Julie Ferreira de Carvalho
55
Documents
Identifiants chercheurs
- julie-ferreira-de-carvalho
- IdRef : 16778384X
- 0000-0001-6200-3344
Présentation
**INRAE Researcher**
**Currently @UMR IRHS : Research Institute in Horticulture and Seeds**
***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
Publications
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The Intertwined Chloroplast and Nuclear Genome Coevolution in PlantsPlant Growth and Regulation - Alterations to Sustain Unfavorable Conditions, InTech Open, 2018, 978-1-78984-285-2. ⟨10.5772/intechopen.75673⟩
Chapitre d'ouvrage
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Polyploid evolution in Spartina: Dealing with highly redundant genomesPamela S. Soltis, Douglas E. Soltis. Polyploidy and Genome Evolution, Springer, pp.225-244, 2012, 978-3-642-31441-4
Chapitre d'ouvrage
hal-01110233v1
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Structural and functional evolutionary dynamics of duplicated genes and genomes in nascent and natural B. napus21st Crucifer Genetics Conference on Brassica - Brassica 2018, Jul 2019, Saint-Malo, France
Communication dans un congrès
hal-03318226v1
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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
Communication dans un congrès
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Structural and functional consequences of transposable elements after multiple Whole-Genome Duplication eventsDynamique des Génomes végétaux, 2018, Rennes, France
Communication dans un congrès
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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
Communication dans un congrès
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How a polyploid becomes a new species: example from the Brassica model.International Conference on Environmental and Agronomical Genomics, 2018, Paris, France
Communication dans un congrès
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Cytonuclear interactions overcome inter-genomic conflict resulting from interspecific hybridization and genome doublingSecond Joint Congress on Evolutionary Biology, Aug 2018, Montpellier, France
Communication dans un congrès
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Genome merger and duplication as springboards for plant invasion: Lessons from SpartinaInternational Conference on Ecological Sciences, SFEcologie2018, SFEcologie, Oct 2018, Rennes, France
Communication dans un congrès
hal-02436817v1
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Transcriptomic responses to challenging environments in Spartina alterniflora populationsWorkshop DYNAGEV2017, Jun 2017, Montpellier, France
Communication dans un congrès
hal-02435012v1
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Genome merger as evolutionary springboard: Insights from recurrent hybridization and polyploidy in SpartinaInternational Conference on Hybridization and Polyploidy (ICPHB-2016), Apr 2016, Rovinj, Croatia
Communication dans un congrès
hal-02422781v1
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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
Communication dans un congrès
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Polyploidy, genome evolution and functional novelty in genus SpartinaI (Poaceae)International Conference « Evolution of Plant Phenotypes: from genomes to traits », Mar 2015, Barcelone, Spain
Communication dans un congrès
hal-01162082v1
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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
Communication dans un congrès
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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
Communication dans un congrès
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Recurrent polyploidy in the salt marsh genus Spartina: Lessons and challengesPAG XXII Plant and Animal Genome Conference, Jan 2014, San Diego, United States. 1 p
Communication dans un congrès
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Bac sequencing analyses in the hexaploid Spartina maritime (Poaceae): Homoeolog divergence and microsynteny in the grass familyRéunion du groupe « Cytogénétique et Polyploïdie », May 2014, Clermont-Ferrand, France
Communication dans un congrès
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Transcriptomic response to hydrocarbon stress in Spartina alternifloraInternational Conference on Invasive Spartina 2014, UMR CNRS 6553 ECOBIO, Jul 2014, Rennes, France
Communication dans un congrès
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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
Communication dans un congrès
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Hybridation, polyploidie et evolution des génomes : le cas des spartines envahissant les marais salésColloque de lancement du Groupement de Recherches CNRS « Invasions Biologiques », UMR CNRS 6553 ECOBIO, Oct 2014, Rennes, France
Communication dans un congrès
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Polyploidy speciation and genome evolution: Lessons from recent allopolyploidsXVIIth Evolutionary Biology Meeting, Sep 2013, Marseille, France
Communication dans un congrès
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Evolutionary dynamics of the chloroplast genome: Insights from comparative analyses in the legume familyColloque « Génomique Environnementale », Nov 2013, Rennes, France
Communication dans un congrès
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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
Communication dans un congrès
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Population level study of genetic and epigenetic variability of rRNA genes in invasive species Spartina anglicaFrench Annual Polyploidy and Cytogenetics Meeting, May 2013, Rennes, France
Communication dans un congrès
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Ecological genomics of invasive polyploids: Case study from hexaploid and allo-dodecaploid Spartina species colonizing salt marshesInternational Conference of Ployploidy, Hybridization and Biodiversity (ICPHB), May 2012, Pruhonice, Czech Republic
Communication dans un congrès
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Ecological genomics of the recent Spartina hybrids and allopolyploid invading salt-marshes13th Congress of the European Society for Evolutionary Biology, European Society for Evolutionary Biology, Aug 2011, Tübingen, Germany
Communication dans un congrès
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Vers la caractérisation des compartiments codant et répété du génome des spartines polyploïdes par séquençage en masseColloque « Biodiversité, Histoire des Espèces, Evolution des Génomes », Jun 2011, Rennes, France
Communication dans un congrès
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Évolution du génome des spartines polyploïdes envahissant les marais salés : apport des nouvelles techniques de séquençage haut-débitSciences agricoles. Université Rennes 1, 2013. Français. ⟨NNT : 2013REN1S002⟩
Thèse
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