Cross-species transcriptomics uncovers genes underlying genetic accommodation of developmental plasticity in spadefoot toads
Creators: name: Liedtke, H. Christoph
name: Harney, Ewan
name: Gomez-Mestre, Ivan
Publisher: name: Zenodo
Year: 2021
Subjects: edgeR
WGCNA
functional enrichment
Pelobates cultripes
Scaphiopus couchii

description: That hardcoded genomes can manifest as plastic phenotypes responding to environmental perturbations is a fascinating feature of living organisms. How such developmental plasticity is regulated at the molecular level is beginning to be uncovered aided by the development of -omic techniques. Here, we compare the transcriptome-wide responses of two species of spadefoot toads with differing capacity for developmental acceleration of their larvae in the face of a shared environmental risk: pond drying. By comparing gene expression profiles over time and performing cross-species network analyses, we identified orthologues and functional gene pathways whose environmental sensitivity in expression have diverged between species. Genes related to lipid, cholesterol and steroid biosynthesis and metabolism make up most of a module of genes environmentally responsive in one species, but canalized in the other. The evolutionary changes in the regulation of the genes identified through these analyses may have been key in the genetic accommodation of developmental plasticity in this system.
description: The uploaded files correspond to the following datasets/supporting information: SI 1: Schematic of bioinformatic workflow conducted in this study (PDF). SI 2: Excel file of raw counts of reads mapped to Trinity 'genes' by Kallisto for Pelobates cultripes (spreadsheet 1) and Scaphiopus couchii(spreadsheet 2). The first data column is the Trinity gene identifier for the specie-specific transcriptome, followed by columns of raw counts per sample. The design matrix (spreadsheet 3) indicates which samples belong to which treatment, species and time point. SI 3: Excel file of differential gene expression results as calculated by edgeR's exactTest() function with default settings. Results show pairwise comparisons for each time point (24, 48 or 72 hours; see spreadsheet names) after exposure to reduced water levels to the 24-hour high water control. The data columns refer to: gene_id = Trinity gene identifier, logFC = log fold change, logCPM = log counts per million, FDR = false discovery rate (q value) SI 4: Excel spreadsheet of functional enrichment results from gProfiler. Results show enriched terms for each set of genes (two species and up to three time points, separated into five spreadsheets) identified as differentially expressed by edgeR (SI 2). For descriptions of data columns, see https://biit.cs.ut.ee/gprofiler/gost. The last spreadsheet summarizes overlap of significant enrichment of terms across all five sets. SI 5: Complete lists of ortholgoues detected using the HaMStR pipeline and orhoDB v.9, for Pelobates cultripes (first spreadsheet) and Scaphiopus couchii (second spreadsheet). The data columns refer to: Transcript_ID = Trinity peptide transcript identifiers, OG/OG_name = orthoDB ortholog group identifier/name, DB = orthoDB database, OG_origin = ortholog group origin. SI 6: Thresholding power and dynamic tree cutting for Weighted Gene Correlation Network Analysis (WGCNA). (PDF). SI 7: Excel file of functional enrichment results from gProfiler. Results show enriched terms for each WGCNA module (separated into different spreadsheets). For descriptions of data columns, see https://biit.cs.ut.ee/gprofiler/gost. The last spreadsheet summarizes the significantly enriched terms per module and the response variables that were significantly correlated (p values) with the module eigengene expression (see manuscript text for details). SI 8: Excel file of orthologs that had a significant water effect based on the WGCNA. The data columns refer to: Module = WGCNA module, Ortholog = orthoDB ID (see SI 5), Short Name/ Ortholog description = ortholog name/description, Ensembl = ensembl peptide ID, Gene sig (water) P-Value = gene significance for "water effect" (see manuscript), Edge above 0.025 = boolean if expression correlations &gt; 0.025 (see manuscript), Reactome Pathways = enriched Reactome pathways (for only cyan module). Funding provided by: Ministerio de Economía, Industria y Competitividad, Gobierno de España<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100010198<br>Award Number: CGL2017-83407-P