Epigenetic changes associated with real-time mobilization of transposable elements in grapevine embryogenic cells

As is generally the case for eukaryotes, the coding portion of the grapevine genome is dwarfed by an abundance of repetitive DNA sequences, known as transposable elements (TEs). These sequences have accumulated throughout evolutionary history as a result of their mobilisation and replication, restructuring their genetic and epigenetic environments in the process. Recently, systems have been identified in plants by which the mutagenic activity of transposons is specifically suppressed in gametes1. However, the clonal propagation of agricultural crops by cuttings allows the indefinite accumulation of somatic TE-derived mutations, which have led to valuable new phenotypes2. To study endogenous TE activity in real-time, we regenerated a population of ‘Pinot noir’ grape vines from totipotent somatic embryogenic callus cultures, some of which had been treated with environmental stressors. Whole-genome resequencing of 20 of these plants revealed a high degree of TE polymorphism in comparison with the parental material. Transposon mobility was not limited to stressed cultures and new insertions were attributed to, a diverse range of TE types contributed to the new insertions. We identified new insertions from eight out of nine TE superfamilies, with helitrons the exception. Epigenetic silencing is thought to have arisen as a host response to the mutagenic capacity of TEs3. We therefore used bisulphite sequencing to compare the epigenetic states of TEs in embryogenic callus (EC) versus vegetative material (young leaves). Obvious differences, particularly at transposable elements, were observed between the two tissue types. Although CpG methylation of TEs was high in both tissues, a decrease in inherited CHG methylation was observed across TEs that were situated within genes in EC tissue. Furthermore, CHH methylation, which must be applied de novo after each cell division was high in EC tissue, but almost absent in leaf tissue. CHH methylation was particularly high across those TE families responsible for the highest number of new mutations. These results provide the first real-time evidence, that TE-derived mutagenesis is not a rare phenomenon limited to specific TE families, but is characteristic of the dynamic nature of a diverse section of the mobilome, as indicated by historical genomic data4. Much of the mobilome retain mutagenic capacity which can be released in certain tissues. In the case of grapevine, the totipotent state of embryogenic callus is associated with a reduction of epigenetic silencing in TEs particularly within genes. This is accompanied by the accumulation of new TE insertions and de novo methylation of active TE families