• Appendix D
  • 1 WGS, mRNA-seq, and ChIP-seq
    • 1.1 WGS
    • 1.2 mRNA-seq
    • 1.3 ChIP-seq
  • 2 Transcriptomic Analyses
    • 2.1 Differential gene expression analysis
    • 2.2 WGCNA
  • 3 Allele-Specific Transcriptomic Analyses
    • 3.1 SNPs and transcripts
    • 3.2 POE gene lists
    • 3.3 192hpf WL & QL - allelic transcriptomics
      • 3.3.1 Block 1
      • 3.3.2 Block 2
    • 3.4 24hpf eggs - allelic transcriptomics
      • 3.4.1 Block 3
      • 3.4.2 Block 4
  • 4 ChIP-seq Analysis
    • 4.1 Enrichment across promoters and gene bodies
    • 4.2 Differential enrichment analysis
      • 4.2.1 H3K27me3
      • 4.2.2 H3K27ac
      • 4.2.3 H3K4me3
  • 5 Allele-Specific ChIP-seq Analyses
    • 5.1 SNPs and peaks
    • 5.2 POE peak lists
      • 5.2.1 H3K27me3
      • 5.2.2 H3K27ac
      • 5.2.3 H3K4me3
    • 5.3 H3K27me3
      • 5.3.1 Gene bodies
      • 5.3.2 Promoters
    • 5.4 H3K27ac
      • 5.4.1 Gene bodies
      • 5.4.2 Promoters
    • 5.5 H3K4me3
      • 5.5.1 Gene bodies
      • 5.5.2 Promoters
    • 5.6 Combined results
      • 5.6.1 Block 1
      • 5.6.2 Block 2
  • 6 HPTM-transcription dynamics
    • 6.1 H3K27me3
      • 6.1.1 Gene bodies
      • 6.1.2 Promoters
    • 6.2 H3K27ac
      • 6.2.1 Gene bodies
      • 6.2.2 Promoters
    • 6.3 H3K4me3
      • 6.3.1 Gene bodies
      • 6.3.2 Promoters
  • 7 POE HPTM enrichment-POE transcription dynamics
    • 7.1 Block 1
      • H3K27me3
      • H3K27ac
      • H3K4me3
    • 7.2 Block 2
      • H3K27me3
      • H3K27ac
      • H3K4me3
    • 7.3 Logistic regression
      • H3K27me3 (gene body)
      • H3K27me3 (promoter)
      • H3K27ac (gene body)
      • H3K27ac (promoter)
      • H3K4me3 (gene body)
      • H3K4me3 (promoter)
  • 8 GO enrichment analyses
    • 8.1 DEGs & POE genes
    • 8.2 WGCNA modules
    • 8.3 HPTM differentially enriched regions
  • 9 POE gene feature assessment
    • 9.1 Spatial clustering
    • 9.2 Intron feature analyses
      • Recombination rate
      • % intron
      • Intron GC
      • Intron CpG density
  • Published with bookdown

Supplementary Materials: Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)

Supplementary Materials: Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)

Sean T. Bresnahan, Shaun Mahony, Kate Anton, Brock Harpur, Christina M. Grozinger

2024-05-07