp_ALL.csv

python3 sex_bias_asex_edgeR_tidier.py -i Output/DE_10sp/ -s \
    TTT_lrt_Tbi_sex_bias_LG.csv,TTT_lrt_Tce_sex_bias_LG.csv,TTT_lrt_Tcm_sex_bias_LG.csv,TTT_lrt_Tpa_sex_bias_LG.csv,TTT_lrt_Tps_sex_bias_LG.csv \
	-a sex_asex -o Output/DE_joined_10sp/ALL_LG_10sp_disp_allsepar_wCPM -c cpm_df_LG_10sp_ALL.csv

• plot:
  • Sex_bias_plotsetc_10sp_orths.R
  • N_SB_genes_10sp.R

Adding virgin females

• get SB genes, cluster virgin and mated samples

  • sex_bias_edgeR_10sp_withVIfemales.R
  • bring expression data together:

   mkdir Output/DE_10sp_joined_Virgin	
   for sp in Tbi Tce Tcm Tpa Tps; do
   	for tiss in WB; do
  
   	python3 sex_bias_asex_edgeR_tidier.py \
   		-i Output/DE_10sp_Virgin -s \
   		"TTT_lrt_"$sp"_sex_bias_"$tiss".csv" -a sex_asex -o "Output/DE_10sp_joined_Virgin/"$sp"_"$tiss"_10sp_disp_allsepar"
   	done
   done
  

  • plot
    • Sex_bias_edgeR_10sp_orths_virgin_mated_asexual_heatmap.R
    • Sex_bias_plotsetc_10sp_withVIfemales.R

Analyses without filtering genes with low expression in asexual females

• Get Sex-biased genes:

  • Sex_bias_edgeR_nocpmfilteronasex.R

• bring expression data together:

mkdir Output/DE_joined_nocpmfilteronasex
for sp in Tbi Tce Tcm Tpa Tps; do
	for tiss in WB RT LG; do
	
	python3 sex_bias_asex_edgeR_tidier.py \
		-i Output/DE_nocpmfiltonasex -s \
		"TTT_lrt_"$sp"_sex_bias_"$tiss".csv" -a sex_asex -o "Output/DE_joined_nocpmfilteronasex/"$sp"_"$tiss"_RBBH_disp_allsepar" 
	done
done

• plot
  • Sex_bias_plotsetc_nocpmfilteronasex.R

Analyses using full transcriptome references

• Using the sexual references

  • Sex_bias_edgeR_sexual_ref.R

• bring expression data together:

mkdir Output/DE_joined_sexual_ref	
for sp in Tbi Tce Tcm Tpa Tps; do
	for tiss in WB RT LG; do
	
	python3 sex_bias_asex_edgeR_tidier.py \
		-i Output/DE_sexual_ref -s \
		"TTT_lrt_"$sp"_sex_bias_"$tiss".csv" -a sex_asex -o "Output/DE_joined_sexual_ref/"$sp"_"$tiss"_longest_iso_disp_allsepar" \
		 -x $sp"_"$tiss"_N_FPKM_longest_iso_1.csv"
	done
done

• plot

  • Sex_bias_plotsetc_sexual_ref.R

• Using the asexual references

  • Sex_bias_edgeR_asexual_ref.R

• bring expression data together:

mkdir Output/DE_joined_asexual_ref	
for sp in Tbi Tce Tcm Tpa Tps; do
	for tiss in WB RT LG; do
	
	python3 sex_bias_asex_edgeR_tidier.py \
		-i Output/DE_asexual_ref -s \
		"TTT_lrt_"$sp"_sex_bias_"$tiss".csv" -a sex_asex -o "Output/DE_joined_asexual_ref/"$sp"_"$tiss"_longest_iso_disp_allsepar" \
		 -x $sp"_"$tiss"_N_FPKM_longest_iso_1.csv"
	done
done

• plot
  • Sex_bias_plotsetc_asexual_ref.R

Analyses on Autosomes only

• Sex_bias_plotsetc_withchrinfo.R

GO term analyses

• TopGO.R | for the main GO term analyses
• TopGO_10sp.R | for the GO term analyses using only the 10 species orthologs

dN/dS analyses

• dnds_SBGE.R

Additional scripts

• B2G_to_topGO.py | Script for converting Blast2GO output into a format usable by topGO
• Get_GO_term_parent_and_child_overlap_adjuster.py | Script for dealing with topographically close GO terms
• Get_GO_term_parent_and_child_overlap_adjuster_test_data_expl.R | Script explaining the logic of Get_GO_term_parent_and_child_overlap_adjuster.py
• super_exact_test_multitest_corrector.py | Script to correct the p-values of SuperExactTest for multiple tests
• super_exact_test_table_parser.py | Script to tidy up the output of super_exact_test_multitest_corrector.py

Infomation on running scripts

General

• All scripts should be run from the directory they are in. Output directories will be created to store Output as the code is run.
• All python scripts were made using python 3.5. All contain help information which can be displayed by specifying no command line arguments.

Abbreviations

Species names:

Species name	Abbreviation	Reproductive mode
Timema bartmani	Tbi	sexual
Timema tahoe	Tte	asexual
Timema cristinae	Tce	sexual
Timema monikensis	Tms	asexual
Timema poppensis	Tps	sexual
Timema douglasi	Tdi	asexual
Timema californicum	Tcm	sexual
Timema shepardi	Tsi	asexual
Timema podura	Tpa	sexual
Timema genevievae	Tge	asexual

Tissues:

Tissue	Abbreviation
Whole-body	WB
Reproductive tract	RT
Legs	LG