Data from "Assisted gene flow yields Acropora palmata corals with robust physiological performance"

This repository contains supplemental data for the paper "Assisted gene flow yields Acropora palmata corals with robust physiological performance". Table S1: Detected Symbiodiniaceae in A. palmata tissue samples. The raw signal intensities for each sample (in rows) and probe (columns D - AM) are given. Each sample is identified by the automatically generated sample id (Column A), the user specimen ID (Column B), and the cohort (Column C). The first five linear discriminants of the linear discriminant analysis are listed in Columns AN - AR. Their combination yields the assignment of Symbiodiniacea to clades (Columns AS - AX) following Kitchen et al., 2020. Dataset S1: Differential gene expression (DEG) results from baseline and heat stress contrasts. Tabs S1A–S1F summarize baseline DEGs between each pair of coral cohorts (CU × PR, CU × CU, CU × FL, FL × FL) at baseline (ambient) conditions, fit with the model Expression ~ Cohort. Tabs S1G–S1K present between-cohort DEGs following thermal stress (Expression ~ Cohort * Treatment). Tabs S1L–S1O list within-cohort DEGs under heat stress, with contrasts extracted from the interaction term. Each sheet includes gene ID, baseMean expression, log₂FoldChange, standard error, test statistic, unadjusted p-value, adjusted p-value (Benjamini-Hochberg FDR), and gene annotation. Log₂FoldChange represents expression relative to the control condition and/or the second group in each contrast. Genes were retained if they had ≥10 counts across all samples. Gene annotations follow the Acropora palmata reference genome and DEGs were identified using DESeq2 (Love et al., 2014). Dataset S#/Dataset S2: Functional enrichment of significant DEGs from baseline and heat stress contrasts. Tabs S2A–S2F summarize GO terms significantly enriched (p < 0.05) among DEGs identified at baseline between each pair of coral cohorts (CU × PR, CU × CU, CU × FL, FL × FL). Tabs S2G–S2I show enrichment results for DEGs identified within each cohort following thermal stress (Treatment vs. Control). Tabs S2J–S2M contain enrichment terms from pairwise comparisons of the treatment effect (Cu × PR, Cu × FL, etc.), based on the interaction term in the model. Each sheet includes GO ID, ontology category (BP = Biological Process, MF = Molecular Function, CC = Cellular Component), GO term description, number of DEGs annotated to that term (GeneRatio), total background genes annotated (BgRatio), raw p-value, FDR-adjusted p-value (Benjamini-Hochberg), q-value, and corresponding gene IDs. GO terms are separated by whether DEGs were upregulated or downregulated in the contrast of interest. Gene annotations follow the Acropora palmata reference genome. Enrichment analyses were performed using the clusterProfiler R package (Yu et al., 2012). Dataset S2: Raw CEL files used to generate genotyping calls for population genetic analyses of Acropora palmata samples. DNA was sent to ThermoFisher for genotyping using the Applied Biosystems Axiom Coral Genotyping Array -- 550962 following Kitchen et al. 2020. Quality control analyses were performed by ThermoFisher. 19,969 probes on the array were designed to resolve the population genomic structure of A.palmata and A.cervicornis. Subsequent analyses were performed using this set. Associated metadata is included in this dataset. AGF_Phenotype_Data: A suite of physiological parameters measured to assess the phenotypes of the different cohorts under the ambient and high temperature conditions. Columns A through F include metadata associated with each coral measured during the experiment. Columns K through AN include the raw phenotype data. See publication for methods associated with phenotype data collection and final metrics utilized.