Chargée de Recherche

CEFE
Campus du CNRS
1919, route de Mende
34293 Montpellier 5

aline.muyle[at]cefe.cnrs.fr

Twitter @Aline_Muyle

Mastodon @This email address is being protected from spambots. You need JavaScript enabled to view it.

ResearcheGate

Linkedin

Workshops

I teach a 3 days workshop on the analysis of DNA methylation : https://instats.org/seminar/analysis-of-dna-methylation2?source=social

Research

I study plant epigenetics and genetics using bioinformatic approaches. I investigate how separate sexes and sex chromosomes evolve and how epigenetics can impact this evolution.

I work mostly on the Silene genus (Caryophyllaceae). In the past I have worked on rice, maize, strawberry and Arabidopsis thaliana.

Currently supervised Students

Suzie Tallon (2024-present, PhD student co-supervised with Thomas Lenormand).

Mathias Laizé (2022-present, PhD student co-supervised with Pierre-André Crochet).

Past students and Postdocs

Alexis Ryo David (2024, M1 student in Evolutionary Ecology at Poitiers University, co-supervised with Mathilde Dufaÿ).

Mattéo Todaro (2024, L2 student in Montpellier University, co-supervised with Mathilde Dufaÿ).

Vanina Tonzo (2023-2024, Postdoc co-supervised with Patrik Nosil).

Lila Maladesky (2023, M2 MEME student, co-supervised with Thomas Lenormand).

Eddy Mendoza-Galindo (2023, M1 MEME student).

Paul Jay (2016, Master internship at LBBE, Université Lyon 1, co-supervised with Gabriel Marais and Jos Käfer).

Cécile Fruchard (2014, Master internship at LBBE, Université Lyon 1, co-supervised with Gabriel Marais).

Brief CV (full version here)

Education
2012 – 2015: PhD in Biology, LBBE (Laboratoire de Biométrie et Biologie Évolutive), Université Lyon 1.
2011 – 2012: Agrégation SVSTU, ENS Lyon (Ecole Normale Supérieure), National rank: 2nd.
2009 – 2011: Master’s degree in Biosciences, ENS Lyon, rank: 1st.
2008 – 2009: Licence in fundamental Biology, ENS Lyon.
2006 – 2008: Classe préparatoire BCPST, Lycée du Parc, Lyon.

Research experiences
September 2022 – Present: CNRS researcher, CEFE, Montpellier.
May 2021 – August 2022: CNRS researcher, LBBE, Lyon.
November 2017 – April 2021: Postdoctoral position under the supervision of Brandon Gaut, University of California Irvine.
October 2015 – September 2017: Postdoctoral position under the supervision of Gabriel Marais, LBBE, Lyon, France.
September 2012 – September 2015: PhD under the supervision of Gabriel Marais, LBBE, Lyon, France.
February – June 2011: Master’s internship under the supervision of Gabriel Marais, LBBE, Lyon, France.
February – December 2010: Master’s internships under the supervision of Sylvain Glémin, ISEM, Montpellier, France.
June – July 2009: Licence internship under the supervision of Mathilde Dufay, GEPV, Lille, France.

Fellowships and Scholarships
November 2018 – April 2021: HFSP Postdoctoral Fellowship.
February 2018 – October 2018: EMBO Postdoctoral Long Term Fellowship.
2008-2015: Élève normalienne, ENS Lyon, France.

Awards
November 2021: Paoletti’s Award, CNRS, France.
June 2019: Dean’s Early Career Research Excellence Award, UCI, USA.
June 2019: FASEB travel award, Mobile DNA Conference, Palm Springs, USA.
October 2016: L’Oréal-UNESCO for Women in Science, encouraging talents, Paris, France.
July 2015: Walter M. Fitch Award, Society for Molecular Biology and Evolution (SMBE), Vienna, Austria.

Ongoing funding
2024-2029: Coordinator of the ANR JCJC IMPRINT. The project aims to study genomic imprinting and separate sexes evolution.
2024-2029: Collaborator on Thomas Lenormand’s ERC project on the evolution of cis and trans-regulators in eukaryotes (acronym RegEvol).
2024-2029: Collaborator on Patrice DAVID’s ANR project on fast Renewed Inbreeding Depression in Animals (acronym FRIDA).

Academic service
01/2024-present: Treasurer of the SMBE.
01/2024-present: Membre de la section 23 du comité national du CNRS.

Publications

Preprints

• Moraga C, Branco C, Rougemont Q, Veltsos P, Jedlička P, Muyle A, Hanique M, Tannier E, Liu X, Mendoza-Galindo E, et al. 2023. The Silene latifolia genome and its giant Y chromosome. BioRxiv 2023.09.21.558754.
• Prentout D*, Muyle A*, Zemp N, Filali A el, Boussau B, Touzet P, Widmer A, Käfer J, Marais GAB. 2023. Evolution of sex-biased gene expression during transitions to separate sexes in the Silene genus. BioRxiv 2023.10.02.560480. (* co-first authors).

Articles

• Martin GT, Solares E, Guadardo-Mendez J, Muyle A, Bousios A, Gaut BS. 2023. miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression. Genome Research 33:1932–1946. PubMed PMID: 37918960.
• Song Y, Peng Y, Liu L, Li G, Zhao X, Wang X, Cao S, Muyle A, Zhou Y, Zhou H. 2023. Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes. Horticulture Research uhad252.
• Aline Muyle, Gabriel Marais, Václav Bačovský, Roman Hobza, Thomas Lenormand. 2022. Dosage compensation in plants: theories, controversies, mechanisms and emerging evolutionary patterns. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 377, 20210222. PubMed PMID: 35306896.
• Aline Muyle, Danelle Seymour, Yuanda Lv, Bruno Huettel, Brandon Gaut. 2022. Gene-body methylation in plants: mechanisms, functions and important implications for understanding evolutionary processes. Genome Biol. Evol. evac038. PubMed PMID: 35298639.
• Muyle A, Ross-Ibarra J, Seymour DK, Gaut BS. 2021. Gene body methylation is under selection in Arabidopsis thaliana. Genetics 218:iyab061. PubMed PMID: 33871638. Featured in Genetics Highlights.
• Muyle A, Seymour D, Darzentas N, Primetis E, Gaut BS, Bousios A. 2021. Gene capture by transposable elements leads to epigenetic conflict in maize. Molecular Plant 14:237–252. PubMed PMID: 33171302.
• Muyle A, Bachtrog D, Marais GAB, Turner JMA. 2021. Epigenetics drive the evolution of sex chromosomes in animals and plants. Philosophical Transactions of the Royal Society B 376:20200124. PubMed PMID: 33866802.
• Muyle A*, Martin H*, Zemp N, Mollion M, Gallina S, Tavares R, Silva A, Bataillon T, Widmer A, Glémin S, Touzet P, Marais GA. 2021. Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus Silene. Molecular Biology and Evolution 38:805–818. PubMed PMID: 32926156. (* co-first authors).
• Boquete MT, Muyle A, Alonso C. 2021. Plant epigenetics: phenotypic and functional diversity beyond the DNA sequence. American Journal of Botany 108:553–558. PubMed PMID: 33887061.
• He L, Jia K-H, Zhang R-G, Wang Y, Shi T-L, Li Z-C, Zeng S-W, Cai X-J, Wagner ND, Hörandl E, Muyle A, Yang K, Charlesworth D, Mao JF. 2021. Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7. Molecular Ecology Resources. PubMed PMID: 33609314.
• Fruchard C, Badouin H, Latrasse D, Devani RS, Muyle A, Rhoné B, Renner SS, Banerjee AK, Bendahmane A, Marais GAB. 2020. Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System. Genes (Basel) 11. PubMed PMID: 32668777.
• Massonnet M, Cochetel N, Minio A, Vondras AM, Muyle A, Lin J, Garcia JF, Zhou Y, Delledonne M, Riaz S, Figueroa-Balderas R, Gaut BS, Cantu D. 2020. The genetic basis of sex determination in grapevines. Nat Commun. 11, 2902. PubMed PMID: 32518223.
• Roessler K*, Muyle A*, Diez CM, Gaut GRJ, Bousios A, Stitzer MC, Seymour DK, Doebley JF, Liu Q, Gaut BS. 2019. The genome-wide dynamics of purging during selfing in maize. Nature Plants 5:980–990. PubMed PMID: 31477888. (* co-first authors).
• Muyle A. 2019. How different is the evolution of sex-biased gene expression between plants and animals? A commentary on: “Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb.” Annals of Botany 123:iv–v. PubMed PMID: 31282546.
• Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas P, Hudzieczek V, Hobza R, Vyskot B, et al. 2019. Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis annua. Genetics 212:815–835. PubMed PMID: 31113811.
• Martin H, Carpentier F, Gallina S, Godé C, Schmitt E, Muyle A, Marais GA, Touzet P. 2019. Evolution of young sex chromosomes in two dioecious sister plant species with distinct sex determination systems. Genome Biology and Evolution, doi: 10.1093/gbe/evz001. PubMed PMID: 30649306.
• Aline Muyle and Brandon S. Gaut. 2019. Loss of gene body methylation in Eutrema salsugineum is associated with reduced gene expression. Molecular Biology and Evolution 36:155–158. PubMed PMID: 30398664.
• Muyle, A.*, Zemp, N.*, Fruchard, C., Cegan, R., Vrana, J., Deschamps, C., Tavares, R., Picard, F., Hobza, R., Widmer, A., Marais, G. 2018. Genomic imprinting mediates dosage compensation in a young plant XY system. Nature Plants, 4(9):677–680. PubMed PMID: 30104649. Recommended by PCI Evol Biol. Highlighted in Nature Plants News and views: Bergero R. 2018. How to solve the gender expression gap. Nature Plants 4:637–638. (* co-first authors)
• Aline Muyle, Rylan Shearn , Gabriel Marais. 2017. The evolution of sex chromosomes and dosage compensation in plants (review). Genome Biology and Evolution, 9(3), 627–645. PubMed PMID: 28391324.
• Muyle, A., Käfer, J., Zemp, N., Mousset, S., Picard, F., Marais, G. 2016. SEX-DETector: a probabilistic approach to uncover sex chromosomes in non-model organisms. Genome Biology and Evolution, 29;8(8):2530-43. PubMed PMID: 27492231.
• Zemp, N., Tavares, R., Muyle, A., Charlesworth, D., Marais, G., Widmer, A. 2016. Evolution of sex-biased gene expression in a dioecious plant. Nature Plants, 2(11):16168. PubMed PMID: 27808231.
• Blavet, N.*, Blavet, H.*, Muyle, A.*, Kafer, J., Cegan, R., Deschamps, C., Zemp, N., Mousset, S., Aubourg, S., Bergero, R., Charlesworth, D., Hobza, R., Widmer, A., Marais, G. 2015. Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia. BMC Genomics, 16:546. PubMed PMID: 26223308. (* co-first authors)
• Sylvain Glémin and Aline Muyle. 2014. Mating systems and selection efficacy: a test using chloroplastic sequence data in Angiosperms. Journal of Evolutionary Biology, 27(7):1386-99. PubMed PMID: 24674012.
• Aline Muyle*, Niklaus Zemp*, Clothilde Deschamps, Sylvain Mousset, Alex Widmer, and Gabriel A. B. Marais. 2012. Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes. PLoS Biology, 10(4):e1001308. PubMed PMID: 22529744. (* co-first authors). Selected by F1000 and part of the Editors’ choice.
• Aline Muyle, Laurana Serres-Giardi, Adrienne Ressayre, Juan Escobar, and Sylvain Glémin. 2011. GC-biased gene conversion and selection affect GC content in the Oryza genus (rice). Molecular Biology and Evolution, 28(9):2695–2706. PubMed PMID: 21504892.

Peer-reviewed book chapters

• Aline Muyle and Gabriel Marais. 2016. Breeding systems and genome evolution in plants. In R. Kliman (head editor), Encyclopedia of Evolutionary Biology, 1st Edition, Elsevier.
• Yongfeng Zhou, Aline Muyle and Brandon Gaut. 2019. Evolutionary Genomics and the Domestication of Grapes. The grape genome, Springer.

Chargée de Recherche

My research interests include mechanisms that promote phenotypic variation as well as potential for and constraints on adaptation, framing those questions at the edge between evolutionary and conservation biology. 

Read more: Céline TEPLITSKY

Chargé de Recherche
Evolutionary genetics and genomics.   My main current researchinterests include evolution in spatially structured populations, evolution of ageing, and evolution of reproductive modes. I combine experiments with the analysis of NGS data. My main empirical study systems are the small crustaceans Daphnia and Artemia.   christoph.haag[at]cefe.cnrs.fr

Read more: Christoph HAAG

Directeur de Recherche / Senior scientist

I study the evolution of adaptive diversity, using colour patterns in butterflies as a model. In my group, we integrate many different approaches, including ecology, genetics, and modelling, to try and untangle how multiple factors influence the evolution and maintenance of diversity and polymorphisms.

This email address is being protected from spambots. You need JavaScript enabled to view it.

Read more: Mathieu JORON