Long-term m5C methylome dynamics parallel phenotypic adaptation in the cyanobacterium Trichodesmium [RNA-seq]

Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS) and RNA-Seq (i.e. transcriptomics) to examine the long-term epigenomic dynamics of an experimenta evolution study under high CO2 in the marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly change in response to short-term high CO2 exposure, which are then maintained for 4.5 years even after adaptation (i.e. trait canalization). After 7 years of CO2 selection, high-CO2 triggered methylation levels return to ancestral, low-CO2 levels, consistent with genetic assimilation theory and observations in eukaryotic model systems. These data suggest a potential role for m5C methylation in prokaryotic trait canalization and identify genetic assimilation as an evolutionary mechanism of potential biogeochemical importance under global change factors. Overall design: Experimental design can be found at Walworth, N. G., Lee, M. D., Fu, F.-X., Hutchins, D. A., & Webb, E. A. (2016). Molecular and physiological evidence of genetic assimilation to high CO2 in the marine nitrogen fixer Trichodesmium. Proceedings of the National Academy of Sciences of the United States of America, 201605202–8. http://doi.org/10.1073/pnas.1605202113. For whole-genome bisulfite samples (WGBS), we sampled the founding ancestral population (T0). We then sampled WGBS biological replicates 4.5 years later (another time point near the time of Walworth et al. PNAS 2016) from the 380-selected cell lines (adapted to low-CO2), the 380s-to-750 cell lines (380-selected cell lines transferred to 750 µatm CO2 to 2 weeks), the 750-selected cell lines (adapted to high CO2), and the 750s-to-380 cell lines (750-selected cell lines transferred to 380 µatm CO2 for 2 weeks). Here, we also sequenced two biological replicate samples for RNA-Seq for all treatments at this time point (n=4 treatments). The 380-selected an 380s-to-750 raw reads can be found in another GEO project with accession number GSE86992. Within the GSE86992, the specific samples for the 380-selected and 380s-to-750 have sample accession numbers of GSM2318497, GSM2318498, GSM2318499, GSM2318500. The rest of the RNA-Seq samples and their metadata are below. Both these RNA samples and the GSE86992 samples were sampled simultaneously. Finally, we sampled for WGBS again 2.5 years later for both the 380-selected cell lines (adapted to low-CO2) and 750-selected cell lines (adapted to high CO2). All WGBS metadata is described in the other spreadsheet associated with this accession number