DOI: 10.5061/dryad.73n5tb2t8
title: Data from: Transcriptomic plasticity of mesophotic corals among natural populations and transplants of Montastraea cavernosa in the Gulf of Mexico and Belize

description: While physiological responses to low-light environments have been studied
 among corals on mesophotic coral ecosystems worldwide (MCEs; 30–150 m),
 the mechanisms behind acclimatization and adaptation to depth are not well
 understood for most coral species. Transcriptomic approaches based on RNA
 sequencing are useful tools for quantifying gene expression plasticity,
 particularly in slow-growing species such as scleractinian corals, and for
 identifying potential functional differences among conspecifics. A
 tag-based RNA-Seq (Tag-Seq) pipeline was applied to quantify
 transcriptional variation in natural populations of the scleractinian
 coral Montastraea cavernosa from mesophotic and
 shallower environments across five sites in Belize and the Gulf of Mexico:
 Carrie Bow Cay, West and East Flower Garden Banks, Pulley Ridge, and Dry
 Tortugas. Regional site location was a stronger driver of gene expression
 patterns than depth. However, mesophotic corals among all sites shared
 similar regulation of metabolic and cell growth functional pathways that
 may represent common physiological responses to environmental conditions
 at depth. Additionally, in a transplant experiment at West and East Flower
 Garden Banks, colonies transplanted from mesophotic to shallower habitats
 diverged from the control mesophotic group over time, indicating
 depth-regulated plasticity of gene expression. When the shallower depth
 zone experienced a bleaching event, bleaching severity did not differ
 significantly between transplants and shallow controls, but gene
 expression patterns indicated variable regulation of stress responses
 among depth treatments. Coupled observational and experimental studies of
 gene expression among mesophotic and shallower M.
 cavernosa provide insights into the ability of this
 depth-generalist coral species to persist under varying environmental
 conditions. 
description: <strong>Gene expression counts and
 <em>DESeq2</em> designs</strong>
 Workbook containing spreadsheets for (in this order):
 <em>DESeq2</em> design for natural populations, gene counts
 for host natural populations, gene counts for symbiont natural
 populations, <em>DESeq2</em> design for transplant
 experiment, gene counts for host transplant experiment, gene counts for
 symbiont transplant experiment, read counts for all samples, and raw gene
 counts for all samples.
 Studivan-and-Voss_allcounts_design.xlsx
 <strong><em>DESeq2</em> R scripts for host and
 symbiont natural populations</strong> R script
 containing outlier detection, data normalization, data visualzation, and
 statistical analyses of differential expression among
 populations.
 Studivan-and-Voss_deseq2_enviro_mcav.R
 Studivan-and-Voss_deseq2_enviro_zoox.R
 <strong><em>DESeq2</em> R scripts for host and
 symbiont transplant experiment</strong> R script
 containing outlier detection, data normalization, data visualzation, and
 statistical analyses of differential expression among transplant
 experiment factors (shallow controls, mesophotic controls,
 mesophotic-to-shallow transplants).
 Studivan-and-Voss_deseq2_trans_mcav.R
 Studivan-and-Voss_deseq2_trans_zoox.R
 <strong><em>KOG-MWU</em> R scripts for host and
 symbiont natural populations</strong> R script
 containing statistical analyses and visualization of eukaryotic
 orthologous group (KOG) pathways among populations.
 Studivan-and-Voss_kogmwu_enviro_mcav.R
 Studivan-and-Voss_kogmwu_enviro_zoox.R
 <strong>Symbiont and chlorophyll data for transplant
 experiment</strong> Workbook containing
 spreadsheets for symbiont and chlorophyll metrics and bleaching responses
 from the transplant experiment.
 Studivan-and-Voss_symbiont_chlorophyll.xlsx
 <strong>R script for symbiont and chlorophyll
 analyses</strong> R script containing statistical
 analyses and visualization of symbiont and chlorophyll metrics from
 transplant experiment.
 Studivan-and-Voss_symbiont_chlorophyll_script.R
 <strong>Temperature and light data for transplant
 experiment</strong> Workbook containing
 datasheets for truncated temperature and light data, summary statistics,
 and raw logger data from transplant experiment.
 Studivan-and-Voss_temp_light.xlsx <b>R
 script for temperature and light analyses</b> R
 script containing statistical analyses and visualization of temperature
 and light data from transplant experiment.
 Studivan-and-Voss_temp_light_script.R