Potato cytosine methylation and gene expression changes induced by a beneficial bacterial endophyte, Burkholderia phytofirmans strain PsJN

► We assess differential potato responses to a beneficial bacterial endophyte. ► Cytosine methylation and transcript differences occur with different responses. ► High plant responsiveness is associated with slight overall methylation changes. ► Poor plant responsiveness is associated with increased cytosine methylation. ► Different gene transcript levels vary between highly- and poorly-responsive plants.