Antoine Branca

Position: Lecturer
Detailed position: U-PSUD Lecturer HDR

Team: Evolutionary genetics and ecology

Contact details:
Laboratoire Écologie, Systématique, Évolution
Bât. 360, rue du Doyen André Guinier
91405 Orsay Cedex

Tel: +33 (0)1 69 15 49 91


Email: antoine.branca (at)

Laboratoire Ecologie, Systématique et Evolution

Research interests

  • Host-parasite coevolution
  • Population genomics
  • Comparative genomics
  • Evolutionary Ecology

Current topic of research :

Adaptation of Penicillium molds to fermented food

Cheese is a fermented food product that is the result of the transformation of milk by a variety of microorganisms. Two Penicillium fungi are used for the maturation of cheese:

  • Penicillium roqueforti, the blue mould, used for producing blue cheese
  • Penicillium camemberti, the white mold, used for the production of Camembert-type cheese.

Dry-cured meat is also a fermented food product that make use of two Penicillium species to give some protection against spoiling agents and produce flavours:

  • Penicillium nalgiovense, is an industrial species

We use comparative genomics to understand the genetic basis of parallel adaptation of these four species to fermented food products.

We also use population genomics to unravel the history of domestication of Penicillium roqueforti (

For media coverage see :

New-York Times
Le Monde (in french)
France Inter (Radio interview in french)

The genetic basis of gall induction by gall wasps (Hymenoptera:Cynipidae)

Gall wasps are little insects that are capable of inducing the formation of differentiated tissue by their host plants.

Hence, the gall gives a shelter and food for the larvae of the wasp.

I was recently awarded a young researcher 4-year grant (ANR JCJC) to start working on the genetic basis of gall induction

Laboratoire Ecologie, Systématique et Evolution

Career path

Since Sept. 2012 Lecturer/Assistant Professor at Laboratoire Ecologie, Systématique et Evolution in OrsayTopic: Population and comparative genomics of cheese fungi
Oct. 2010 – Aug. 2012 Post Doc at the Institute for Evolution and Biodiversity, in Münster, Germany in Evolutionary Bioinformatics Group, Prof. Erich Bornberg-Bauer; Research Scientist of the DFG-SPP “Host Parasite Coevolution”Topic: Population genomics of Bacillus thuringiensis/ Caenorhabditis elegans host-parasite experimental coevolution
Jun. 2009 – Aug. 2010 Post Doc at the University of Minnesota, Department of Plant Biology in Saint-Paul in the group of Dr. Peter TiffinTopic: Analysis of the pattern of diversity of Medicago truncatula and his associated Sinorhizobium symbionts
Feb. 2009 PhD degree at the Université Pierre et Marie Curie in ParisTopic: Ecological diversification of the African parasitoid Cotesia sesamiae: Role of symbiotic partners
Sep. 2005 – Feb. 2009 PhD studies under the supervision of Dr. Stéphane Dupas at the Laboratory Evolution, Genome and Speciation in Gif-sur-Yvette
Laboratoire Ecologie, Systématique et Evolution


Journal articles


  • Branca Antoine, Le Ru Bruno, Calatayud Paul-André, Obonyo Julius, Musyoka Boaz, Capdevielle-Dulac Claire, Kaiser-Arnauld Laure, Silvain Jean-François, Gauthier Jérémy, Paillusson Corentin, Gayral Philippe, Herniou Elisabeth A., Dupas Stéphane 2019 “Relative Influence of Host, Wolbachia, Geography and Climate on the Genetic Structure of the Sub-saharan Parasitic Wasp Cotesia sesamiae ” Frontiers in Ecology and Evolution 7 (309)


  • Fortuna, Taiadjana M, Alice Namias, Alodie Snirc, Antoine Branca, Michael E Hood, Christian Raquin, Jacqui A Shykoff, and Tatiana Giraud. 2018. “Multiple Infections, Relatedness and Virulence in the Anther-smut Fungus Castrating Saponaria Plants.” Molecular Ecology 27 (23): 4947–59. doi:10.1111/mec.14911
  • Dumas, Emilie, Alice Feurtey, Ricardo C Rodriguez de la Vega, Stéphanie Le Prieur, Alodie Snirc, Monika Coton, Anne Thierry, Emmanuel Coton, Mélanie Le Piver, Daniel Roueyre, Jeanne Ropars, Antoine Branca# and Tatiana Giraud#. 2018. “Independent Domestication Events in the Blue-Cheese Fungus Penicillium Roqueforti.” BioRxiv, 451773.


  • Badouin, Helene, Pierre Gladieux, Jerome Gouzy, Sophie Siguenza, Gabriela Aguileta, Alodie Snirc, Stéphanie Le Prieur, Celine Jeziorski, Antoine Branca, and Tatiana Giraud. 2017. “Widespread Selective Sweeps throughout the Genome of Model Plant Pathogenic Fungi and Identification of Effector Candidates.” Molecular Ecology 26 (7): 2041–62. doi: 10.1111/mec.13976
  • Kaiser, L, Stéphane Dupas, Antoine Branca, Elisabeth A Herniou, Catherine W Clarke, Claire Capdevielle-Dulac, Julius Obonyo, Romain Benoist, Jérémy Gauthier, and Paul-André Calatayud. 2017. “The Cotesia sesamiae Story: Insight into Host-Range Evolution in a Hymenoptera Parasitoid and Implication for Its Use in Biological Control Programs.” Genetica 145 (6): 455–68. doi:10.1007/s10709-017-9989-3


  • Greenwood, Jenny M, Alberto Lopez Ezquerra, Sarah Behrens, Antoine Branca, and Ludovic Mallet. 2016. “Current Analysis of Host–Parasite Interactions with a Focus on next Generation Sequencing Data.” Zoology 119 (4): 298–306. doi:10.1016/j.zool.2016.06.010


  • Ropars, J. *, Rodríguez de la Vega, R.C.*, López-Villavicencio, M., Gouzy, J., Sallet, E., Dumas, E., Lacoste, S., Debuchy, R., Dupont, J., Branca, A.#, Giraud T#. (2015) “Adaptive horizontal gene transfers between multiple cheese-associated fungi” Current Biology DOI:…
  • Masri, L.*, Branca, A.*, Sheppard, A.E.*, Papkou, A., Laehnemann, D., Günther, P.S., Prahl, S., Saebelfeld, M., Crain, P.R., Strauß, J., Hollensteiner, J., Liesegang, H., Brzuszkiewicz, E., Daniel, R., Michiels, N.K., Schulte,R.D., Kurtz, J., Rosenstiel, P., Telschow, A., Bornberg-Bauer, E., Schulenburg, H. (2015) “Host–Pathogen Coevolution: The Selective Advantage of Bacillus thuringiensis Virulence and Its Cry Toxin Genes?” PLoS Biology DOI: 10.1371/journal.pbio.1002169
  • Badouin, H., Hood, M. E., Gouzy, J., Aguileta, G., Siguenza, S., Perlin, M. H., Cuomo, C. A., Fairhead, C., Branca, A., Giraud, T. (2015). Chaos of rearrangements in the mating-type chromosomes of the anther-smut fungus Microbotryum lychnidis-dioicae. Genetics, 200(4), 1275-1284.
  • Gillot, G., Jany, J. L., Coton, M., Le Floch, G., Debaets, S., Ropars, J., López-Villavicencio, Dupont, J., Branca, A., Giraud, T., Coton, E. (2015). Insights into Penicillium roqueforti morphological and genetic diversity. PloS one, 10(6), e0129849.
  • Leforestier, D., Ravon, E., Muranty, H., Cornille, A., Lemaire, C., Giraud, T., Durel C.-E., Branca, A. (2015). Genomic basis of the differences between cider and dessert apple varieties. Evolutionary Applications.
  • Kaiser, L., Le Ru, B., Kaoula, F., Paillusson, C., Capdevielle?Dulac, C., Obonyo, J., Herniou, E., Jancek, S., Branca, A., Calatayud, P.-A., Silvain, J.-F., Dupas, S. (2015). Ongoing ecological speciation in Cotesia sesamiae, a biological control agent of cereal stemborers. Evolutionary Applications.


  • Dupas, S., Le Ru, B., Branca, A., Faure, N., Gigot, G., Campagne, P., Sezonlin, M., Ndemah, R., Ong’amo, G., Silvain, J. F. (2014). Phylogeography in continuous space: coupling species distribution models and circuit theory to assess the effect of contiguous migration at different climatic periods on genetic differentiation in Busseola fusca (Lepidoptera: Noctuidae). Molecular ecology, 23(9), 2313-2325.
  • Gladieux, P., Ropars, J., Badouin, H., Branca, A., Aguileta, G., Vienne, D. M., Rodríguez de la Vega, R.C.*, Branco, S., Giraud, T. (2014). Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Molecular ecology, 23(4), 753-773.
  • Cheeseman, K., Ropars, J., Renault, P., Dupont, J., Gouzy, J., Branca, A., Abraham, A.-L., Ceppi, M., Conseiller, E., Debuchy, R., Malagnac, F., Goarin, A., Silar, P., Lacoste, S., Sallet, E., Bensimon, A., Giraud, T., Brygoo, Y. (2014) “Multiple recent horizontal transfers of a large genomic region in cheese making fungi.” Nature Communications 5 2876. doi:10.1038/ncomms3876



  • O Ong’amo, G., Le Ru, B. P., Campagne, P., Branca, A., Calatayud, P.-A., Capdevielle-Dulac, C., Silvain, J.-F. (2012) “Genetic Diversity and Population Structure of Busseola segeta Bowden (Lepidoptera; Noctuidae): A Case Study of Host Use Diversification in Guineo-Congolian Rainforest Relic Area (Kenya)” 3(4) :1156-1170
  • Epstein, B., Branca, A., Mudge, J., Bharti, A. K., Briskine, R. T., Farmer, A. D., Sugawara, M., Young, N. D., Sadowsky, M. J., Tiffin, P. (2012) “Population genomics of the facultatively mutualistic bacteria Sinorhizobium meliloti and S. medicae” PLoS Genetics
  • Paape, T.D., Zhou, P., Branca, A., Briskine, R., T., Young, N.D., Tiffin, P. (2012) “Fine scale population recombination rates, hotspots and correlates of recombination in the Medicago truncatula genome” Genome Biology and Evolution 4 (5): 726-737


  • Branca, A., Paape, T.D., Zhou, P., Briskine, R., Farmer, A.D., Mudge, J., Bharti, A.K., Woodward, J.E., May, G.D., Gentzbittel, L., Ben, C., Denny, R., Sadowsky, M.J., Ronfort, J., Bataillon, T., Young, N.D., Tiffin, P. (2011) “Whole-genome nucleotide diversity, recombination,,linkage disequilibrium in the model legume Medicago truncatula” PNAS 108 (42) E864-E870
  • Branca, A. , Le Rü, B. P., Vavre F., Silvain J.-F., Dupas, S. (2011) “Intraspecific specialization of the generalist parasitoid Cotesia sesamiae revealed by polyDNAvirus polymorphism and associated with different Wolbachia infections.” Molecular Ecology 20 (5) 959–971



  • Faure N., Branca, A., Gigot, G., Dupas, S., Silvain, J-F. (2009) “Isolation and characterization of ten microsatellite loci in Cotesia sesamiae (Cameron) (Hymenoptera: Braconidae), a parasitoid of African stem borer pests.” Molecular Ecology Resources 9 (5) 1375-1379.
  • Branca, A., Vavre F., Silvain J.-F., Dupas, S. (2009) “Maintenance of adaptive differentiation by Wolbachia induced bidirectional cytoplasmic incompatibility: sib-mating and reproductive system matter.” BMC Evolutionary Biology 9:185.


  • Dupas, S., Gitau, C. W., Branca, A., Le Rü, B. P., Silvain, J.-F. (2008) ” Evolution of a Polydnavirus Gene in Relation to Parasitoid-Host Species Immune Resistance.” Journal of Heredity 99(5):491-499.



  • Branca, A., Dupas, S. (2006) ” A model for the study of Wolbachia pipientis Hertig(Rickettsiales:Rickettsiaceae)-induced cytoplasmic incompatibility in arrhenotokous haplodiploid populations: Consequences for biological control.” Annales de la Société entomologique de France 42:443-448.


  • Lopez-Villavicencio, M., Branca, A., Giraud, T., Shykoff, J. (2005) “Sex-specific effect of Microbotryum violaceum (Uredinales) spores on healthy plants of the gynodioecious Gypsophila repens (Caryophyllaceae).” American Journal of Botany 92: 896-900.

Book Chapters:

  • Branca, A., Gitau, C. W., Dupas, S. (2011) “Maintenance of specialized parasitoid populations through polyDNAviruses” In: Parasitoid Viruses: Symbionts and Pathogens (eds N. E. Beckage and J.-M. Drezen), Elsevier