Whole organism integrated DNA methylation and transcriptomics analysis of butterfly metamorphosis

Metamorphosis is one of the most fascinating developmental processes in the natural world. The underlying molecular events resulting in the transformation of a caterpillar into a butterfly, including the epigenetic and transcriptomic programs, remain elusive. By integrating DNA and RNA long-read sequencing of the entire body of five consecutive stages from larval to late-pupal development in a laboratory butterfly, we characterise the fundamental metabolic and developmental transitions taking place. We identify a progression from lipid metabolism in larvae towards an up-regulation of muscle formation and mitochondrial energy generation in pupae. Intra-genic CpG methylation correlates with, but does not appear to dictate, gene expression. The level of 5-hydroxymethlcytosine modification detected was very low. The use of long-read mRNA sequencing provided access to complete transcript isoform sequences, and differential isoform usage was notably detected in genes for energy metabolism, and for muscle and neural development during the metamorphic process.