The dataset consists of three comma-delimited plain text files corresponding to (i) Epigenotypic data of maternal modules, (ii) phenotypic data of maternal modules, and (iii) phenotypic data of the subprogenies obtained in the greenhouse, for different modules from adult, wild-grown, field-sampled plants of the shrub Lavandula latifolia (Lamiaceae). Five modules, each consisting of a terminal branchlet bearing one inflorescence and its subtending leaves, were collected from each of 15 wild-growing L. latifolia plants from a large population growing near Arroyo Aguaderillos in the Sierra de Cazorla (Jaén province, southeastern Spain; geographical coordinates 37.96157 N, 2.88389 W). Each module was characterized epigenotypically by the methylation state of methylation-sensitive amplified fragment length polymorphism markers (MS-AFLP), and phenotypically by fecundity-related traits (inflorescence length, and size, number and mass of seeds produced). Seeds from the different modules were sown in the greenhouse and resulting ‘subprogenies’ characterized phenotypically (germination probability and time to emergence, seedling size, susceptibility to fungal disease). For MS-AFLP data, each column refer to a specific (although anonymous) marker, identified by primer combination and size (base pairs)., This dataset includes three files containing (i) Epigenotypic data of maternal modules, (ii) phenotypic data of maternal modules, and (iii) phenotypic data of greenhouse subprogenies for different modules of 15 adult, wild-grown, field-sampled plants of the shrub Lavandula latifolia., Partial support for this study was provided by grants PID2019-104365GB-I00 (Ministerio de Ciencia e Innovación, Spanish Government) and P18-FR-4413 (Consejería de Transformación Económica, Industria, Conocimiento y Universidades, Andalusian Government)., Five modules, each consisting of a terminal branchlet bearing one inflorescence and its subtending leaves, were collected from each of 15 wild-growing L. latifolia plants from a large population growing near Arroyo Aguaderillos in the Sierra de Cazorla (Jaén province, southeastern Spain; geographical coordinates 37.96157 N, 2.88389 W). Each module was characterized epigenotypically by the methylation state of methylation-sensitive amplified fragment length polymorphism markers (MS-AFLP), and phenotypically by fecundity-related traits (inflorescence length, and size, number and mass of seeds produced). Seeds from the different modules were sown in the greenhouse and resulting ‘subprogenies’ characterized phenotypically (germination probability and time to emergence, seedling size, susceptibility to fungal disease). For MS-AFLP data, each column refer to a specific (although anonymous) marker, identified by primer combination and size (base pairs). Further details can be obtained in Herrera, Carlos M.; Medrano, Mónica; Bazaga, Pilar; Alonso, Conchita. 2022. Ecological significance of intraplant variation: epigenetic mosaicism in Lavandula latifolia plants predicts extant and transgenerational variability of fecundity-related traits. Journal of Ecology (in press)., Peer reviewed

Intraindividual epigenetic mosaicism is probably widespread among long-lived plants, yet its ecological significance as a potential source of variation in fitness-related traits in plant populations remains virtually unexplored. This paper examines the hypothesis that extant epigenetic variation within plants can have both current and transgenerational fecundity correlates which could eventually translate into fitness variations among different parts of the same individual and their respective offspring.
Five modules, each consisting of a terminal branchlet bearing one inflorescence and its subtending leaves, were collected from each of 15 wild-growing Lavandula latifolia (Lamiaceae) plants. They were characterized epigenotypically by the methylation state of methylation-sensitive amplified fragment length polymorphism (MS-AFLP) markers, and phenotypically by fecundity-related traits (inflorescence length, and size, number and mass of seeds produced). Seeds from the different modules were sown in the greenhouse and resulting ‘subprogenies’ characterized phenotypically (germination probability and time to emergence, seedling size, susceptibility to fungal disease).
All plants sampled were internally heterogeneous with regard to the methylation state of 1%–13% of MS-AFLP markers. Predictable relationships were found between epigenotypic and phenotypic variation across the extant modules of individual L. latifolia shrubs. Phenotypes of subprogenies from different modules of the same plant grown under homogeneous conditions in the greenhouse were predictably related to the epigenotype of the maternal module which produced the seeds.
Synthesis. The variable epigenotypes of different modules in the same plant not only predicted extant phenotypic variation among the modules themselves, but also phenotypic differences among the subprogenies produced by different modules. These relationships linking intraplant epigenotypic mosaicism with both extant and transgenerational heterogeneity in fitness-related traits support the ‘epigenetic mosaicism hypothesis’ for plant variation, and also suggest hitherto unexplored ecological consequences of epigenotypically enhanced variation in the context of plant populations and communities., Partial support for this work was provided by grants PID2019-104365GB-I00 (Ministerio de Ciencia e Innovación, Spanish Government) and P18-FR-4413 (Consejería de Transformación Económica, Industria, Conocimiento y Universidades, Andalusian Government)., Peer reviewed

Plant metabolic pathways and gene networks involved in the response to herbivory are well-established, but the impact of epigenetic factors as modulators of those responses is less understood. Here, we studied the role of DNA cytosine methylation on phenotypic responses after short-term herbivory in Thlaspi arvense plants with two contrasting flowering phenotypes. We investigated the effect of experimental demethylation and herbivory treatments following a 2x3 factorial design. First, half the seeds were submerged in a water solution of the demethylating agent 5-azacytidine and the other half only in water, as controls. Then, we assigned control and demethylated plants to three herbivory categories (i) insect herbivory, (ii) artificial herbivory, and (iii) undamaged plants. The effects of the demethylation and herbivory treatments were assessed by quantifying genome-wide global DNA cytosine methylation, concentration of leaf glucosinolates, final stem biomass, fruit and seed production, and seed size. For most of the plant traits analysed, individuals from the two plant-types responded differently. In late-flowering plants, global DNA methylation did not differ between control and demethylated plants but it was significantly reduced by herbivory. Conversely, in early-flowering plants, demethylation at seed stage was still evident in leaf genomes of reproductive individuals whereas herbivory did not affect their global DNA methylation. In late-flowering plants, artificial herbivory imposed a stronger reduction than insect herbivory in global DNA methylation and final stem biomass, and induced higher concentration of aliphatic glucosinolates. In early-flowering plants, the effects of herbivory were non-significant for the same traits. Finally, the effect of herbivory on reproductive parameters varied with the level of demethylation and the plant flowering-type. The complexity of our results suggests that the genetic background of experimental plants can affect the responses to treatments and it points towards multifaceted genetic-epigenetic interactions in determining herbivory-induced phenotypic plasticity., This work was supported and funded by the European Union’s Horizon 2020 research and innovation program via the Marie Sklodowska-Curie ETN ‘EpiDiverse’ (grant agreement No 764965) and CSIC Open Access Publication Support Initiative (Unit of Information Resources for Research). C.A. and M.M. were also supported by the Spanish Government through the Research Project ‘Epinter’ (PID2019-104365GB-I00, Ref.
619 AEI/10.13039/501100011033)., No

Plant metabolic pathways and gene networks involved in the response to herbivory are well-established, but the impact of epigenetic factors as modulators of those responses is less understood. Here, we use the demethylating agent 5-azacytidine to uncover the role of DNA cytosine methylation on phenotypic responses after short-term herbivory in Thlaspi arvense plants that came from two European populations with contrasting flowering phenotypes expected to differ in the response to experimental demethylation. The experimental design followed a 2 × 3 factorial design, that was replicated for each flowering-type. First, half the seeds were submerged in a water solution of 5-azacytidine and the other half only in water, as controls. Then, we assigned control and demethylated plants to three herbivory categories (i) insect herbivory, (ii) artificial herbivory, and (iii) undamaged plants. The effects of the demethylation and herbivory treatments were assessed by quantifying genome-wide global DNA cytosine methylation, concentration of leaf glucosinolates, final stem biomass, fruit and seed production, and seed size. For most of the plant traits analysed, individuals from the two flowering-types responded differently. In late-flowering plants, global DNA methylation did not differ between control and demethylated plants but it was significantly reduced by herbivory. Conversely, in early-flowering plants, demethylation at seed stage was still evident in leaf DNA of reproductive individuals whereas herbivory did not affect their global DNA methylation. In late-flowering plants, artificial herbivory imposed a stronger reduction than insect herbivory in global DNA methylation and final stem biomass, and induced higher concentration of aliphatic glucosinolates. In early-flowering plants, the effects of herbivory were non-significant for the same traits. Finally, the effect of herbivory on reproductive parameters varied with the level of demethylation and the plant flowering-type. Although further investigations with more populations and families are required to confirm our results, they suggest that the genetic background of experimental plants and timing of damage can affect the response to herbivory and point towards multifaceted genetic-epigenetic interactions in determining herbivory-induced phenotypic plasticity., This work was supported and funded by the European Union's Horizon 2020 research and innovation program via the Marie Sklodowska-Curie ITN ‘EpiDiverse’ (grant agreement No 764965). C.A. and M.M. were also supported by the Spanish Government through the Research Project ‘Epinter’ (PID2019-104365GB-I00, Ref. AEI/10.13039/501100011033)., Peer reviewed

Changes in epigenetic states can allow individuals to cope with environmental changes. If such
changes are heritable, this may lead to epigenetic adaptation. Thus, it is likely that in sessile
organisms such as plants, part of the spatial epigenetic variation found across individuals will
reflect the environmental heterogeneity within populations. The departure of the spatial epigenetic
structure from the baseline genetic variation can help in understanding the value of epigenetic
regulation in species with different breadth of optimal environmental requirements. Here we
hypothesize that in plants with narrow environmental requirements epigenetic variability should be
less structured in space given the lower variability in suitable environmental conditions. We
performed a multispecies study that considered seven pairs of congeneric plant species, each
encompassing a narrow endemic with habitat specialization and a widespread species. In three
populations per species we used AFLP and methylation-sensitive AFLP markers to characterise the
spatial genetic and epigenetic structures. Narrow endemics showed a significantly lower epigenetic
than genetic differentiation between populations. Within populations, epigenetic variation was less
spatially structured than genetic variation, mainly in narrow endemics. In these species, structural
equation models revealed that such pattern was associated to a lack of correlation between
epigenetic and genetic information. Altogether, these results show a greater decoupling of the
spatial epigenetic variation from the baseline spatial genetic pattern in endemic species. These
findings highlight the value of studying genetic and epigenetic spatial variation to better understand
habitat specialisation in plants., This work was supported by the Consejería de Innovación Ciencia y Empresa, Junta de Andalucía [P18-FR-4413] and the Ministerio de Ciencia e Innovación, Spanish Government [PID2019-104365GB-I00/AEI/10.13039/501100011033 and SUMHAL-LIFEWATCH-2019-09-CSIC-4, through European Regional Development Funds POPE 2014-2020]., Peer reviewed

In flowering plants, pollinators contribute to gene flow while they also respond to variation in plant traits together determined by genetic, epigenetic and environmental sources of variation. Consequently, a correlation between abundance and diversity of pollinators and the genetic and epigenetic characteristics of plant populations such as diversity or distinctiveness is expected. However, no study has explored these long-term dimensions of plant–pollinator interactions. Mediterranean narrow endemics often exhibit unexpectedly high levels of population genetic and epigenetic diversity. We hypothesize that pollinators may contribute to explain this pattern. Specifically, given the higher sensitivity of small, isolated population to gene flow, we expect a stronger association of pollinators with population genetic and epigenetic variability in narrow endemics than in widely distributed congeners. We studied five pairs of congeneric plant species, consisting of one narrow endemic with a restricted distribution and one widespread congener, found in the Sierra de Cazorla mountains (SE Spain). We characterized the pollinators in up to three populations per species to estimate their diversity and visitation rates. Additionally, we calculated the genetic and epigenetic diversity and distinctiveness of each population using AFLP markers and methylation-sensitive AFLP markers (MSAP), respectively. We assessed the relationship between pollinator diversity and visitation rates. The diversity of pollinators did not vary according to the plant´s distribution range, but visitation rate was higher in widespread species. As predicted, only narrow endemics showed a significant association between pollinators and their population genetic and epigenetic characteristics. Specifically, higher pollinator diversity and visitation rates entailed higher population genetic diversity and lower epigenetic distinctiveness. This work shows the importance of investigating the relationship between pollinator diversity and population genetics and epigenetics to better understand the evolution of plant rarity., This work was supported by the Consejería de Innovación Ciencia y Empresa, Junta de Andalucía [P18-FR-4413] and the Ministerio de Ciencia e Innovación, Spanish Government [PID2019-104365GB-I00/AEI/10.13039/501100011033 and SUMHAL, LIFEWATCH-2019-09-CSIC-4, through European Regional Development Funds POPE 2014-2020]., Peer reviewed

In flowering plants, pollinators contribute to gene flow while they also respond to variation in plant traits together determined by genetic, epigenetic and environmental sources of variation. Consequently, a correlation between abundance and diversity of pollinators and the genetic and epigenetic characteristics of plant populations such as diversity or distinctiveness is expected. However, no study has explored these long-term dimensions of plant–pollinator interactions. Mediterranean narrow endemics often exhibit unexpectedly high levels of population genetic and epigenetic diversity. We hypothesize that pollinators may contribute to explain this pattern. Specifically, given the higher sensitivity of small, isolated population to gene flow, we expect a stronger association of pollinators with population genetic and epigenetic variability in narrow endemics than in widely distributed congeners. We studied five pairs of congeneric plant species, consisting of one narrow endemic with a restricted distribution and one widespread congener, found in the Sierra de Cazorla mountains (SE Spain). We characterized the pollinators in up to three populations per species to estimate their diversity and visitation rates. Additionally, we calculated the genetic and epigenetic diversity and distinctiveness of each population using AFLP markers and methylation-sensitive AFLP markers (MSAP), respectively. We assessed the relationship between pollinator diversity and visitation rates. The diversity of pollinators did not vary according to the plant´s distribution range, but visitation rate was higher in widespread species. As predicted, only narrow endemics showed a significant association between pollinators and their population genetic and epigenetic characteristics. Specifically, higher pollinator diversity and visitation rates entailed higher population genetic diversity and lower epigenetic distinctiveness. This work shows the importance of investigating the relationship between pollinator diversity and population genetics and epigenetics to better understand the evolution of plant rarity., Junta de Andalucía : P18-FR-4413; Consejería de Innovación Ciencia y Empresa
Ministerio de Ciencia, Innovación y Universidades : PID2019- 104365GB-I00/AEI/10.13039/50110001103;
Ministerio de Ciencia, Innovación y Universidades : SUMHAL-LIFEWATCH-2019-09-CSIC-4, CSIC - European Regional Development Funds POPE 2014-2020, Peer reviewed

This dataset contains amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) data from geo-referenced plant individuals belonging to 14 plant species and up to three populations per species., Consejería de Innovación Ciencia y Empresa, Junta de Andalucía [P18-FR-4413]; Ministerio de Ciencia e Innovación, Spanish Government [PID2019-104365GB-I00/AEI/10.13039/501100011033]; Ministerio de Ciencia e Innovación, Spanish Government [SUMHAL-LIFEWATCH-2019-09-CSIC-4], Peer reviewed

1. Johannsen.dataset1.csv [line, class.seed.mother, mean.seed.progeny, stdev.seed.progeny, freq]

This dataset includes results of experiments for each pure line showing the mean and standard deviation of seed weight, broken down by the weight class of the initial mother seeds ("Muttersamen", 1901 crop) (Johannsen 1903, p. 21-24, tables Linie A through Linie T). Detailed information on the variables to be found in the original source., 2. Johannsen.dataset2.csv [line, class.seed.progeny, freq]

This dataset consists of the distribution of seeds among weight classes, separately for each pure line (Johannsen 1903, Uebersichtstabelle I, p. 25). Detailed information on the variables to be found in the original source., FocScales, PROMETEO-2021/040; EPINTER, PID2019-104365GB-I00, Peer reviewed

[Data availability] The bisulfite sequencing raw data is deposited in the ENA Sequence Read Archive Repository (https://www.ebi.ac.uk/ena/) under study accession numbers PRJEB51853 (https://www.ebi.ac.uk/ena/browser/view/PRJEB51853) and PRJEB51623 (https://www.ebi.ac.uk/ena/browser/view/PRJEB51623). The Populus nigra cv. ‘italica’ reference genome used is available also at ENA project PRJEB44889 (https://www.ebi.ac.uk/ena/browser/view/PRJEB44889). Extended methods (sample metadata; custom scripts, and other relevant data) will be given upon request from the corresponding author., DNA methylation is a key epigenetic mechanism in plants, reported to be involved in regulating responses and local adaptation to abiotic and biotic stressors that could be particularly beneficial for long-lived tree species. Given that climate change is predicted to promote insect outbreaks, epigenetic studies of herbivory responses in trees may be vital for forest management and conservation. Here, we study changes in DNA methylation in response to herbivory in the clonal tree Populus nigra cv. ‘italica’ (Lombardy poplar). Cuttings were collected from three distant geographical locations (Spain, Italy, Poland), clonally replicated and grown in a common environment. We used reduced representation bisulfite sequencing to assess methylation changes between three experimental categories: (i) insect and (ii) artificial herbivory, and (iii) undamaged plants. Our results indicate that DNA methylation in poplars from different provenance, despite being genetically very similar, responded differently to experimental herbivory with plant origin accounting for 17.2% of the variation across CG, CHG, and CHH contexts. Both insect and artificial herbivory induced a significantly higher response in CHH context. When we explore loci with contrasting methylation levels (differentially methylated cytosines, DMCs), Spanish poplars were the most responsive to insect damage while Polish trees to artificial herbivory. DMCs were primarily located in gene bodies and their flanking regions (CG, CHG) or intergenic regions (CHH). Further, about one-third of DMCs obtained in CHH context were associated with transposable elements (TEs). Our findings suggest that for a better understanding of the role of the epigenetics in plant responses to herbivory we may need to take into account history of exposure, and highlight the importance of incorporating epigenetic knowledge to manage natural forests and tree plantations to help them cope with their environmental challenges., Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This work was supported and funded by the European Union’s Horizon 2020 research and innovation program via the Marie Sklodowska-Curie ITN ‘EpiDiverse’ (grant agreement No 764965) < https://cordis.europa.eu/project/id/764965 >. C.A. and M.M. were also supported by the Spanish Government through the Research Projects ‘Epinter’ (PID2019-104365 GB-I00) and ‘Distepic’ (PID2022-141530NB-C21, Ministerio de Ciencia e Innovación)., Peer reviewed

There is mounting evidence that plant responses to environmental stress are mediated by epigenetic factors, including DNA methylation. Understanding relationships between DNA methylation, plant development and individual fitness in contrasting environments is key to uncover potential impacts of epigenetic regulation on plant adaptation. Here, we used an experimental approach combining controlled alteration of epigenetic features with exposure to stress.
Two provenances of Erodium cicutarium were exposed to a demethylating agent (5-azacytidine) and recurrent drought, and effects on above- and belowground phenotypic traits related to early development, phenology and fitness assessed.
Application of 5-azacytidine significantly reduced DNA methylation in leaf and root tissues. This slowed plant development, delayed flowering, and reduced the number of inflorescences produced, independent of water regime. Recurrent drought reduced final above- and belowground biomass and inflorescence production, regardless of the 5-azacytidine exposure. Increased fruit and seed-set were the only adaptations to drought in E. cicutarium, together with an increased number of flowers per inflorescence in water-stressed plants previously treated with 5-azacytidine.
Epigenetic effects can desynchronize plant growth, flowering and senescence in both favourable and adverse environments. Future studies should focus on understanding intraspecific variation in ability to change the plant methylome in response to stress, and transgenerational transmission of such responses., Financial support was provided by grants EPIECOL-CGL2013-43352-P, EPIENDEM-CGL2016-76605-P, EPINTER-PID2019-104365GB-I00 and DISTEPIC-PID2022-141530NB-C22 (Ministerio de Ciencia e Innovación, Spanish Government). We acknowledge support for the publication fee from the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI)., Peer reviewed

[Data availability] The E. cicutarium genomic data are publicly available at the NCBI genome repository under genome project accession JBDFRG000000000, with the raw reads hosted at the NCBI Sequence Read Archive (SRA) repository under accession number SRR28842229. Protein sequences used in the phylogenetic analysis are available at Supplementary Methods 2 in this journal. RNA-seq raw reads are available at the NCBI SRA repository under accession numbers SRR29751957-SRR29751979. Scripts to analyze the data are publicly available at GitHub (https://github.com/rmblazquez/erodium-cicutarium-Transcriptomics-ebd). All Supplementary Figures 1 to 6, Supplementary Methods 1 to 3, Supplementary Results 1 and Supplementary Tables 1 to 12 are available at https://doi.org/10.25387/g3.30621302., Epigenetic regulation, and particularly modifications in DNA methylation, plays critical roles in plant adaptation. DNA methylation inhibitors have been used to investigate the relationship between DNA methylation and plastic plant phenotypes. However, their effect in gene expression regulation throughout the lifetime remains understudied in nonmodel plants. Here, we analyze the effects of seed exposure to the hypomethylating agent 5-azacytidine (5-azaC) in plant transcriptome. Seeds of Erodium cicutarium were soaked in either a solution of 5-azaC in DMSO or water with DMSO (control, hereafter) before sowing. Subsequently, RNA was extracted from juvenile roots, juvenile leaves, and adult leaves, and their transcriptomes were sequenced. Differential gene expression analysis was performed between control and treated samples for all tissues together and separately, presuming that changes between treatments will be substantially weaker than among tissues and developmental stages. Beforehand, a draft genome of E. cicutarium was assembled as reference for the transcriptome analysis. We found that 5-azaC upregulated chromomethylase CMT1 across all treated samples, and domain rearranged DNA methyltransferase DRM2 in juvenile roots. Furthermore, adult leaves showed more differentially expressed genes between control and 5-azaC-treated samples compared to juvenile leaves. Finally, gene co-expression network analysis revealed a module of co-expressed genes with differential gene expression linked to 5-azaC treatment in juvenile roots, pointing toward activation of genes associated with transposable elements. These results show how experimental treatment with 5-azaC at seed stage has both short and long-term effects in the plant transcriptome, potentially broadening phenotype variation due to nondirectional effects of 5-azaC on gene expression., This study was supported by the Spanish Ministerio de Ciencia, Innovación y Universidades, through the “Proyectos de I+D+i” program, with references PID2019-104365GB-I00 and PID2022-141530NB-C22. We acknowledge support of the publication fee by the CSIC through its Open Access Publication Support Initiative developed by the Unit of Information Resources for Research (URICI)., Peer reviewed