Supplemental Tables and Notes: Host Plant and Light Regime Shape Limited, Whole-Body Transcriptional Rhythmicity in the Bird Cherry-Oat Aphid (Rhopalosiphum padi)
Year: 2026
Type: supplementary-materials
Abstract: This dataset provides the supplemental tables and supplemental text accompanying the manuscript: Host Plant and Light Regime Shape Limited, Whole-Body Transcriptional Rhythmicity in the Bird Cherry-Oat Aphid (Rhopalosiphum padi)Daniel Kunk and Vamsi Nalam (Colorado State University) Overview of Included Files This record contains 11 Supplemental Tables and 1 Supplemental Note: Supplemental Note S1: Extended discussion and methodological comparison evaluating rhythmicity detection across dryR, Cosinor, and JTK_CYCLE (specifically assessing the sensitivity and fragility of rhythmic signals detected under constant darkness on wheat). Table S1. Artificial diet composition and ingredients: Excel file containing the list of ingredients used to prepare the artificial diet, including supplier, catalog number, and amount added per 100 mL of diet. The table is organized by component class (sugar, amino acids, vitamins, and salts/other ingredients). Table S2. Survival and performance assay raw data and statistical results: Excel file containing the raw survival and performance assay datasets, including the daily counts of surviving adults and cumulative nymphs for diet-fed aphids and endpoint (96 h) counts for all treatments. Additional sheets report the full statistical results for each hypothesis test conducted. Table S3. RNA-seq quality metrics and sample metadata: Excel file containing per-sample MultiQC summary statistics for read preprocessing (fastp) and quantification (Salmon) (sheet 1) and sample metadata for each library (sheet 2), including FASTQ filenames, sample name, timepoint (ZT), biological replicate, sequencing batch, host treatment (i.e., wheat or diet), and light treatment (LD or DD). Table S4. dryR rhythmicity results, model summaries, and filtering statistics: Large Excel file containing dryR results for wheat and artificial diet experiments. dryR transcript-level results for wheat (sheet 1) and diet (sheet 2). Model-level summaries (sheet 3), including transcript counts per model and descriptive statistics for each experiment. Filtering summary for transcripts assigned to model R0 (sheet 4), including the reason(s) for filtering/low rhythmicity support. Table S5. Nitecap results: Large Excel file containing Nitecap results. Each sheet includes the input expression matrix and the Nitecap results for each experiment and light condition: LD – Wheat (sheet 1), DD – Wheat (sheet 2), LD – Diet (sheet 3), and DD – Diet (sheet 4). Table S6. dryR model comparisons and transition counts between wheat and artificial diet: Large Excel file summarizing dryR model correspondence for transcripts in wheat and artificial diet. This file contains the list of transcript model assignments between wheat and diet, excluding model R1 (sheet 1) and including R1 (sheet 2). Counts of model-to-model transitions from wheat to diet used in Sankey analysis (e.g., Wheat R1 → Diet R2) are also provided (sheet 3). Table S7. GO term enrichment results and associated transcript IDs for dryR rhythmicity models: Large Excel file containing Gene Ontology (GO) enrichment outputs for dryR rhythmicity models in wheat (R2–R5) and artificial diet (R2–R4). For each model, two sheets are provided: the first sheet contains GO enrichment results (starting with Wheat R2), and the following sheet lists the transcript IDs associated with each enriched GO term from the preceding sheet. In total, the workbook contains 14 sheets (two per model). Table S8. KEGG pathway enrichment results and associated transcript IDs for dryR rhythmicity models: Large Excel file containing KEGG pathway enrichment outputs for dryR rhythmicity models in wheat (R2–R5) and artificial diet (R2–R4). For each model, two sheets are provided: the first sheet contains KEGG enrichment results (starting with Wheat R2), and the following sheet lists the transcript IDs associated with each enriched pathway from the preceding results sheet. In total, the workbook contains 14 sheets (two per model). Table S9. FIMO motif scan outputs for dryR rhythmicity models: Excel file containing FIMO results from promoter motif scanning across dryR rhythmicity models in wheat (R1–R5) and artificial diet (R1–R4). Meme file motif definitions used for the scan are provided on sheet 1. Subsequent sheets contain the FIMO results tables for each model in wheat and diet. Table S10. XSTREME motif discovery results for dryR rhythmicity models: Excel file containing XSTREME output tables for promoter motif discovery across dryR rhythmicity models in wheat (R2–R5) and artificial diet (R2–R4). Separate sheets provide the XSTREME results for each model. Table S11. Rhythmicity profiles of canonical insect circadian clock transcript homologs in R. padi: Excel file containing tables summarizing dryR and Nitecap rhythmicity results for R. padi transcript isoforms identified as homologs of canonical insect circadian clock genes. Results are shown for aphids feeding on wheat and artificial diet under light-dark (LD) and constant darkness (DD) conditions. The dryR classifications indicate inferred rhythmic models and associated parameters, and Nitecap results report transcript rhythmicity statistics and associated parameters for each condition. Associated Code & Repositories Code used to process sequence data, model transcript rhythmicity, and conduct promoter motif analyses is available at the following GitHub repositories: RNA-seq preprocessing & quantification: https://github.com/dankunk/tango-public/ Rhythmicity modeling & downstream functional enrichment (dryR): https://github.com/dankunk/Rpadi_Wheat-Diet_LD-DD_Analysis Promoter sequence extraction & motif analysis: https://github.com/dankunk/RhythmicPromoterAnalysis Raw Sequencing Data All raw paired-end RNA-seq reads and associated BioSample metadata are deposited in the NCBI Sequence Read Archive (SRA) under BioProject accession PRJNA1413204.
Author: Kunk, Daniel
Institution: Colorado State University
Language: English
Subfield: Endocrine and Autonomic Systems
Field: Neuroscience
Domain: Life Sciences
SDG: Zero hunger
Open Access status: green
OpenAlex ID: W7221048429