Methylation and Gene Expression Differences Between Reproductive Castes of the Bumblbee, Bombus terrestris.

This is a repository for the code used in the following publication:
Marshall, H., Lonsdale, Z. N. & Mallon, E.B. (2019). Methylation and Gene Expression Differences Between Reproductive Castes of Bumblbee Workers. Evolution Letters. 3 (5); p485-499

Phenotypic plasticity is the production of multiple phenotypes from a single genome and is notably observed in social insects. Multiple epigenetic mechanisms have been associated with social insect plasticity, with methylation being explored to the greatest extent. Methylation is known to play a role in caste determination in Apis mellifera, and other social insects, but there is limited knowledge on it's role in other bee species. In this study we analysed whole genome bisulfite sequencing and RNA-seq data sets from head tissue of reproductive and sterile castes of the eusocial bumblebee Bombus terrestris.

Project Team:

This project is part of the work from the Social Epigenetics group at the Unviersity of Leicester, headed by Dr. Eamonn Mallon, see website. Data was generated by Hollie Marshall and Dr. Zoe Lonsdale. Dr. Hollie Marshall carried out all analyses.

Project Structure and Scripts

• Differential Expression
  • Read trimming and alignment (Cutadapt and STAR)
  • Read counting (HTSeq)
  • Differential expression (DEseq2)
  • Differential exon expression (DEXseq)
• Differenial Methylation
  • Read trimming and alignment (Bismark)
  • Methylation information extraction (Bismark)
  • Annotation of methyaltion calls with genomic features (custom R)
  • Differential methylation (MSC and methylKit)
  • Permutation (custom R and methylKit)
• GO Analysis
  • Blast to Drosophilia (Blast2GO)
  • Fisher's exact test (custom R)
• Comparative Analyses
  • Hypergeometric tests (custom R)
  • Honeybee reciprocal blast (Blast+ and custom R)
  • Methylation and expression comparison (custom R)

Additional Info

If you would like to use any of the custom code found here please cite this paper:

Citation: Marshall, H., Lonsdale, Z. N. & Mallon, E.B. (2019). Methylation and Gene Expression Differences Between Reproductive Castes of Bumblbee Workers. Evolution Letters. 3 (5); p485-499

If you have any questions/comments etc. feel free to contact me at:

• email: [email protected]
• twitter: @mooholl