echille / genotype_dominates_transcriptomic_response_pacu Goto Github PK

Erin E. Chille (1), Timothy G. Stephens (1), Deeksha Misri (2), Emma L. Strand (3), Hollie M. Putnam (3), and Debashish Bhattacharya (1)

1. Department of Biochemistry and Microbiology, Rutgers University; New Brunswick, NJ 08901, USA.
2. Department of Genetics, Rutgers University, New Brunswick, NJ 08901, USA.
3. Department of Biological Sciences, University of Rhode Island; Kingston, RI 02881, USA.

This repository provides data and scripts to analyze Monitpora capitata and Pocillopora acuta gene expression across two months of exposure to thermal and/or low pH stress conditions. This analysis provides genotype-controlled gene expression data characterizing the population-level response to stress of colonies inhabiting the sheltered Kāneʻohe Bay, Hawaiʻi. The RNA-seq data are available from NCBI’s SRA repository (BioProject: PRJNA731596). Genome assemblies and predicted genes are available from http://cyanophora.rutgers.edu/montipora/ (Version 3) and http://cyanophora.rutgers.edu/Pocillopora_acuta/ (Version 2). Read processing scripts are available at https://doi.org/10.5281/zenodo.8077955. The color score data and scripts are available at https://github.com/hputnam/Acclim_Dynamics.

Transcriptome data are frequently used to investigate coral bleaching, however, the factors controlling gene expression in natural populations of these species is poorly understood. We studied two corals, Montipora capitata and Pocillopora acuta, that inhabit the sheltered Kāneʻohe Bay, Hawaiʻi. M. capitata colonies in the bay are outbreeding diploids, whereas P. acuta is a mixture of clonal diploids and triploids. Populations were sampled from six reefs and subjected to thermal and pH stress. RNA-seq data were generated to test two competing hypotheses: 1) gene expression is largely independent of genotype, reflecting a shared treatment-driven response (TDE) or, 2) genotype dominates gene expression, regardless of treatment (GDE). Our results strongly support the GDE model, even under severe stress. We suggest that post-transcriptional processes (e.g., control of translation, protein turnover) modify the signal from the transcriptome, and may underlie the observed differences in coral bleaching sensitivity via the downstream proteome and metabolome.

Execute all scripts in Rproj and knit to project

This repository is organized by Genome_Info, Manuscript, Output, Sample_Info, and Scripts.

Sample_Info includes data table summarizing sample metadata. Genome_Info includes transcript count matrices and relevant genomic data (e.g. functional annotations). Scripts and Output include all R scripts and results, respectively from all gene expression analyses. Manuscript includes all final figures and produced for the associated manuscript.

Any questions about this project and the contents of this repository can be directed to Erin Chille at erin_chille (at) scarletmail.rutgers.edu.