Epigenetic divergence of key genes associated with water temperature and salinity in a highly invasive model ascidian

Invasive species offer good models for studying mechanisms of response to rapid changing environments in the wild. DNA methylation is considered to be one of crucial drivers for rapid local adaptation. However, the extent of epigenetic variation and the factors driving such variation remain largely unexplored in biological invasions. Here we used direct bisulfite sequencing to investigate DNA methylation patterns of five key genes corresponding to two important environmental factors in marine ecosystems, water temperature and salinity, in a model invasive ascidian Ciona robusta (=C. intestinalis spA). Our results clearly showed that DNA methylation mainly occurred in gene bodies, rather than promoters, at regions with low values of CpG O/E. We detected significant variation of DNA methylation among populations in two genes (heat shock protein 90 and Na+-K+-2Cl(-) cotransporter). Interestingly, significant correlation was detected between methylation levels and the two environmental factors at some CpGs in these two genes. When the data of all CpGs was subjected to principal component analysis, individuals were assigned back to their population orgins. All the results suggest that environmental factors likely contribute, at least partially, to the observed DNA methylation variation. Such variation, either by some loci alone or through gene networks, might be involved in rapid local adaptation during biological invasions.