Cristian Peña-Ponton

Cristian Peña-Ponton MSc

PhD Candidate
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Visiting Address

Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands



I am a PhD student working on the identification of DNA methylation and gene expression patterns induced by abiotic and biotic factors in the Lombardy poplar. I am specially focused in the study of drought and rust infection effects and their interaction.


I am from Ecuador, after finishing my Bachelor in Plant Biotechnology at Universidad de las Fuerzas Armadas UFA-ESPE (Ecuador), I worked part-time as plant tissue culture instructor at UFA-ESPE and part-time as teak micropropagation manager at Neoforests S.A.
Then, I discovered my passion for bioinformatics and moved to Australia where I obtained my Master's degree in Bioinformatics at the University of Melbourne. Next, I returned to Ecuador and became a lecturer of bioinformatics and plant tissue culture at UFA-ESPE.
In 2018, I started my PhD at the NIOO-KNAW in the Terrestrial Ecology Department and at the University of Wageningen in the Nematology Department. My doctoral project is part of the European Training Network EPIDIVERSE funded by the EU Horizon 2020 program under Marie Skłodowska-Curie actions.
During my PhD, I have had the opportunity to perform two secondments in Germany: Leipzig University and Philipps-Universität Marburg, where I have received training in bioinformatics, whole genome bisulfite sequencing and data integration.

Research groups


Peer-reviewed publications

  • PLoS ONE

    Herbivory induced methylation changes in the Lombardy poplar

    A. Niloya Troyee, Cristian Peňa, Mónica Medrano, Koen Verhoeven, Conchita Alonso

    DNA cytosine methylation is an epigenetic mechanism involved in regulation of plant responses to biotic and abiotic stress and its ability to change can vary with the sequence context in which a cytosine appears (CpG, CHG, CHH, where H = Adenine, Thymine, Cytosine). Quantification of DNA methylation in model plant species is frequently addressed by Whole Genome Bisulfite Sequencing (WGBS), which requires a good-quality reference genome. Reduced Representation Bisulfite Sequencing (RRBS) is a cost-effective potential alternative for ecological research with limited genomic resources and large experimental designs. In this study, we provide for the first time a comprehensive comparison between the outputs of RRBS and WGBS to characterize DNA methylation changes in response to a given environmental factor. In particular, we used epiGBS (recently optimized RRBS) and WGBS to assess global and sequence-specific differential methylation after insect and artificial herbivory in clones of Populus nigra cv. 'italica'. We found that, after any of the two herbivory treatments, global methylation percentage increased in CHH, and the shift was detected as statistically significant only by epiGBS. As regards to loci-specific differential methylation induced by herbivory (cytosines in epiGBS and regions in WGBS), both techniques indicated the specificity of the response elicited by insect and artificial herbivory, together with higher frequency of hypo-methylation in CpG and hyper-methylation in CHH. Methylation changes were mainly found in gene bodies and intergenic regions when present at CpG and CHG and in transposable elements and intergenic regions at CHH context. Thus, epiGBS succeeded to characterize global, genome-wide methylation changes in response to herbivory in the Lombardy poplar. Our results support that epiGBS could be particularly useful in large experimental designs aimed to explore epigenetic changes of non-model plant species in response to multiple environmental factors.
  • Journal of Evolutionary Biology

    Environmental and genealogical effects on DNA methylation in a widespread apomictic dandelion lineage

    Verónica Noé Ibañez, Morgane Van Antro, Cristian Peňa, Slavica Milanovic-Ivanovic, Niels C. A. M. Wagemaker, F. Gawehns, Koen Verhoeven
    DNA methylation in plant genomes occurs in different sequences and genomic contexts that have very different properties. DNA methylation that occurs in CG (mCG) sequence context shows transgenerational stability and high epimutation rate, and can thus provide genealogical information at short time scales. However, due to meta-stability and because mCG variants may arise due to other factors than epimutation, such as environmental stress exposure, it is not clear how well mCG captures genealogical information at micro-evolutionary time scales. Here, we analysed DNA methylation variation between accessions from a geographically widespread, apomictic common dandelion (Taraxacum officinale) lineage when grown experimentally under different light conditions. Using a reduced-representation bisulphite sequencing approach, we show that the light treatment induced differentially methylated cytosines (DMCs) in all sequence contexts, with a bias towards transposable elements. Accession differences were associated mainly with DMCs in CG context. Hierarchical clustering of samples based on total mCG profiles revealed a perfect clustering of samples by accession identity, irrespective of light conditions. Using microsatellite information as a benchmark of genetic divergence within the clonal lineage, we show that genetic divergence between accessions correlates strongly with overall mCG profiles. However, our results suggest that environmental effects that do occur in CG context may produce a heritable signal that partly dilutes the genealogical signal. Our study shows that methylation information in plants can be used to reconstruct micro-evolutionary genealogy, providing a useful tool in systems that lack genetic variation such as clonal and vegetatively propagated plants.

Projects & collaborations


EpiDiverse: Epigenetic contribution to phenotypic plasticity in Populus nigra


In long-lived sessile organisms such as trees, phenotypic plasticity is an important requirement for successful persistence in changing or variable environments. Epigenetic mechanisms have the potential to mediate long-term plastic responses to environmental change. However, the importance of epigenetic mechanisms such as DNA methylation as regulators of adaptive plasticity is not well known. In this project we will experimentally evaluate effects of stress exposure on DNA methylation, transposable element activity and gene expression in black poplar (Populus nigra), with the aim to (1) identify genomic loci that show stress-induced epigenetic modification with functional consequences, and (2) evaluate the temporal stability of such loci, for example across growing seasons. Making use of clonally propagated trees that have grown in contrasting environments, we will also investigate to what extent environment-induced epigenetic differences are transmitted to offspring via clonal propagation (cuttings) versus via sexual reproduction through seeds, using WGBS and epiGBS analysis. Experiments will be carried out in close interaction with other Populus nigra projects within the EpiDiverse consortium (at Marburg University, Germany and at the Institute of Applied Genomics, Udine, Italy).


  • Herbivory effects on the DNA methylome of the Lombardy poplar


    We collaborate with PhD student Anupoma Niloya Troyee, Dr. Conchita Alonso and Dr. Mónica Medrano from EBD-CSIC (Sevilla, Spain) to unravel the effects of natural and artificial herbivory on the DNA methylation variation. Our plant system is the Lombardy poplar and we mainly use epiGBS and WGBS technologies.


  • Natural and stress-induced methylation variation in the Lombardy poplar


    We collaborate with PhD student Bárbara Díez Rodríguez, Dr. Lars Opgenoorth and Dr. Katrin Heer from Philipps-Universität Marburg (Marburg, Germany) to identify and integrate DNA methylation patterns induced by natural and artificial environments. Our study system involves hundreds of clonal  Lombardy poplars collected from multiple European regions, and we mainly analyze WGBS, phenotypic and climate data.