#Outline

##Introduction

- Start with phenotypic plasticity? Or go right into epigenetics and DNA methylation?
- DNA methylation in general
- DNA methylation in invertebrates: gene body methylation - functions, potential role in phenotypic plasticity
- DNA methylation in corals and why it is of interest: potential basis of phenotypic plasticity/acclimatization/resilience to env change
- Introduce objectives of the study: explore patterns of germline methylation in coral transcriptomes and env response genes

##Methods

- Description of datasets, including table
- Description of methods used to annotate transcriptomes
- Description of methods used to calculate CpG and analyze graphically/statistically

##Results

- For each species, compare CpG O/E of whole-transcriptome to env response genes. 
    - For each species, show density plot with env response gene profile superimposed over transcriptome CpG O/E
      - Compare density profiles statistically using some kind of bootstrapping technique
  - For each species, show bar plot of CpG O/E by GOslim bin for both whole transcriptome and env response genes
  - Show summary plot with ranking of GOslim bin by mean CpG O/E

###Discussion

- This content will become more clear once results are complete, however likely topics include hypotheses for patterns of germline methylation in transcriptomes and env response genes.