Transcriptomic and DNA Methylation Profiles of Alternative Aphid Morphs and Genotypes

Pea aphids can develop alternative morphs when exposed to stressful conditions, showing differences between genotypes in their stress responses. Although several biological pathways regulating alternative morph production have been investigated, the role of epigenetic mechanisms remains understudied in genotype dependent stress responses. Understanding the underlying differences in stress response between aphid genotypes may provide clues to their adaptation. Here, we use RNA-seq and MBD-seq to analyse the transcriptome and DNA methylome profile of alternative morphs in two aphid lineages that differ in their life history and stress response. While most differentially expressed genes between morphs were linked to either wing development or stress responses, these expression differences were not associated with clear DNA methylation profiles. In addition, the transcriptome profile reveals some possible genes in the neuroendocrine pathway and histone modification that could play an important role in regulating the stress response between aphid genotypes. Overall, our study reveals both novel genes and pathways associated with polyphenism in aphids but finds no association between DNA methylation and gene expression.