TY - JOUR
T1 - High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive transposable element superfamilies in the clonal Lombardy poplar
AU - Peña-Ponton, Cristian
AU - Diez-Rodriguez, Barbara
AU - Perez-Bello, Paloma
AU - Becker, Claude
AU - McIntyre, Lauren M.
AU - van der Putten, Wim H.
AU - De Paoli, Emanuele
AU - Heer, Katrin
AU - Opgenoorth, Lars
AU - Verhoeven, Koen J.F.
N1 - Data archiving: NIOO data, komt nog in portal
PY - 2024/9/27
Y1 - 2024/9/27
N2 - DNA methylation is environment-sensitive and can mediate stress responses. In trees, changes in the environment might cumulatively shape the methylome landscape over time. However, because high-resolution methylome studies usually focus on single environmental cues, the stress-specificity and long-term stability of methylation responses remain unclear. Here, we studied the methylome plasticity of a Populus nigra cv. ‘Italica’ clone widely distributed across Europe. Adult trees from different geographic locations were clonally propagated in a common garden experiment and exposed to cold, heat, drought, herbivory, rust infection, and salicylic acid treatments. Whole-genome bisulfite sequencing revealed stress-induced and naturally occurring DNA methylation variants. In CG/CHG contexts, the same genomic regions were often affected by multiple stresses, suggesting a generic methylome response. Moreover, these variants showed striking overlap with naturally occurring methylation variants between trees from different locations. Drought treatment triggered CHH hypermethylation of transposable elements, affecting entire superfamilies near drought-responsive genes. Thus, we revealed genomic hotspots of methylation change that are not stress-specific and that contribute to natural DNA methylation variation, and identified stress-specific hypermethylation of entire transposon superfamilies with possible functional consequences. Our results underscore the importance of studying multiple stressors in a single experiment for recognizing general versus stress-specific methylome responses.
AB - DNA methylation is environment-sensitive and can mediate stress responses. In trees, changes in the environment might cumulatively shape the methylome landscape over time. However, because high-resolution methylome studies usually focus on single environmental cues, the stress-specificity and long-term stability of methylation responses remain unclear. Here, we studied the methylome plasticity of a Populus nigra cv. ‘Italica’ clone widely distributed across Europe. Adult trees from different geographic locations were clonally propagated in a common garden experiment and exposed to cold, heat, drought, herbivory, rust infection, and salicylic acid treatments. Whole-genome bisulfite sequencing revealed stress-induced and naturally occurring DNA methylation variants. In CG/CHG contexts, the same genomic regions were often affected by multiple stresses, suggesting a generic methylome response. Moreover, these variants showed striking overlap with naturally occurring methylation variants between trees from different locations. Drought treatment triggered CHH hypermethylation of transposable elements, affecting entire superfamilies near drought-responsive genes. Thus, we revealed genomic hotspots of methylation change that are not stress-specific and that contribute to natural DNA methylation variation, and identified stress-specific hypermethylation of entire transposon superfamilies with possible functional consequences. Our results underscore the importance of studying multiple stressors in a single experiment for recognizing general versus stress-specific methylome responses.
KW - Abiotic stress
KW - biotic stress
KW - differentially methylated region
KW - drought
KW - Lombardy poplar
KW - Melampsora larici-populina
KW - Populus nigra
KW - short interspersed nuclear element (SINE)
KW - whole genome bisulfite sequencing (WGBS)
U2 - 10.1093/jxb/erae262
DO - 10.1093/jxb/erae262
M3 - Article
AN - SCOPUS:85205363105
SN - 0022-0957
VL - 75
SP - 5839
EP - 5856
JO - Journal of Experimental Botany
JF - Journal of Experimental Botany
IS - 18
ER -