FISH 546 - Compendium

A Differential Gene Expression analysis of Montipora capitata corals from two life-history stages DOI

Author

Sarah Tanja

Published

June 1, 2023

Overview

In this analysis, we are going to look at the differentially expressed genes, and their functions, between coral larvae and coral recruits. The data for this is borrowed from Dr. Ariana Huffmyer’s study on Montipora capitata Early Life History Energetics.

I will compare RNA expression between 4 larvae, and 4 recruits.

Two Pocillopora damicronis larvae floating against a black background. The larvae are torpedo-shaped, and have a brown core like a chocolate-filled eclair. The brown color is from the algal symbionts which enter the Pocillopora damicornis larvae before they are released during brooder spawning by adult corals.

Pocillopora damicornis larvae. E. Rivest/VIMS

Coral recruits like a small droplets of jelly with radial symmetry speckle a black background.

Coral recruits. Heyward & Negri, AIMS

End Goal

The end goal of this analysis is to develop a heatmap that shows the top 20 differentially expressed gene functions between the coral larvae life stage and the coral recruit life stage.

Code Pipeline

Step 1. Get Sequence & Genome Data using curland wget

Step 2. Align Sequences to a Genome using kallisto

Step 3. Identify Differential Gene Expression using DESeq2

Step 4. Annotate the Reference Transcriptome using UniProt and BLAST

Step 5. Merge the Annotated Transcriptome with the List of Differentially Expressed Genes

Step 6. Visualize the Top Differentially Expressed Genes and their Functions