This study evaluated the transcriptomic responses of corals with different morphological characteristics in response to different types of sediment stress. Six coral species (Acropora cervicornis, Montestraea cavernosa, Montipora capitata, Orbicella faveolata, Pocillopora acuta, and Porites lobata) were assessed at two locations (Florida and Hawai’i). Floridian corals (A. cervicornis, M. cavernosa and O. faveolata) were exposed to sterilized white carbonate sediment for 18 days, whereas Hawaiian corals (M. capitata, P. acuta and P. lobata) were exposed to unsterilized terrigenous red soil for up to 7 days.
Bioinf- contains scripts for bioinformatic analysesSTAR- scripts for read alignment using the STAR alignment software for the Hawai’i coral speciesOrthoFinder.md- scripts for running OrthoFinder to identify orthologous genes between speciesRNASeq_pipeline_FL.md- scripts for RNAseq analysis for Florida coral speciesRNASeq_pipeline_HI.md- scripts for RNAseq analysis for Hawai’i coral speciesTranscriptLengths.md- script to calculate transcript lengths of each gene and protein. This information was used in the GOSeq scripts.wgetgenomes.md- download information for all reference genomes used
DataNCBI_upload- information on NCBI sequences uploadnoaa_buoy- water temperature data from NOAA in Florida and Hawai’i during the times of the experimentsFL_sediment_metadata_raw.csv- metadata from the Florida experimentHI_sediment_metadata_raw.csv- metadata from the Hawai’i experimentacerv_metadata_filtered.csv- metadata from A. cervicornis from the Florida experimentmcap_metadata_filtered.csv- metadata from M. capitata from the Hawai’i experimentmcav_metadata_filtered.csv- metadata from M. cavernosa from the Florida experimentofav_metadata_filtered.csv- metadata from O. faveolata from the Florida experimentpacuta_metadata_filtered.csv- metadata from P. acuta from the Hawai’i experimentplob_metadata_filtered.csv- metadata from P. lobata from the Hawai’i experiment
Images- pipeline, QC and workflow imagesOutput- output from gene expression analyses.DESeq2- differential gene expression outputacerv- differential gene expression output for A. cervicornis from the Florida experimentmcap- differential gene expression output for M. capitata from the Hawai’i experimentmcav- differential gene expression output for M. cavernosa from the Florida experimentofav- differential gene expression output for O. faveolata from the Florida experimentpacuta- differential gene expression output for P. acuta from the Hawai’i experimentplob- differential gene expression output for P. lobata from the Hawai’i experiment
Figs- figure outputGOslim- figures for GO slimPCA- PCA figures of differentiall expressed genes for Florida and Hawai’i coralsTemperature- temperature figures from NOAA data from Florida and Hawai’i experimental periodsVenn- Venn diagram figures of shared GO terms and orthogroups between speciesacerv- PCAs, heatmaps and GO plots for all genes and DEGs for A. cervicornis from the Florida experimentmcap- PCAs, heatmaps and GO plots for all genes and DEGs for M. capitata from the Hawai’i experimentmcav- PCAs, heatmaps and GO plots for all genes and DEGs for M. cavernosa from the Florida experimentofav- PCAs, heatmaps and GO plots for all genes and DEGs for O. faveolata from the Florida experimentpacuta- PCAs, heatmaps and GO plots for all genes and DEGs for P. acuta from the Hawai’i experimentplob- PCAs, heatmaps and GO plots for all genes and DEGs for P. lobata from the Hawai’i experimentupset- upset plots of shared GO terms and orthogroups between species
GOSeq- gene ontology outputacerv- gene ontology output for A. cervicornis from the Florida experimentmcap- gene ontology output for M. capitata from the Hawai’i experimentmcav- gene ontology output for M. cavernosa from the Florida experimentofav- gene ontology output for O. faveolata from the Florida experimentpacuta- gene ontology output for P. acuta from the Hawai’i experimentplob- gene ontology output for P. lobata from the Hawai’i experimentall.go.BP.slim_20220417.csv- gene ontology output for Biological Processes for all speciesall.go.CC.slim_20220417.csv- gene ontology output for Cellular Components for all speciesall.go.MF.slim_20220417.csv- gene ontology output for Molecular Functions for all speciesall.go.slim_20220417.csv- gene ontology output for all species
OrthoFinder- OrthoFinder outputacerv- orthofinder and DEG output for A. cervicornis from the Florida experimentmcap- orthofinder and DEG output for M. capitata from the Hawai’i experimentmcav- orthofinder and DEG output for M. cavernosa from the Florida experimentofav- orthofinder and DEG output for O. faveolata from the Florida experimentpacuta- orthofinder and DEG output for P. acuta from the Hawai’i experimentplob- orthofinder and DEG output for P. lobata from the Hawai’i experimentspecies_compare- files comparing each species against one anotherAllSpecies_DEGs_ortho_20221020.csv- DEGs and corresponding orthogroups for all speciesOrthogroups.tsv- raw data from orthofinder comparison for all species
QC- multiQC output for raw and trimmed readsSuppTables- supplementary tables for the associated manuscriptAlignmentOutput.csv- raw and clean read counts, % of reads mapped to genomeAlignmentOutput_Averages.csv- averages of raw and clean read counts, % of reads mapped to genomeDEG_GO_Orthogroup_SummaryTable.csv- summary counts of DEG, GO and orthogroups for each speciesOrthogroups_DEGs.csv- summary table with the number of orthogroups with DEGs and number of DEGs in orthogroupsShared_GO_terms.csv- GO terms shared between speciesShared_GO.xlsx- GO terms shared between species in manuscript ready table
RAnalysis- R scripts for data analysesacerv- DESeq2 and GOSeq scripts for A. cervicornis from the Florida experimentgff_wrangling- scripts for manipulating GFFs for use with STAR softwaremcap- DESeq2 and GOSeq scripts for M. capitata from the Hawai’i experimentmcav- DESeq2 and GOSeq scripts for M. cavernosa from the Florida experimentofav- DESeq2 and GOSeq scripts for O. faveolata from the Florida experimentpacuta- DESeq2 and GOSeq scripts for P. acuta from the Hawai’i experimentplob- DESeq2 and GOSeq scripts for P. lobata from the Hawai’i experimentDEG_GO_summary.Rmd- script summarizing DEG and GO informationGOslim.Rmd- script assigning GO terms into GO slim binsNOAA_temperatures- script plotting NOAA temperatures from Florida and Hawai’iOrthogroups.Rmd- script analyzing orthogroups in the context of DEGs for each speciesPCA_plots.Rmd- script to make PCA figure for manuscriptRNASeqPower.Rmd- script to run power analysis on RNASeq data