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Data from: Transcriptomic plasticity of mesophotic corals among natural populations and transplants of Montastraea cavernosa in the Gulf of Mexico and Belize

Citation

Studivan, Michael S; Voss, Joshua D (2020), Data from: Transcriptomic plasticity of mesophotic corals among natural populations and transplants of Montastraea cavernosa in the Gulf of Mexico and Belize, Dryad, Dataset, https://doi.org/10.5061/dryad.73n5tb2t8

Abstract

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. 

Usage Notes

Gene expression counts and DESeq2 designs

Workbook containing spreadsheets for (in this order): DESeq2 design for natural populations, gene counts for host natural populations, gene counts for symbiont natural populations, DESeq2 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

DESeq2 R scripts for host and symbiont natural populations

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

DESeq2 R scripts for host and symbiont transplant experiment

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

KOG-MWU R scripts for host and symbiont natural populations

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

Symbiont and chlorophyll data for transplant experiment

Workbook containing spreadsheets for symbiont and chlorophyll metrics and bleaching responses from the transplant experiment.

Studivan-and-Voss_symbiont_chlorophyll.xlsx

R script for symbiont and chlorophyll analyses

R script containing statistical analyses and visualization of symbiont and chlorophyll metrics from transplant experiment.

Studivan-and-Voss_symbiont_chlorophyll_script.R

Temperature and light data for transplant experiment

Workbook containing datasheets for truncated temperature and light data, summary statistics, and raw logger data from transplant experiment.

Studivan-and-Voss_temp_light.xlsx

R script for temperature and light analyses

R script containing statistical analyses and visualization of temperature and light data from transplant experiment.

Studivan-and-Voss_temp_light_script.R

Funding

National Oceanic and Atmospheric Administration, Award: NA09OAR4320073,NA11NOS4780045,NA14OAR4320260

Florida Atlantic University