DOI: 10.5061/dryad.cnp5hqc3z
title: Cross-species transcriptomics uncovers genes underlying genetic accommodation of developmental plasticity in spadefoot toads

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).