Methylome changes in Lolium perenne associated with long-term colonisation by the endophytic fungus Epichloë sp. Lp TG-3 strain AR37

Flavia Pilar Forte; Marta Malinowska; Istvan Nagy; Jan Schmid; Paul Dijkwel; David E Hume; Richard D Johnson; Wayne R Simpson; Torben Asp

doi:10.3389/fpls.2023.1258100

Methylome changes in Lolium perenne associated with long-term colonisation by the endophytic fungus Epichloë sp. Lp TG-3 strain AR37

Front Plant Sci. 2023 Sep 22:14:1258100. doi: 10.3389/fpls.2023.1258100. eCollection 2023.

Authors

Flavia Pilar Forte¹, Marta Malinowska¹, Istvan Nagy¹, Jan Schmid^{2

3}, Paul Dijkwel², David E Hume⁴, Richard D Johnson⁴, Wayne R Simpson⁴, Torben Asp¹

Affiliations

¹ Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Aarhus, Denmark.
² Ferguson Street Laboratories, Palmerston North, New Zealand.
³ School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
⁴ AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.

Abstract

Epichloë spp. often form mutualistic interactions with cool-season grasses, such as Lolium perenne. However, the molecular mechanisms underlying this interaction remain poorly understood. In this study, we employed reduced representation bisulfite sequencing method (epiGBS) to investigate the impact of the Epichloë sp. LpTG-3 strain AR37 on the methylome of L. perenne across multiple grass generations and under drought stress conditions. Our results showed that the presence of the endophyte leads to a decrease in DNA methylation across genomic features, with differentially methylated regions primarily located in intergenic regions and CHH contexts. The presence of the endophyte was consistently associated with hypomethylation in plants across generations. This research sheds new light on the molecular mechanisms governing the mutualistic interaction between Epichloë sp. LpTG-3 strain AR37 and L. perenne. It underscores the role of methylation changes associated with endophyte infection and suggests that the observed global DNA hypomethylation in L. perenne may be influenced by factors such as the duration of the endophyte-plant association and the accumulation of genetic and epigenetic changes over time.

Keywords: DNA methylation; Epichloë sp.; Lolium perenne; artificial association; drought stress; endophytic fungi; generation effect; plant-microbe interactions.

Grants and funding

The authors declare financial support was received for the research, authorship, and/or publication of this article. This study received funding from the European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie grant agreement number 676480, and Innovation Fund Denmark grant number 6150‐00020B.