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  • Twitter: @DrJulieFerreira
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52

Julie Ferreira de Carvalho


INRAE Researcher

Currently @UMR IGEPP : Institut de Génétique Environnement et Protection des Plantes (le Rheu)

Research interests

  • Studying the bases of phenotypic diversity and how plants cope with challenging and fluctuating environments is essential to improve resilience and sustainability of biological systems. Using complex polyploid plant models I investigate the functional and structural consequences of hybridisation and genome doubling on plant genomes in an evolutionary and ecological framework. As all Angiosperms have experienced at least one round of genome doubling and as most important crops have multiple sets of chromosomes, it is paramount to dive into their genomes in the light of this complex and redundant ecosystem. I have been interested in determining the molecular (genetic, epigenetic) bases of polyploid plant phenotypes and adaptation to various environmental cues (both abiotic and biotic). I utilize multidisciplinary approaches combining quantitative genetics, evolutionary biology, ecology, experimental and molecular biology, and bioinformatics to inform the genetic and epigenetic bases of polyploid speciation and tackle important questions in plant adaptation and evolution. In the last ten years, I pushed forward the knowledge frontier around three main questions:
    • What are the consequences of interspecific hybridization and polyploidy on genome organization, and how do these changes contribute to functional diversification and adaptation to the environment?
    • How important is epigenetics in fostering new functional traits and adapted phenotypes to contrasted environments and herbivory?
    • What is the extent of the unexplored diversity (structural variants, genetics and epigenetics) at the intraspecific and interspecific levels, and how much of this diversity could be harvested to enhance plant response to biotic and abiotic cues?

Scientific Skills

  • Comparative genomics and transcriptomics: Bioinformatics analyses, assemblies, annotations, differential gene transcription, SNP calling and identification of promoter regions and Transposable Elements
    • Phylogeny, Quantitative and Population Genetics: Neighbor Joining, Maximum Likelihood and Maximum Parsimony, Population structure, Genome Wide Association Studies, Genotyping analyses (DNA-Seq and DNA microarrays)
    • Bio-statistics and environments: Experimental designs (RCBD), parametric and non-parametric tests, linear models, mixed models. R programming, Rstudio, Galaxy and Unix, knowledge in Python programming
    • Molecular Biology: DNA, RNA extractions, cDNA synthesis, PCR, real-time quantitative PCR and derived methods, cloning and sequencing, library preparation for different sequencing platforms
    • Epigenomics: Bisulfite treatment and sequencing (WGBS, Epi-GBS), differential methylation level analyses, smallRNA extraction and analyses


Journal articles18 documents

  • Julie Ferreira de Carvalho, Solenn Stoeckel, Frédérique Eber, Maryse Lodé-Taburel, Marie-Madeleine Gilet, et al.. Untangling structural factors driving genome stabilization in nascent Brassica napus allopolyploids. New Phytologist, Wiley, 2021, 230 (5), pp.2072-2084. ⟨10.1111/nph.17308⟩. ⟨hal-03227311⟩
  • Julien Boutte, Loeiz Maillet, Thomas Chaussepied, Sébastien Letort, Jean-Marc Aury, et al.. Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa. Frontiers in Plant Science, Frontiers, 2020, 11, pp.577536. ⟨10.3389/fpls.2020.577536⟩. ⟨hal-03137565⟩
  • Thanina Azibi, Houria Hadj-Arab, Maryse Lodé-Taburel, Julie Ferreira de Carvalho, Gwenn Trotoux, et al.. Impact of whole genome triplication on the evolutionary history and the functional dynamics of regulatory genes involved in Brassica self-incompatibility signalling pathway. Sexual Plant Reproduction, Springer Verlag, 2020, 33 (1), pp.43-58. ⟨10.1007/s00497-020-00385-x⟩. ⟨hal-02784702⟩
  • Mathieu Rousseau-Gueutin, Caroline Belser, Corinne Da silva, Gautier Richard, Benjamin Istace, et al.. Long-read assembly of the Brassica napus reference genome Darmor-bzh. GigaScience, BioMed Central, 2020, 9 (12), pp.giaa137. ⟨10.1093/gigascience/giaa137⟩. ⟨hal-03283975⟩
  • Julie Ferreira de Carvalho, Jérémy Lucas, Gwenaëlle Deniot, Cyril Falentin, Olivier Filangi, et al.. Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica. Plant Journal, Wiley, 2019, 98 (3), pp.434-447. ⟨10.1111/tpj.14228⟩. ⟨hal-02019346⟩
  • Mariano Alvarez, Julie Ferreira de Carvalho, Armel Salmon, Malika L Ainouche, Armand Cavé-Radet, et al.. Transcriptome response of the foundation plant Spartina alterniflora to the Deepwater Horizon oil spill. Molecular Ecology, Wiley, 2018, 27 (14), pp.2986-3000. ⟨10.1111/mec.14736⟩. ⟨hal-01811051v2⟩
  • Koen Verhoeven, Eline Verbon, Thomas van Gurp, Carla Oplaat, Julie Ferreira de Carvalho, et al.. Intergenerational environmental effects: functional signals in offspring transcriptomes and metabolomes after parental jasmonic acid treatment in apomictic dandelion. New Phytologist, Wiley, 2018, 217 (2), pp.871-882. ⟨10.1111/nph.14835⟩. ⟨hal-03292207⟩
  • Julie Ferreira de Carvalho, Julien Boutte, Pierre Bourdaud, Houda Chelaifa, Kader Ainouche, et al.. Gene expression variation in natural populations of hexaploid and allododecaploid Spartina species (Poaceae). Plant Systematics and Evolution, Springer Verlag (Germany), 2017, 303 (8), pp.1061-1079. ⟨10.1007/s00606-017-1446-3⟩. ⟨hal-01631555⟩
  • Elsa Desnoues, Julie Ferreira de Carvalho, Constantin Zohner, Thomas Crowther. The relative roles of local climate adaptation and phylogeny in determining leaf-out timing of temperate tree species. Forest Ecosystems, Springer, 2017, 4 (1), ⟨10.1186/s40663-017-0113-z⟩. ⟨hal-03292321⟩
  • Lionel Morgado, Veronica Preite, Carla Oplaat, Sarit Anava, Julie Ferreira de Carvalho, et al.. Small RNAs Reflect Grandparental Environments in Apomictic Dandelion. Molecular Biology and Evolution, Oxford University Press (OUP), 2017, 34 (8), pp.2035-2040. ⟨10.1093/molbev/msx150⟩. ⟨hal-03292326⟩
  • Julien Boutte, Benoît Aliaga, Oscar Lima, Julie Ferreira de Carvalho, Abdelkader Aïnouche, et al.. Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima. G3, Genetics Society of America, 2016, 6 (1), pp.29--40. ⟨10.1534/g3.115.023242⟩. ⟨hal-01269912⟩
  • Julie Boutte, Julie Ferreira de Carvalho, Mathieu Rousseau-Gueutin, Julie Poulain, Corinne da Silva, et al.. Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae). Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2016, 8 (9), pp.3030-3044. ⟨10.1093/gbe/evw209⟩. ⟨hal-01412081⟩
  • Dalibor Huska, Ilia J. Leitch, Julie Ferreira de Carvalho, Andrew R. Leitch, Armel Salmon, et al.. Persistence, dispersal and genetic evolution of recently formed Spartina homoploid hybrids and allopolyploids in Southern England. Biological Invasions, Springer Verlag, 2016, 18 (8), pp.2137-2151. ⟨10.1007/s10530-015-0956-6⟩. ⟨hal-01371822⟩
  • Julie Ferreira de Carvalho, Carla Oplaat, Nikolaos Pappas, Martijn Derks, Dick de Ridder, et al.. Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants. BMC Genomics, 2016, 17 (1), ⟨10.1186/s12864-016-2524-6⟩. ⟨hal-03292408⟩
  • Julie Ferreira de Carvalho, Victor de Jager, Thomas van Gurp, Niels Wagemaker, Koen Verhoeven. Recent and dynamic transposable elements contribute to genomic divergence under asexuality. BMC Genomics, 2016, 17 (1), ⟨10.1186/s12864-016-3234-9⟩. ⟨hal-03292332⟩
  • Guillaume E. Martin, Mathieu Rousseau-Gueutin, Solenn Cordonnier, Oscar Lima, Sophie Michon-Coudouel, et al.. The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family. Annals of Botany, Oxford University Press (OUP), 2014, 113 (7), pp.1197-1210. ⟨10.1093/aob/mcu050⟩. ⟨hal-01061902⟩
  • Julie Ferreira de Carvalho, Julie Poulain, Corinne da Silva, Patrick Wincker, Sophie Michon-Coudouel, et al.. Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae). Heredity, Nature Publishing Group, 2013, 110 (2), pp.181-193. ⟨10.1038/hdy.2012.76⟩. ⟨hal-00797941⟩
  • Julie Ferreira de Carvalho, Houda Chelaifa, Julien Boutte, Julie Poulain, Arnaud Couloux, et al.. Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis. Plant Molecular Biology, Springer Verlag (Germany), 2013, 83 (6), pp.606. ⟨10.1007/s11103-013-0111-7⟩. ⟨hal-00943497⟩

Book sections2 documents

  • Mathieu Rousseau-Gueutin, Jean Keller, Julie Ferreira de Carvalho, Abdelkader Ainoüche, Guillaume Martin. The Intertwined Chloroplast and Nuclear Genome Coevolution in Plants. Plant Growth and Regulation - Alterations to Sustain Unfavorable Conditions, InTech Open, 2018, 978-1-78984-285-2. ⟨10.5772/intechopen.75673⟩. ⟨hal-02787510⟩
  • Malika L. Aïnouche, Houda Chelaifa, Julie Ferreira de Carvalho, Sidonie Bellot, Abdelkader Aïnouche, et al.. Polyploid evolution in Spartina: Dealing with highly redundant genomes. Pamela S. Soltis, Douglas E. Soltis. Polyploidy and Genome Evolution, Springer, pp.225-244, 2012, 978-3-642-31441-4. ⟨hal-01110233⟩

Conference papers25 documents

  • Mathieu Rousseau-Gueutin, Jérémy Lucas, France Denoeud, Julie Ferreira de Carvalho, Zhesi He, et al.. Structural and functional evolutionary dynamics of duplicated genes and genomes in nascent and natural B. napus. 21st Crucifer Genetics Conference on Brassica - Brassica 2018, Jul 2019, Saint-Malo, France. ⟨hal-03318226⟩
  • Mathieu Rousseau-Gueutin, Julie Ferreira de Carvalho, Jérémy Lucas, Gwenaëlle Deniot, Cyril Falentin, et al.. Co-evolution of chloroplast and nuclear genomes in flowering plants and impact of allopolyploidy on fine tune cytonuclear interactions.. International Conference on Polyploidy, Jun 2019, Ghent, Belgium. ⟨hal-03318182⟩
  • Mathieu Rousseau-Gueutin, Julie Ferreira de Carvalho, Solenn Stoeckel, Jérôme Morice, Marie-Madeleine Gilet, et al.. Impact of structural variations on the meiotic stability and plant fertility of the allotetraploid B. napus (oilseed rape). Second Joint Congress on Evolutionary Biology, Aug 2018, Montpellier, France. ⟨hal-03318231⟩
  • Julie Ferreira de Carvalho, Jérémy Lucas, Cyril Falentin, Gwenaëlle Deniot, Olivier Filangi, et al.. Cytonuclear interactions overcome inter-genomic conflict resulting from interspecific hybridization and genome doubling. Second Joint Congress on Evolutionary Biology, Aug 2018, Montpellier, France. ⟨hal-03318235⟩
  • Malika L. Aïnouche, Armand Cavé-Radet, Delphine Giraud, Alex Baumel, Blanca Gallego-Tévar, et al.. Genome merger and duplication as springboards for plant invasion: Lessons from Spartina. International Conference on Ecological Sciences, SFEcologie2018, SFEcologie, Oct 2018, Rennes, France. ⟨hal-02436817⟩
  • Mathieu Rousseau-Gueutin, Julie Ferreira de Carvalho, J. Lucas, F. Denoued, Fabrice Legeai, et al.. How a polyploid becomes a new species: example from the Brassica model.. International Conference on Environmental and Agronomical Genomics, 2018, Paris, France. ⟨hal-03318223⟩
  • Julie Ferreira de Carvalho, Thomas Chaussepied, Sébastien Letort, Anne-Marie Chèvre, Mathieu Rousseau-Gueutin. Structural and functional consequences of transposable elements after multiple Whole-Genome Duplication events. Dynamique des Génomes végétaux, 2018, Rennes, France. ⟨hal-03318224⟩
  • Christina L. Richards, Mariano Alvarez, Julie Ferreira de Carvalho, Armand Cavé-Radet, Abdelhak El Amrani, et al.. Transcriptomic responses to challenging environments in Spartina alterniflora populations. Workshop DYNAGEV2017, Jun 2017, Montpellier, France. ⟨hal-02435012⟩
  • Malika L. Aïnouche, Alex Baumel, Blanca Gallego-Tévar, Jesus Castillo, Mathieu Rousseau-Gueutin, et al.. Unending hybridization and polyploid speciation stories: Lessons from Spartina (Poaceae). XV OPTIMA Meeting, Organization for the Phyto-Taxonomic Investigation of the Mediterranean Area, Jun 2016, Montpellier, France. ⟨hal-02422822⟩
  • Malika L. Aïnouche, Houda Chelaifa, Mathieu Rousseau-Gueutin, Julien Boutte, Hélène Rousseau, et al.. Genome merger as evolutionary springboard: Insights from recurrent hybridization and polyploidy in Spartina. International Conference on Hybridization and Polyploidy (ICPHB-2016), Apr 2016, Rovinj, Croatia. ⟨hal-02422781⟩
  • Malika Ainouche, Mathieu Rousseau-Gueutin, Hélène Rousseau, Julien Boutte, Sidonie Bellot, et al.. Polyploidy, genome evolution and functional novelty in genus SpartinaI (Poaceae). International Conference « Evolution of Plant Phenotypes: from genomes to traits », Mar 2015, Barcelone, Spain. ⟨hal-01162082⟩
  • Armel Salmon, Julien Boutte, Julie Ferreira de Carvalho, Mathieu Rousseau-Gueutin, Malika Ainouche. The challenges of genomics in polyploidy Spartina species: How to deal with hybrid genomes and high redundancy?. PAG XXIII Plant and Animal Genome Conference, Jan 2015, San Diego, United States. ⟨hal-01162085⟩
  • Armel Salmon, Julien Boutte, Julie Ferreira de Carvalho, Mathieu Rousseau-Gueutin, Malika L. Aïnouche. The challenges of genomics in polyploidy Spartina species: How to deal with hybrid genomes and high redundancy?. PAG XXIII Plant and Animal Genome Conference, Jan 2015, San Diego, United States. ⟨hal-02422739⟩
  • Malika Ainouche, Julie Ferreira de Carvalho, Julien Boutte, Sidonie Bellot, Mathieu Rousseau-Gueutin, et al.. Recurrent polyploidy in the salt marsh genus Spartina: Lessons and challenges. PAG XXII Plant and Animal Genome Conference, Jan 2014, San Diego, United States. 1 p. ⟨hal-01108383⟩
  • Mariano Alvarez, Armel Salmon, Julie Ferreira de Carvalho, Malika Ainouche, Christina L. Richards. Transcriptomic response to hydrocarbon stress in Spartina alterniflora. International Conference on Invasive Spartina 2014, UMR CNRS 6553 ECOBIO, Jul 2014, Rennes, France. ⟨hal-01108408⟩
  • Armel Salmon, Julien Boutte, Julie Ferreira de Carvalho, Mathieu Rousseau-Gueutin, Malika Ainouche. The challenges of genomics in polyploid Spartina species: How to deal with hydrid genomes and high redundancy?. International Conference on Invasive Spartina 2014, Jul 2014, Rennes, France. ⟨hal-01108413⟩
  • Malika Ainouche, Armel Salmon, Mathieu Rousseau-Gueutin, Julien Boutte, Hélène Rousseau, et al.. Hybridation, polyploidie et evolution des génomes : le cas des spartines envahissant les marais salés. Colloque de lancement du Groupement de Recherches CNRS « Invasions Biologiques », UMR CNRS 6553 ECOBIO, Oct 2014, Rennes, France. ⟨hal-01108368⟩
  • Carine Charron, Mathieu Rousseau-Gueutin, Julie Ferreira de Carvalho, Houda Chelaifa, Julien Boutte, et al.. Bac sequencing analyses in the hexaploid Spartina maritime (Poaceae): Homoeolog divergence and microsynteny in the grass family. Réunion du groupe « Cytogénétique et Polyploïdie », May 2014, Clermont-Ferrand, France. ⟨hal-01108395⟩
  • Malika Ainouche, Houda Chelaifa, Julie Ferreira de Carvalho, Julien Boutte, Sidonie Bellot, et al.. Polyploidy speciation and genome evolution: Lessons from recent allopolyploids. XVIIth Evolutionary Biology Meeting, Sep 2013, Marseille, France. ⟨hal-01108428⟩
  • Julien Boutte, Benoit Aliaga, Julie Ferreira de Carvalho, Oscar Lima, Sophie Coudouel, et al.. Automatized detection of duplicated copies from NGS data: Application to 45S rDNA and coding genes in the hexaploid Spartina maritime (Poaceae). Rencontres ALPHY/PhyloSIB, Feb 2013, Lyon, France. ⟨hal-01108442⟩
  • Mathieu Rousseau-Gueutin, Guillaume Martin, Solene Cordonnier, Oscar Lima, Sophie Michon-Coudouel, et al.. Evolutionary dynamics of the chloroplast genome: Insights from comparative analyses in the legume family. Colloque « Génomique Environnementale », Nov 2013, Rennes, France. ⟨hal-01108884⟩
  • D. Huskaz, Julie Ferreira de Carvalho, Andrew Leitch, Malika Ainouche, Ales Kovarik. Population level study of genetic and epigenetic variability of rRNA genes in invasive species Spartina anglica. French Annual Polyploidy and Cytogenetics Meeting, May 2013, Rennes, France. ⟨hal-01108846⟩
  • Julie Ferreira de Carvalho, Julie Poulain, Corinne da Silva, Patrick Wincker, Sophie Coudouel, et al.. Ecological genomics of invasive polyploids: Case study from hexaploid and allo-dodecaploid Spartina species colonizing salt marshes. International Conference of Ployploidy, Hybridization and Biodiversity (ICPHB), May 2012, Pruhonice, Czech Republic. ⟨hal-01108907⟩
  • Malika L. Aïnouche, Houda Chelaifa, Julie Ferreira de Carvalho, Sidonie Bellot, Armel Salmon. Ecological genomics of the recent Spartina hybrids and allopolyploid invading salt-marshes. 13th Congress of the European Society for Evolutionary Biology, European Society for Evolutionary Biology, Aug 2011, Tübingen, Germany. ⟨hal-01108929⟩
  • Julie Ferreira de Carvalho, Houda Chelaifa, Jiri Macas, Oscar Lima, Sophie Coudouel, et al.. Vers la caractérisation des compartiments codant et répété du génome des spartines polyploïdes par séquençage en masse. Colloque « Biodiversité, Histoire des Espèces, Evolution des Génomes », Jun 2011, Rennes, France. ⟨hal-01108953⟩

Poster communications6 documents

  • Julie Ferreira de Carvalho, Julien Boutte, Loeiz Maillet, Thomas Chaussepied, Sébastien Letort, et al.. Functional consequences of transposable elements on duplicated gene transcription and retention in polyploid Brassica species. International Conference on Polyploidy, Jun 2019, Ghent, Belgium. ⟨hal-03318194⟩
  • Thanina Azibi, Mathieu Rousseau-Gueutin, Gwenn Trotoux, Maryse Lodé-Taburel, Julie Ferreira de Carvalho, et al.. Shift to self-compatibility in synthetic allopolyploid Brassica napus. 21st Crucifer Genetics Conference on Brassica - Brassica 2018, Jul 2018, Saint-Malo, France. ⟨hal-03318239⟩
  • Carine Charron, Mathieu Rousseau-Gueutin, Julie Ferreira de Carvalho, Houda Chelaifa, Julien Boutte, et al.. Bac sequencing analyses in the hexaploid Spartina maritime (Poaceae): Homoeolog divergence and microsynteny in the grass family. International Conference on Invasive Spartina 2014, Jul 2014, Rennes, France. 1 p., 2014. ⟨hal-01109652⟩
  • Julie Ferreira de Carvalho, Carine Charron, Houda Chelaifa, Julien Boutte, Mathieu Rousseau-Gueutin, et al.. The hexaploid Spartina maritime (Poaceae, Chloridoidea) genome: Composition and evolution in the grass family. Plant Genome Evolution Meeting, Sep 2013, Amsterdam, Netherlands. 2013. ⟨hal-01110188⟩
  • Julien Boutte, Benoit Aliaga, Julie Ferreira de Carvalho, Oscar Lima, Sophie Coudouel, et al.. Automatized detection of duplicated copies from NGS data: Application to 45S rDNA and coding genes in hexaploid Spartina species (Poaceae). International Conference of Ployploidy, Hybridization and Biodiversity (ICPHB), May 2012, Prague, Czech Republic. ⟨hal-01110201⟩
  • Julie Ferreira de Carvalho, Julie Poulain, Corinne da Silva, Patrick Wincker, Sophie Coudouel, et al.. Genome and transcriptome analyses in hexaploid Spartina species (Poaceae) colonizing salt marshes. PAG XIX Plant and Animal Genome Conference, Jan 2012, San Diego, United States. ⟨hal-01110212⟩

Theses1 document

  • Julie Ferreira de Carvalho. Évolution du génome des spartines polyploïdes envahissant les marais salés : apport des nouvelles techniques de séquençage haut-débit. Sciences agricoles. Université Rennes 1, 2013. Français. ⟨NNT : 2013REN1S002⟩. ⟨tel-00795861⟩