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Julie Ferreira de Carvalho

33
Documents
Identifiants chercheurs

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

mathieu-rousseau-gueutin

Projet BrasExplor : élargir les ressources génétiques du CRB BrACySol pour Brassica oleracea et Brassica rapa

Cyril Falentin , Vincent Richer , Pascal Glory , Gwenaëlle Deniot , Julie Ferreira de Carvalho
NOV'AE, 2022, NS2, pp.21-27. ⟨10.17180/novae-2022-NS02-art03⟩
Article dans une revue hal-03790700v1

Epigenomic and structural events preclude recombination in Brassica napus

Franz Boideau , Gautier Richard , Olivier Coriton , Virginie Huteau , Caroline Belser
New Phytologist, 2022, 234 (2), pp.545-559. ⟨10.1111/nph.18004⟩
Article dans une revue hal-03651949v1
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Untangling structural factors driving genome stabilization in nascent Brassica napus allopolyploids

Julie Ferreira de Carvalho , Solenn Stoeckel , Frédérique Eber , Maryse Lodé-Taburel , Marie-Madeleine Gilet
New Phytologist, 2021, 230 (5), pp.2072-2084. ⟨10.1111/nph.17308⟩
Article dans une revue hal-03227311v1
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Long-read assembly of the Brassica napus reference genome Darmor-bzh

Mathieu Rousseau-Gueutin , Caroline Belser , Corinne Da silva , Gautier Richard , Benjamin Istace
GigaScience, 2020, 9 (12), pp.giaa137. ⟨10.1093/gigascience/giaa137⟩
Article dans une revue hal-03283975v1
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Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa

Julien Boutte , Loeiz Maillet , Thomas Chaussepied , Sébastien Letort , Jean-Marc Aury
Frontiers in Plant Science, 2020, 11, pp.577536. ⟨10.3389/fpls.2020.577536⟩
Article dans une revue hal-03137565v1

Impact of whole genome triplication on the evolutionary history and the functional dynamics of regulatory genes involved in Brassica self-incompatibility signalling pathway

Thanina Azibi , Houria Hadj-Arab , Maryse Lodé-Taburel , Julie Ferreira de Carvalho , Gwenn Trotoux
Sexual Plant Reproduction, 2020, 33 (1), pp.43-58. ⟨10.1007/s00497-020-00385-x⟩
Article dans une revue hal-02784702v1
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Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica

Julie Ferreira de Carvalho , Jérémy Lucas , Gwenaëlle Deniot , Cyril Falentin , Olivier Filangi
Plant Journal, 2019, 98 (3), pp.434-447. ⟨10.1111/tpj.14228⟩
Article dans une revue hal-02019346v1
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Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae)

Julie Boutte , Julie Ferreira de Carvalho , Mathieu Rousseau-Gueutin , Julie Poulain , Corinne da Silva
Genome Biology and Evolution, 2016, 8 (9), pp.3030-3044. ⟨10.1093/gbe/evw209⟩
Article dans une revue hal-01412081v1
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Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima

Julien Boutte , Benoît Aliaga , Oscar Lima , Julie Ferreira de Carvalho , Abdelkader Aïnouche
G3, 2016, 6 (1), pp.29--40. ⟨10.1534/g3.115.023242⟩
Article dans une revue hal-01269912v1
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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

Guillaume E. Martin , Mathieu Rousseau-Gueutin , Solenn Cordonnier , Oscar Lima , Sophie Michon-Coudouel
Annals of Botany, 2014, 113 (7), pp.1197-1210. ⟨10.1093/aob/mcu050⟩
Article dans une revue hal-01061902v1

The Intertwined Chloroplast and Nuclear Genome Coevolution in Plants

Mathieu Rousseau-Gueutin , Jean Keller , Julie Ferreira de Carvalho , Abdelkader Ainoüche , Guillaume Martin
Plant Growth and Regulation - Alterations to Sustain Unfavorable Conditions, InTech Open, 2018, 978-1-78984-285-2. ⟨10.5772/intechopen.75673⟩
Chapitre d'ouvrage hal-02787510v1

Co-evolution of chloroplast and nuclear genomes in flowering plants and impact of allopolyploidy on fine tune cytonuclear interactions.

Mathieu Rousseau-Gueutin , Julie Ferreira de Carvalho , Jérémy Lucas , Gwenaëlle Deniot , Cyril Falentin
International Conference on Polyploidy, Jun 2019, Ghent, Belgium
Communication dans un congrès hal-03318182v1

Structural and functional evolutionary dynamics of duplicated genes and genomes in nascent and natural B. napus

Mathieu Rousseau-Gueutin , Jérémy Lucas , France Denoeud , Julie Ferreira de Carvalho , Zhesi He
21st Crucifer Genetics Conference on Brassica - Brassica 2018, Jul 2019, Saint-Malo, France
Communication dans un congrès hal-03318226v1

Structural and functional consequences of transposable elements after multiple Whole-Genome Duplication events

Julie Ferreira de Carvalho , Thomas Chaussepied , Sébastien Letort , Anne-Marie Chèvre , Mathieu Rousseau-Gueutin
Dynamique des Génomes végétaux, 2018, Rennes, France
Communication dans un congrès hal-03318224v1

Impact of structural variations on the meiotic stability and plant fertility of the allotetraploid B. napus (oilseed rape)

Mathieu Rousseau-Gueutin , Julie Ferreira de Carvalho , Solenn Stoeckel , Jérôme Morice , Marie-Madeleine Gilet
Second Joint Congress on Evolutionary Biology, Aug 2018, Montpellier, France
Communication dans un congrès hal-03318231v1

Genome merger and duplication as springboards for plant invasion: Lessons from Spartina

Malika L. Aïnouche , Armand Cavé-Radet , Delphine Giraud , Alex Baumel , Blanca Gallego-Tévar
International Conference on Ecological Sciences, SFEcologie2018, SFEcologie, Oct 2018, Rennes, France
Communication dans un congrès hal-02436817v1

How a polyploid becomes a new species: example from the Brassica model.

Mathieu Rousseau-Gueutin , Julie Ferreira de Carvalho , J. Lucas , France Denoeud , Fabrice Legeai
International Conference on Environmental and Agronomical Genomics, 2018, Paris, France
Communication dans un congrès hal-03318223v1

Cytonuclear interactions overcome inter-genomic conflict resulting from interspecific hybridization and genome doubling

Julie Ferreira de Carvalho , Jérémy Lucas , Cyril Falentin , Gwenaëlle Deniot , Olivier Filangi
Second Joint Congress on Evolutionary Biology, Aug 2018, Montpellier, France
Communication dans un congrès hal-03318235v1

Unending hybridization and polyploid speciation stories: Lessons from Spartina (Poaceae)

Malika L. Aïnouche , Alex Baumel , Blanca Gallego-Tévar , Jesus Castillo , Mathieu Rousseau-Gueutin
XV OPTIMA Meeting, Organization for the Phyto-Taxonomic Investigation of the Mediterranean Area, Jun 2016, Montpellier, France
Communication dans un congrès hal-02422822v1

Genome merger as evolutionary springboard: Insights from recurrent hybridization and polyploidy in Spartina

Malika L. Aïnouche , Houda Chelaifa , Mathieu Rousseau-Gueutin , Julien Boutte , Hélène Rousseau
International Conference on Hybridization and Polyploidy (ICPHB-2016), Apr 2016, Rovinj, Croatia
Communication dans un congrès hal-02422781v1

Polyploidy, genome evolution and functional novelty in genus SpartinaI (Poaceae)

Malika Ainouche , Mathieu Rousseau-Gueutin , Hélène Rousseau , Julien Boutte , Sidonie Bellot
International Conference « Evolution of Plant Phenotypes: from genomes to traits », Mar 2015, Barcelone, Spain
Communication dans un congrès hal-01162082v1

The challenges of genomics in polyploidy Spartina species: How to deal with hybrid genomes and high redundancy?

Armel Salmon , Julien Boutte , Julie Ferreira de Carvalho , Mathieu Rousseau-Gueutin , Malika L. Aïnouche
PAG XXIII Plant and Animal Genome Conference, Jan 2015, San Diego, United States
Communication dans un congrès hal-02422739v1

The challenges of genomics in polyploidy Spartina species: How to deal with hybrid genomes and high redundancy?

Armel Salmon , Julien Boutte , Julie Ferreira de Carvalho , Mathieu Rousseau-Gueutin , Malika Ainouche
PAG XXIII Plant and Animal Genome Conference, Jan 2015, San Diego, United States
Communication dans un congrès hal-01162085v1

Recurrent polyploidy in the salt marsh genus Spartina: Lessons and challenges

Malika Ainouche , Julie Ferreira de Carvalho , Julien Boutte , Sidonie Bellot , Mathieu Rousseau-Gueutin
PAG XXII Plant and Animal Genome Conference, Jan 2014, San Diego, United States. 1 p
Communication dans un congrès hal-01108383v1

Hybridation, polyploidie et evolution des génomes : le cas des spartines envahissant les marais salés

Malika Ainouche , Armel Salmon , Mathieu Rousseau-Gueutin , Julien Boutte , Hélène Rousseau
Colloque de lancement du Groupement de Recherches CNRS « Invasions Biologiques », UMR CNRS 6553 ECOBIO, Oct 2014, Rennes, France
Communication dans un congrès hal-01108368v1

Bac sequencing analyses in the hexaploid Spartina maritime (Poaceae): Homoeolog divergence and microsynteny in the grass family

Carine Charron , Mathieu Rousseau-Gueutin , Julie Ferreira de Carvalho , Houda Chelaifa , Julien Boutte
Réunion du groupe « Cytogénétique et Polyploïdie », May 2014, Clermont-Ferrand, France
Communication dans un congrès hal-01108395v1

The challenges of genomics in polyploid Spartina species: How to deal with hydrid genomes and high redundancy?

Armel Salmon , Julien Boutte , Julie Ferreira de Carvalho , Mathieu Rousseau-Gueutin , Malika Ainouche
International Conference on Invasive Spartina 2014, Jul 2014, Rennes, France
Communication dans un congrès hal-01108413v1

Polyploidy speciation and genome evolution: Lessons from recent allopolyploids

Malika Ainouche , Houda Chelaifa , Julie Ferreira de Carvalho , Julien Boutte , Sidonie Bellot
XVIIth Evolutionary Biology Meeting, Sep 2013, Marseille, France
Communication dans un congrès hal-01108428v1

Evolutionary dynamics of the chloroplast genome: Insights from comparative analyses in the legume family

Mathieu Rousseau-Gueutin , Guillaume Martin , Solene Cordonnier , Oscar Lima , Sophie Michon-Coudouel
Colloque « Génomique Environnementale », Nov 2013, Rennes, France
Communication dans un congrès hal-01108884v1