README.md

Sediment Stress

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.

Experimental design

Bioinformatic pipeline

Repository overview

• Bioinf - contains scripts for bioinformatic analyses
  • STAR - scripts for read alignment using the STAR alignment software for the Hawai’i coral species
  • OrthoFinder.md - scripts for running OrthoFinder to identify orthologous genes between species
  • RNASeq_pipeline_FL.md - scripts for RNAseq analysis for Florida coral species
  • RNASeq_pipeline_HI.md - scripts for RNAseq analysis for Hawai’i coral species
  • TranscriptLengths.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
• Data
  • NCBI_upload - information on NCBI sequences upload
  • noaa_buoy - water temperature data from NOAA in Florida and Hawai’i during the times of the experiments
  • FL_sediment_metadata_raw.csv - metadata from the Florida experiment
  • HI_sediment_metadata_raw.csv - metadata from the Hawai’i experiment
  • acerv_metadata_filtered.csv - metadata from A. cervicornis from the Florida experiment
  • mcap_metadata_filtered.csv - metadata from M. capitata from the Hawai’i experiment
  • mcav_metadata_filtered.csv - metadata from M. cavernosa from the Florida experiment
  • ofav_metadata_filtered.csv - metadata from O. faveolata from the Florida experiment
  • pacuta_metadata_filtered.csv - metadata from P. acuta from the Hawai’i experiment
  • plob_metadata_filtered.csv - metadata from P. lobata from the Hawai’i experiment
• Images - pipeline, QC and workflow images
• Output - output from gene expression analyses.
  • DESeq2 - differential gene expression output
    • acerv - differential gene expression output for A. cervicornis from the Florida experiment
    • mcap - differential gene expression output for M. capitata from the Hawai’i experiment
    • mcav - differential gene expression output for M. cavernosa from the Florida experiment
    • ofav - differential gene expression output for O. faveolata from the Florida experiment
    • pacuta - differential gene expression output for P. acuta from the Hawai’i experiment
    • plob - differential gene expression output for P. lobata from the Hawai’i experiment
  • Figs - figure output
    • GOslim - figures for GO slim
      • BP - GO slim figures for Biological Processes
      • CC - GO slim figures for Cellular Components
      • MF - GO slim figures for Molecular Functions
    • PCA - PCA figures of differentiall expressed genes for Florida and Hawai’i corals
    • Temperature - temperature figures from NOAA data from Florida and Hawai’i experimental periods
    • Venn - Venn diagram figures of shared GO terms and orthogroups between species
    • acerv - PCAs, heatmaps and GO plots for all genes and DEGs for A. cervicornis from the Florida experiment
    • mcap - PCAs, heatmaps and GO plots for all genes and DEGs for M. capitata from the Hawai’i experiment
    • mcav - PCAs, heatmaps and GO plots for all genes and DEGs for M. cavernosa from the Florida experiment
    • ofav - PCAs, heatmaps and GO plots for all genes and DEGs for O. faveolata from the Florida experiment
    • pacuta - PCAs, heatmaps and GO plots for all genes and DEGs for P. acuta from the Hawai’i experiment
    • plob - PCAs, heatmaps and GO plots for all genes and DEGs for P. lobata from the Hawai’i experiment
    • upset - upset plots of shared GO terms and orthogroups between species
  • GOSeq - gene ontology output
    • acerv - gene ontology output for A. cervicornis from the Florida experiment
    • mcap - gene ontology output for M. capitata from the Hawai’i experiment
    • mcav - gene ontology output for M. cavernosa from the Florida experiment
    • ofav - gene ontology output for O. faveolata from the Florida experiment
    • pacuta - gene ontology output for P. acuta from the Hawai’i experiment
    • plob - gene ontology output for P. lobata from the Hawai’i experiment
    • all.go.BP.slim_20220417.csv - gene ontology output for Biological Processes for all species
    • all.go.CC.slim_20220417.csv - gene ontology output for Cellular Components for all species
    • all.go.MF.slim_20220417.csv - gene ontology output for Molecular Functions for all species
    • all.go.slim_20220417.csv - gene ontology output for all species
  • OrthoFinder - OrthoFinder output
    • acerv - orthofinder and DEG output for A. cervicornis from the Florida experiment
    • mcap - orthofinder and DEG output for M. capitata from the Hawai’i experiment
    • mcav - orthofinder and DEG output for M. cavernosa from the Florida experiment
    • ofav - orthofinder and DEG output for O. faveolata from the Florida experiment
    • pacuta - orthofinder and DEG output for P. acuta from the Hawai’i experiment
    • plob - orthofinder and DEG output for P. lobata from the Hawai’i experiment
    • species_compare - files comparing each species against one another
    • AllSpecies_DEGs_ortho_20221020.csv - DEGs and corresponding orthogroups for all species
    • Orthogroups.tsv - raw data from orthofinder comparison for all species
  • QC - multiQC output for raw and trimmed reads
  • SuppTables - supplementary tables for the associated manuscript
    • AlignmentOutput.csv - raw and clean read counts, % of reads mapped to genome
    • AlignmentOutput_Averages.csv - averages of raw and clean read counts, % of reads mapped to genome
    • DEG_GO_Orthogroup_SummaryTable.csv - summary counts of DEG, GO and orthogroups for each species
    • Orthogroups_DEGs.csv - summary table with the number of orthogroups with DEGs and number of DEGs in orthogroups
    • Shared_GO_terms.csv - GO terms shared between species
    • Shared_GO.xlsx - GO terms shared between species in manuscript ready table
• RAnalysis - R scripts for data analyses
  • acerv - DESeq2 and GOSeq scripts for A. cervicornis from the Florida experiment
  • gff_wrangling - scripts for manipulating GFFs for use with STAR software
  • mcap - DESeq2 and GOSeq scripts for M. capitata from the Hawai’i experiment
  • mcav - DESeq2 and GOSeq scripts for M. cavernosa from the Florida experiment
  • ofav - DESeq2 and GOSeq scripts for O. faveolata from the Florida experiment
  • pacuta - DESeq2 and GOSeq scripts for P. acuta from the Hawai’i experiment
  • plob - DESeq2 and GOSeq scripts for P. lobata from the Hawai’i experiment
  • DEG_GO_summary.Rmd - script summarizing DEG and GO information
  • GOslim.Rmd - script assigning GO terms into GO slim bins
  • NOAA_temperatures - script plotting NOAA temperatures from Florida and Hawai’i
  • Orthogroups.Rmd - script analyzing orthogroups in the context of DEGs for each species
  • PCA_plots.Rmd - script to make PCA figure for manuscript
  • RNASeqPower.Rmd - script to run power analysis on RNASeq data