Embryogenesis is a brief but potentially critical phase in the tree life cycle for adaptive phenotypic plasticity. Using somatic embryogenesis in maritime pine, we found that temperature during the maturation phase affects embryo development and post-embryonic tree growth for up to three years. We examined whether this somatic stress memory could stem from temperature- and/or development-induced changes in DNA methylation. To do this, we developed a 200 Mb custom sequence capture bisulfite analysis of genes and promoters to identify differentially methylated cytosines (DMCs) between temperature treatments (18, 23, and 28 degrees C and developmental stages (immature and cotyledonary embryos, shoot apical meristem of 2-year-old plants) and investigate if these differences can be mitotically transmitted from embryonic to post-embryonic development (epigenetic memory). We identified ten genes involved in defense responses and adaptation, embryo development and chromatin regulation that are candidates for the establishment of a persistent epigenetic memory of temperature sensed during embryo maturation in maritime pine.

This work is part of the Supplementary Materials for the publication Trontin et al https://doi.org/10.1101/2024.06.27.600784

Here, we give the raw data for the 200 Mb custom sequence capture bisulfite (Sup Mat 2) with the sequence of the capture probes (Roche technology) with 3 BEd files corresponding to the capture of the 866 model genes, the promoters and all the Unigenes available on maritime Pine. These 3 subets of sequences are given in the 'reference sequence' file with 2 fasta files and one Bed file.

All the genes analaysez in this study have been evaluated for the Gene Ontology enrichement method (Sup Mat 3) using the software 'Metascape' (https://metascape.org/gp/index.html#/main/step1). The gene ID are given in one file and teh results of the metascape GO enrichement are given in the other file by sample analysis (type of plant matrerial : early somatic embryo, cotyledonary somatic embryo or shoot apical meristem of 2 years old tree) and temperature (18, 23 or 28°C).

Sup Mat 2 : Sequence capture design Sup Mat 3 : GO analysis with Metascape