Data from "Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar"

<strong>Data from : ‘Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar’</strong> An Vanden Broeck*, Tim Meese*, Pieter Verschelde, Karen Cox, Berthold Heinze, Dieter Deforce, Ellen De Meester and Filip Van Nieuwerburgh * These authors contributed equally. -------------------------------------------------- <strong>Background: </strong>Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar (<em>Populus nigra</em> cv. 'Italica' Duroi) offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome. <strong>Results: </strong>We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH-context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe any biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring’s’ phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment. <strong>Conclusions: </strong>Genome-wide cytosine methylation patterns in symmetrical GC-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in GC-context can be used as bio-markers to infer a common ancestor and thus to investigate the environmental history of a specific Lombardy poplar on short time-scales. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world. <strong>ADDITIONAL FILES</strong> 1. <strong>Additional file 1.</strong> CSV-file with information on the Lombardy poplar trees samples used for whole genome bisulfite sequencing (WGBS) in the two methylome experiments (<em>metadata</em>). The raw fastq datafiles obtained by whole genome bisulfite sequencing (WGBS) are available at the Gene Expression Omnibus (GEO) database (submission GSE225596). 2. <strong>Additional file 2. </strong>Zip-folder with html-files of the mapping and methylation statistics of the genomes of the 16 individual Lombardy poplar samples for the three sequence contexts (CpG, CHG, CHH) (bismark reports) (<em>processed data</em>). 3. <strong>Additional file 3</strong>. Zip-folder with: i) excel-files listing the genes in DMRs, and ii) PNG-files with the ‘Biological Coefficient of Variation (BCV)’-plots between any of the six pairwise comparisons of Lombardy poplars grouped per ortet and identified with Bioconductor package edgeR. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (<em>processed data</em>). 4. <strong>Additional file 4</strong>. EXCEL-file with the total list of GO terms that were enriched in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (<em>processed data</em>). 5. <strong>Additional file 5</strong>. Zip-folder with PNG-files representing heatmaps and excel-files with clustered GO terms significant over-represented in promoters and gene regions located in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively. The files were obtained with the Bioconductor package simplifyEnrichment (<em>processed data</em>). 6. <strong>Additional file 6. </strong>CSV-file with the raw data of the bud set observations in the common garden experiment (<em>raw data</em>). 7. <strong>Additional file 7. </strong>HTML-file with the R source codes to reproduce the results of the bud set analysis (<em>code,</em> <em>R script</em>). 8. <strong>Additional file 8. </strong>A text-file representing the Snakefile (i.e. a readable Python-based workflow) including the different steps and rules of the bioinformatics of the WGBS data analyses (<em>code, Snakefile</em>). 9. <strong>Additional file 9. </strong>RMD-file<strong> </strong>with the code to reproduce the analyses to identify differential methylated predefined regions (<em>code,</em> <em>R script</em>). 10. <strong>Additional file 10. </strong>includes the R-script with the code to reproduce the clustering and visualizing of the GO enrichment results (<em>code,</em> <em>R script</em>). -----------------------------------------------------------