DOI: 10.6084/m9.figshare.23661603
title: Supplementary data for manuscript: Day-night gene expression reveals circadian gene <i>disco </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, Andrew J. Mongue, Yi-Ming Weng, 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 RNA extraction and Library Preparation metadata