Skip to content

Investigate the role of mtDNA in the sex determination/development of Potamilus streckersoni, a freshwater mussel with doubly uniparental mitochondrial inheritance. Scripts for DESeq2, WGCNA, GSEA, AlphaFold/AlphaPulldown, and mt-sncRNA validation.

Notifications You must be signed in to change notification settings

raqmejtru/mitonuclear-sd

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

38 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Mitonuclear sex determination/development in Potamilus streckersoni

This project investigates the role of mitochondrial DNA in the sex determination/development of Potamilus streckersoni, a freshwater mussel with doubly uniparental mitochondrial inheritance.

Analyses

This repository hosts scripts for the following analyses:

  • differential gene expression (DESeq2)

  • weighted gene co-expression network analysis (WGCNA)

  • gene set enrichment analysis (GSEA)

  • protein-protein interaction prediction (AlphaFold & AlphaPulldown)

  • mitochondrial short-non coding RNA validation

Analyses were performed by running analysis_workflow.R, and results were synthesized into the visualizations presented below.

Data visualizations


Figure 1
Figure 1. Overview of doubly uniparental mitochondrial inheritance in bivalves. Adapted from Breton et al. (2018).


Figure 2
Figure 2. A) Volcano plot representing differential gene expression across female and male gonadal samples of Potamilus streckersoni. B) Dendrogram of modules from a weighted gene co-expression network. Heat map visualizes the correlation between the eigengene of each module and whether the gonadal sample is female or male.


Figure 3
Figure 3. Gene set enrichment of Hallmark Pathways. Pathways with negative NES values contain genes with female-biased expression, while pathways with positive NES values contain genes with male-biased expression. All shown pathways showed significant enrichment (p-adj < 0.05) in female (orange) and male (blue) gonadal tissue.



Figure 4
Figure 4. A) Volcano plots highlighting the differential expression of genes that are targeted by F and M mitochondrial short non-coding RNAs (mt-sncRNAs). B) Heat map visualizes sncRNAs expressed from mitochondria that were isolated from female and male gonadal samples. The log10 counts per million of each mt-sncRNA are mean-centered, such that a sample with average expression is represented in white.


Figure 5
Figure 5. GCNT1 protein network as predicted by STRING based on the Potamilus streckersoni proteome. Gray lines represent known interactions based on database and experimental evidence. Genes are colored based on expression profiles between female (orange) and male (blue) gonadal tissue with density representing higher differences in gene expression between female and male gonadal tissue. Dark gray coloration represents genes with no expression. Asterisks indicated genes with significant differences in expression (p-adj < 0.05). Protein names with the suffix ‘-like’ are hypothetical and annotated as their best KEGG-hit when applicable. Protein names with an underscore represent protein products from genes with multiple annotated copies.

About

Investigate the role of mtDNA in the sex determination/development of Potamilus streckersoni, a freshwater mussel with doubly uniparental mitochondrial inheritance. Scripts for DESeq2, WGCNA, GSEA, AlphaFold/AlphaPulldown, and mt-sncRNA validation.

Topics

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published