DOI: 10.6084/m9.figshare.23661603.v2
title: Supplementary data for manuscript: Day-night gene expression reveals circadian gene <i>disco</i><i> </i>as a candidate for diel-niche evolution in moths.

description: <br><b>Supporting Information for</b><br>Day-night gene expression reveals circadian gene <i>disco </i>as a candidate for diel-niche evolution in moths.<br><b>Authors</b>: Yash Sondhi, Rebeccah L. Messcher, Anthony J. Bellantuano, Caroline G. Storer, Scott D. Cinel, R. Keating Godfrey, Deborah Glass, Ryan A. St Laurent, Chris A. Hamilton, Chandra Earl, Colin J. Brislawn, Ian J. Kitching, Seth M. Bybee, Jamie C. Theobald, Akito Y. Kawahara<br>Supp_dataset_1: EdgeR: EdgeR sample metadata, analysis parameters (config files for RasFlow), differentially expressed gene sets, annotated DEG sets with <i>Bombyx mori </i>annotations for <i>Anisota pellucida </i>(Ap) and <i>Dryocampa rubicunda </i>(Dr)<i>.</i> Overlapping genes between <i>Anisota </i>and<i> Dryocampa. </i>Analysis performed with de-novo assembly versions 5 for both species.Supp_dataset_2: DESeq2: DESeq2 sample metadata, analysis parameters (R script), differentially expressed gene sets, and annotated DEG sets with <i>Bombyx mori </i>annotations for <i>Anisota pellucida </i>(Ap) and <i>Dryocampa rubicunda </i>(Dr)<i>.</i> Unique and overlapping genes between <i>Anisota </i>and<i> Dryocampa. </i>Analysis performed with de-novo assembly versions 5 for both species.Supp_dataset_3: Supporting_Table_Common_RNAseq: Overlapping genes for both analyses with a pivot table summary of the different unique <i>Bombyx </i>genes and the number of transcripts mapped to each.Supp_dataset_4: Gene_modules_WGCNA: WGCNA identified modules for <i>Anisota </i>and <i>Dryocampa </i>individual count data and combined modules along with annotations of the (grey60, tan, turquoise and blue) modules.Supp_dataset_5: GO_analyses: TopGO, ShinyGo and Revigo analysesSupp_dataset_6:Analyses_combined:All analyses results combined and annotated, with FC&lt;0 and FC&lt;2 for DEGs. Note to combine analyses fold change signs were switched for EdgeR changed.Supp_dataset_7: Overlap_common_genes_annotated_with_sequence: Overlapping transcripts annotated with sequences for both species and <i>Bombyx mori. </i>Note to combine analyses fold change signs were switched for EdgeR changed.Supp_dataset_8_EggNOG_annotations: EggNog annotations of the various sequences in dataset 7 and the GO terms used to query this datasetSupp_datatset_9: GO_lookup_genes: Genes recovered from the GO cross referencing with EggNOG annotationsSupp_dataset_10: Genes of interest for which conservation and protein models were constructedSupp_dataset_11: Assembly_codes: 11a:List of moths and assembly codes used 11b: List of insects and assembly codes used for Orthofinder searchesSupp_dataset_12_Alphafold_Bmor_models: Alphafold predicted models for <i>Bombyx </i>genes of interestSupp_dataset_13_Conservation analyses: Consurf predicted models and conservation analyses for insects and mothsSupp_dataset_14_PyMOL: PyMOL files showcasing the overlapping protein structuresSupp_dataset_15_Protocols: Modified RNA Extraction Protocols<br>Supp_dataset_16_Assemblies: De-novo assemblies and Peptide Files<br>Supp_dataset_17_Samples: Sample metadata