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Epigenetic Diversity in Ecology

Deliverables

Recruitment: vacancies advertised
EpiDiverse publications in open access repositories
Final open conference

Final open conference in Seville or alternatively in online format if an inperson meeting in Seville is not possible due to Covid19

Fact sheets and email list

Ecological Epigenetics fact sheets and email list

Publications

EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics

Author(s): Adam Nunn, Sultan Nilay Can, Christian Otto, Mario Fasold, Bárbara Díez Rodríguez, Noé Fernández-Pozo, Stefan A Rensing, Peter F Stadler, David Langenberger
Published in: NAR Genomics and Bioinformatics, Issue Volume 3, Issue 4, 2021, ISSN 2631-9268
Publisher: Oxford Academic

ANCHOR: A Technical Approach to Monitor Single-Copy Locus Localization in Planta

Author(s): Anis Meschichi; Mathieu Ingouff; Claire Picart; Marie Mirouze; Sophie Desset; Franck Gallardo; Kerstin Bystricky; Nathalie Picault; Stefanie Rosa; Frédéric Pontvianne
Published in: Frontiers in Plant Science, Issue 3, 2021, ISSN 1664-462X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fpls.2021.677849

DNA Methylation Can Mediate Local Adaptation and Response to Climate Change in the Clonal Plant Fragaria vesca: Evidence From a European-Scale Reciprocal Transplant Experiment

Author(s): Sammarco Iris; Münzbergová Zuzana; Latzel Vít
Published in: Frontiers in Plant Sciene, Issue 3, 2022, ISSN 1664-462X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fpls.2022.827166

epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS‐based reduced representation bisulfite sequencing

Author(s): Gawehns, F; Postuma, M; van Antro, M; Nunn, A; Sepers, B; Fatma, S; van Gurp, TP; Wagemaker, CAM; Mateman, AC; Milanovic-Ivanovic, S; Grosse, I; van Oers, K; Vergeer, P; Verhoeven, KJF
Published in: Molecular Ecology Resources, Issue 3, 2022, ISSN 1755-0998
Publisher: Wiley-Blackwell
DOI: 10.1111/1755-0998.13597

Playing with genetic and epigenetic concepts at the school: an Epigenetic Orchestra project

Author(s): Conchita Alonso; Yolanda Palomares
Published in: Evolution: Education and Outreach, Issue 5, 2021, ISSN 1936-6434
Publisher: BioMed Central Ltd
DOI: 10.1186/s12052-021-00146-y

Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis

Author(s): Adam Nunn, Christian Otto, Peter F Stadler, David Langenberger
Published in: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbab021

A Blind and Independent Benchmark Study for Detecting Differentially Methylated Regions in Plants

Author(s): Kreutz, Clemens; Can, Sultan Nilay; Schulze Bruening, Ralf; Meyberg, Rabea; Merai, Zsuzsanna; Fernandez-Pozo, Noe; Rensing, Stefan A.
Published in: BIOINFORMATICS, Issue 3, 2020, ISSN 1460-2059
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa191

Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response

Author(s): Ariadna Picart-Picolo, Stefan Grob, Nathalie Picault, Michal Franek, Christel Llauro, Thierry Halter, Tom R. Maier, Edouard Jobet, Julie Descombin, Panpan Zhang, Vijayapalani Paramasivan, Thomas J. Baum, Lionel Navarro, Martina Dvořáčková, Marie Mirouze, Frédéric Pontvianne
Published in: Genome Research, Issue 30/11, 2020, Page(s) 1583-1592, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.261586.120

Epigenetics in plant organismic interactions

Author(s): Daniela Ramos-Cruz, A. Niloya Troyee, Claude Becker
Published in: Current Opinion in Plant Biology, Issue 61, 2021, Page(s) 102060, ISSN 1369-5266
Publisher: Elsevier BV
DOI: 10.1016/j.pbi.2021.102060

The role of plant epigenetics in biotic interactions

Author(s): Conchita Alonso, Daniela Ramos‐Cruz, Claude Becker
Published in: New Phytologist, Issue 221/2, 2018, Page(s) 731-737, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.15408

Epigenetic targeting of transposon relics: beating the dead horses of the genome?

Author(s): Sammarco Iris; Pieters Janto; Salony Susnata; Toman Izabela; Zolotarov Grygoriy; Lafon Placette Clément
Published in: Epigenetics, Issue 4, 2022, ISSN 1559-2308
Publisher: Taylor & Francis
DOI: 10.1080/15592294.2021.2022066

The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline

Author(s): Sultan Nilay Can, Adam Nunn, Dario Galanti, David Langenberger, Claude Becker, Katharina Volmer, Katrin Heer, Lars Opgenoorth, Noe Fernandez-Pozo and Stefan A. Rensing
Published in: Epigenomes, 2021, ISSN 2075-4655
Publisher: MDPI

Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Author(s): Adam Nunn, Isaac Rodríguez-Arévalo, Zenith Tandukar, Katherine Frels, Adrián Contreras-Garrido, Pablo Carbonell-Bejerano, Panpan Zhang, Daniela Ramos Cruz, Katharina Jandrasits, Christa Lanz, Anthony Brusa, Marie Mirouze, Kevin Dorn, David W Galbraith, Brice A. Jarvis, John C. Sedbrook, Donald L. Wyse, Christian Otto, David Langenberger, Peter F. Stadler, Detlef Weigel, M. David Marks, James A.
Published in: Plant Biotechnology Journal, 2022, Page(s) pp 1-20, ISSN 1467-7652
Publisher: Wiley on line publishers
DOI: 10.1111/pbi.13775

Plant epigenetics: phenotypic and functional diversity beyond the DNA sequence

Author(s): MT Boquete; A Muyle; C Alonso
Published in: American Journal of Botany, Issue 5, 2021, ISSN 1537-2197
Publisher: Botanical Society of America
DOI: 10.1002/ajb2.1645

Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response

Author(s): Picart-Picolo, Ariadna; Grob, Stefan; Picault, Nathalie; Franek, Michal; Llauro, Christel; Halter, Thierry; Maier, Tom R.; Jobet, Edouard; Descombin, Julie; Zhang, Panpan; Paramasivan, Vijayapalani; Baum, Thomas J.; Navarro, Lionel; Dvořáčková, Martina; Mirouze, Marie; Pontvianne, Frédéric
Published in: https://hal-univ-perp.archives-ouvertes.fr/hal-02962580, Issue 3, 2021, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.5167/uzh-196601

ecc_finder: A Robust and Accurate Tool for Detecting Extrachromosomal Circular DNA From Sequencing Data

Author(s): Marie Mirouze; Panpan Zhang; Christel Llauro; Hoaran Peng; Etienne Bucher
Published in: Frontiers in Plant Science, Issue 3, 2021, ISSN 1664-462X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fpls.2021.743742

A Critical Guide for Studies on Epigenetic Inheritance in Plants

Author(s): Daniela Ramos Cruz, Claude Becker
Published in: Plant Epigenetics and Epigenomics - Methods and Protocols, Issue 2093, 2020, Page(s) 261-270, ISBN 978-1-0716-0178-5
Publisher: Springer US
DOI: 10.1007/978-1-0716-0179-2_18

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