Parent-of-origin effect on global gene expression and host-plant adaptation in  Spodoptera frugiperda (Lepidoptera: Noctuidae)
Creators: name: Lan, Laijiao
name: Nam, Kiwoong
name: Robin, Stéphanie
name: Nègre, Nicolas
Publisher: name: Zenodo
Year: 2025

description: Analysis files and scripts for the publication:

Parent-of-origin effect on global gene expression and host-plant adaptation in 

Spodoptera frugiperda (Lepidoptera: Noctuidae)

by

Laijiao Lan1, Stéphanie Robin2,3, Kiwoong Nam1 and Nicolas Nègre1*

1 DGIMI, Univ Montpellier, INRAE, Montpellier, France

2 BIPAA, IGEPP, INRAE, Institut Agro, University of Rennes, Rennes, France

3 IRISA, University of Rennes, INRIA, CNRS, IRISA, Rennes, France

*Correspondence: nicolas.negre@umontpellier.fr





 

 

 
description: Here is a short description of the files available:

The main scripts for RNA-seq analysis and GO and KEGG pathways analyses can be found here:

2502_HybridRNAseq _LAN.Rmd

sorting_GeneID_ProteinID_OGS7.1_20230705_proteins.R

sorting_KAAS_kegg_trans.py

 

The files used from the reference genome on BIPAA (https://bipaa.genouest.org/sp/spodoptera_frugiperda_corn/) to retrieve functional annotations are here:

OGS7.1_20230705_proteins.fa

gene.list.txt

q00001.keg

 

…and compiled in user friendly excel files:

Geneid and feature counts_Lan_RNAseq_Hybrids_Poitout.xlsx

gene_info_blast2GO7.1.xlsx

2403_blast2GO_OGS7.1.xlsx

2403_KAAS_info_Sfu9.xlsx

2406_ALL_Heterosis_Maternal_RR_CC_GENES_INFO.xlsx

240603_LRT_clustering_res_table_sorted.xlsx

 

The data files to perform the analyses are the following:

Data

            2207_larval_weight_Corn_vsPoitout.txt

            2207_larval_weight_Poitout_vsCorn.txt

            2207_survival_rate_Corn_vsPoitout.txt

            2207_survival_rate_Poitout_vsCorn.txt

            240307_Insects_KO_pathway.txt

            2403_KAAS_GID_KO_pathway_Sfu9.txt

            2406_Raw_counts_LRT_group3_top10BP_KEGG_heterosis-RC4.txt

            2406_Raw_counts_LRT_group6_all_BP_RM-RC4.txt

            2406_Raw_counts_Wald_enriched_genes_all_GO_RCvsCR-RC4.txt

            2406_Raw_counts_Wald_enriched_genes_all_KEGG_CCvsRR.txt

            2406_Raw_counts_Wald_enriched_genes_all_KEGG_RRvsCC.txt

            2406_Raw_counts_Wald_enriched_genes_top10GO_KEGG_CRvsRC-RC4.txt

            2406_res_info_CCeffect_genes_2CC_group8-RC4.txt

            2406_res_info_Heterosis_genes_group3-RC4.txt

            2406_res_info_Maternal_genes_RM_group6-RC4.txt

            2406_res_info_RReffect_genes_2RR_group1-RC4.txt

            colData_RCvsCR-RC4.txt

            colData_RRvsCC.txt

            colData-RC4.txt

            colData-RC4+sex.txt

            fertility_2207corn.txt

            fertility_2207PoitoutVScorn.txt

            filtered_2403_KAAS_GID_KO_pathway_Sfu9.txt

            gene_info_blastGO7.1.txt

            integer_4genotypes_chr1_FeatureCounts_Poitout-RC4.txt

            integer_4genotypes_chr29_FeatureCounts_Poitout-RC4.txt

            integer_4genotypes_FeatureCounts_Poitout-RC4.txt

            integer_RCvsCR_FeatureCounts_Poitout-RC4.txt

            integer_RRvsCC_FeatureCounts_Poitout.txt

            lw_d8_2207corn.txt

            lw_d8_2207Poitoutvscorn.txt

            lw_d10_2207corn.txt

            lw_d10_2207Poitoutvscorn.txt

            lw_d12_2207corn.txt

            lw_d12_2207Poitoutvscorn.txt

            lw_d14_2207corn.txt

            lw_d14_2207Poitoutvscorn.txt

            lw_d16_2207corn.txt

            sorted_annotation_blast2GO_OGS7.1.txt

            sorted_geneGO_blast2GO_OGS7.1.txt

           

… and the result files (text and plots) from the analyses are listed here:

RESULTS

            files

                        2406_2CCeffect_GENES_group8-RC4.txt

                        2406_2RReffect_GENES_group1-RC4.txt

                        2406_CCvsRR_ORA_kegg_gene_tables.csv

                        2406_CRvsRC_ORA_BP_gene_tables.csv

                        2406_CRvsRC_ORA_kegg_gene_tables.csv

                        2406_hete_ORA_BP_gene_tables.csv

                        2406_hete_ORA_KEGG_gene_tables.csv

                        2406_Heterosis_GENES_group3-RC4.txt

                        2406_normalized_counts_4genotypes-RC4.txt

                        2406_normalized_counts_HYBRIDS_RCvsCR-RC4.txt

                        2406_normalized_counts_STRAINS_RRvsCC.txt

                        2406_RCvsCR_ORA_BP_gene_tables.csv

                        2406_RCvsCR_res_tableHYBRID_shrunken_no_NA-RC4.csv

                        2406_RCvsCR_sigGENES-RC4.csv

                        2406_RM_GENES_group6-RC4.txt

                        2406_RM_ORA_BP_gene_tables.csv

                        2406_RM_ORA_KEGG_gene_tables.csv

                        2406_RRvsCC_ORA_kegg_gene_tables.csv

                        2406_RRvsCC_res_tableSTRAIN_shrunken_no_NA.csv

                        2406_RRvsCC_sigGENES.csv

                        240603_normalized_counts_4genotypes-RC4.xlsx

                        gene_anno.txt

                        pathway_anno.txt

            plots

                        Fig.1_2406_larval performance of both diets.tiff

                        Fig.2_2502_heterosis_combined_GO_KEGG_clusters.tiff

                        Fig.3_2502_heatmap_LRT_group3_top10BP_KEGG_heterosis-RC4.tiff

                        Fig.4_2502_maternal_RM_combined_GO_KEGG_clusters.tiff

                        Fig.5_2406_heatmap_LRT_group6_all_BP_RM-RC4-2.tiff

                        Fig.6_2406_CRvsRC_combined_PCA_MA-RC4.tiff

                        Fig.7_2406_RCvsCR_combined_ORA-RC4.tiff

                        Fig.8_2406_heatmap_Wald_RCvsCR_gene_silencing.tiff

                        Fig.9_2406_heatmap_Wald_CRvsRC_oxip_GO_KEGG_CRvsRC.tiff

                        Fig.S1_Fertility of both diets.tiff

                        Fig.S8_2406_combined_PCA_heatmap_chromosomes+sex.tiff

                        Fig.S9_2406_combined_RR_CC_effect.tiff

                        Fig.S10_2406_RRvsCC_PCA_MA.tiff

                        Fig.S11_2406_combined_strain_ORA_KEGG.tiff

                        Fig.S12_2406_heatmap_Wald_RRvsCC_all_KEGG_RR.tiff

                        Fig.S13_2406_heatmap_Wald_CCvsRR_all_KEGG_CC.tiff

                        Fig.S15_2406-LRT_overall_ExpressionPatterns-RC4.tiff