Supplementary data for manuscript: Day-night gene expression reveals circadian gene disco as a candidate for diel-niche evolution in moths.

Supporting Information for
Day-night gene expression reveals circadian gene disco as a candidate for diel-niche evolution in moths.

Authors: 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

Supp_dataset_1: EdgeR: EdgeR sample metadata, analysis parameters (config files for RasFlow), differentially expressed gene sets, annotated DEG sets with Bombyx mori annotations for Anisota pellucida (Ap) and Dryocampa rubicunda (Dr). Overlapping genes between Anisota and Dryocampa. 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 Bombyx mori annotations for Anisota pellucida (Ap) and Dryocampa rubicunda (Dr). Unique and overlapping genes between Anisota and Dryocampa. 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 Bombyx genes and the number of transcripts mapped to each.

Supp_dataset_4: Gene_modules_WGCNA: WGCNA identified modules for Anisota and Dryocampa 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 analyses

Supp_dataset_6:Analyses_combined:All analyses results combined and annotated, with FC<0 and FC<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 Bombyx mori. 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 dataset

Supp_datatset_9: GO_lookup_genes: Genes recovered from the GO cross referencing with EggNOG annotations

Supp_dataset_10: Genes of interest for which conservation and protein models were constructed

Supp_dataset_11: Assembly_codes: 11a:List of moths and assembly codes used 11b: List of insects and assembly codes used for Orthofinder searches

Supp_dataset_12_Alphafold_Bmor_models: Alphafold predicted models for Bombyx genes of interest

Supp_dataset_13_Conservation analyses: Consurf predicted models and conservation analyses for insects and moths

Supp_dataset_14_PyMOL: PyMOL files showcasing the overlapping protein structures

Supp_dataset_15_Protocols: Modified RNA Extraction Protocols
Supp_dataset_16_Assemblies: De-novo assemblies and Peptide Files
Supp_dataset_17_Samples: Sample RNA extraction and Library Preparation metadata