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Julie Ferreira de Carvalho

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**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

Identification and Quantification of Glucosinolates and Phenolics in a Large Panel of Brassica napus Highlight Valuable Genetic Resources for Chemical Ecology and Breeding

Anani Amegan Missinou , Julie Ferreira de Carvalho , Nathalie Marnet , Thomas Delhaye , Oumayma Hamzaoui
Journal of Agricultural and Food Chemistry, 2022, 70 (16), pp.5245-5261. ⟨10.1021/acs.jafc.1c08118⟩
Journal articles hal-03700611v1

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⟩
Journal articles hal-03651949v1

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⟩
Journal articles hal-03790700v1
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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⟩
Journal articles hal-03227311v1

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⟩
Journal articles hal-02784702v1
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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⟩
Journal articles hal-03137565v1
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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⟩
Journal articles hal-03283975v1
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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⟩
Journal articles hal-02019346v1

Intergenerational environmental effects: functional signals in offspring transcriptomes and metabolomes after parental jasmonic acid treatment in apomictic dandelion

Koen Verhoeven , Eline Verbon , Thomas van Gurp , Carla Oplaat , Julie Ferreira de Carvalho
New Phytologist, 2018, 217 (2), pp.871-882. ⟨10.1111/nph.14835⟩
Journal articles hal-03292207v1
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Transcriptome response of the foundation plant Spartina alterniflora to the Deepwater Horizon oil spill

Mariano Alvarez , Julie Ferreira de Carvalho , Armel Salmon , Malika L Ainouche , Armand Cavé-Radet
Molecular Ecology, 2018, 27 (14), pp.2986-3000. ⟨10.1111/mec.14736⟩
Journal articles hal-01811051v2

The relative roles of local climate adaptation and phylogeny in determining leaf-out timing of temperate tree species

Elsa Desnoues , Julie Ferreira de Carvalho , Constantin Zohner , Thomas Crowther
Forest Ecosystems, 2017, 4 (1), ⟨10.1186/s40663-017-0113-z⟩
Journal articles hal-03292321v1

Gene expression variation in natural populations of hexaploid and allododecaploid Spartina species (Poaceae)

Julie Ferreira de Carvalho , Julien Boutte , Pierre Bourdaud , Houda Chelaifa , Kader Ainouche
Plant Systematics and Evolution, 2017, 303 (8), pp.1061-1079. ⟨10.1007/s00606-017-1446-3⟩
Journal articles hal-01631555v1

Small RNAs Reflect Grandparental Environments in Apomictic Dandelion

Lionel Morgado , Veronica Preite , Carla Oplaat , Sarit Anava , Julie Ferreira de Carvalho
Molecular Biology and Evolution, 2017, 34 (8), pp.2035-2040. ⟨10.1093/molbev/msx150⟩
Journal articles hal-03292326v1

Recent and dynamic transposable elements contribute to genomic divergence under asexuality

Julie Ferreira de Carvalho , Victor de Jager , Thomas van Gurp , Niels Wagemaker , Koen Verhoeven
BMC Genomics, 2016, 17 (1), ⟨10.1186/s12864-016-3234-9⟩
Journal articles hal-03292332v1

Persistence, dispersal and genetic evolution of recently formed Spartina homoploid hybrids and allopolyploids in Southern England

Dalibor Huska , Ilia J. Leitch , Julie Ferreira de Carvalho , Andrew R. Leitch , Armel Salmon
Biological Invasions, 2016, 18 (8), pp.2137-2151. ⟨10.1007/s10530-015-0956-6⟩
Journal articles hal-01371822v1

Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants

Julie Ferreira de Carvalho , Carla Oplaat , Nikolaos Pappas , Martijn Derks , Dick de Ridder
BMC Genomics, 2016, 17 (1), ⟨10.1186/s12864-016-2524-6⟩
Journal articles hal-03292408v1
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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⟩
Journal articles hal-01269912v1
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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⟩
Journal articles hal-01412081v1
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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⟩
Journal articles hal-01061902v1

Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis

Julie Ferreira de Carvalho , Houda Chelaifa , Julien Boutte , Julie Poulain , Arnaud Couloux
Plant Molecular Biology, 2013, 83 (6), pp.606. ⟨10.1007/s11103-013-0111-7⟩
Journal articles hal-00943497v1

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)

Julie Ferreira de Carvalho , Julie Poulain , Corinne da Silva , Patrick Wincker , Sophie Michon-Coudouel
Heredity, 2013, 110 (2), pp.181-193. ⟨10.1038/hdy.2012.76⟩
Journal articles hal-00797941v1

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⟩
Book sections hal-02787510v1

Polyploid evolution in Spartina: Dealing with highly redundant genomes

Malika L. Aïnouche , Houda Chelaifa , Julie Ferreira de Carvalho , Sidonie Bellot , Abdelkader Aïnouche
Pamela S. Soltis, Douglas E. Soltis. Polyploidy and Genome Evolution, Springer, pp.225-244, 2012, 978-3-642-31441-4
Book sections hal-01110233v1

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
Conference papers hal-03318226v1

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
Conference papers hal-03318182v1

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
Conference papers hal-03318235v1

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
Conference papers 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
Conference papers 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
Conference papers hal-03318223v1

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
Conference papers hal-03318224v1

Transcriptomic responses to challenging environments in Spartina alterniflora populations

Christina L. Richards , Mariano Alvarez , Julie Ferreira de Carvalho , Armand Cavé-Radet , Abdelhak El Amrani
Workshop DYNAGEV2017, Jun 2017, Montpellier, France
Conference papers hal-02435012v1

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
Conference papers hal-02422781v1

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
Conference papers hal-02422822v1

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
Conference papers hal-01162085v1

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
Conference papers hal-02422739v1

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
Conference papers hal-01162082v1

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
Conference papers hal-01108413v1

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
Conference papers 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
Conference papers hal-01108395v1

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
Conference papers hal-01108383v1

Transcriptomic response to hydrocarbon stress in Spartina alterniflora

Mariano Alvarez , Armel Salmon , Julie Ferreira de Carvalho , Malika Ainouche , Christina L. Richards
International Conference on Invasive Spartina 2014, UMR CNRS 6553 ECOBIO, Jul 2014, Rennes, France
Conference papers hal-01108408v1

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
Conference papers hal-01108884v1

Automatized detection of duplicated copies from NGS data: Application to 45S rDNA and coding genes in the hexaploid Spartina maritime (Poaceae)

Julien Boutte , Benoit Aliaga , Julie Ferreira de Carvalho , Oscar Lima , Sophie Coudouel
Rencontres ALPHY/PhyloSIB, Feb 2013, Lyon, France
Conference papers hal-01108442v1

Population level study of genetic and epigenetic variability of rRNA genes in invasive species Spartina anglica

D. Huskaz , Julie Ferreira de Carvalho , Andrew Leitch , Malika Ainouche , Ales Kovarik
French Annual Polyploidy and Cytogenetics Meeting, May 2013, Rennes, France
Conference papers hal-01108846v1

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
Conference papers hal-01108428v1

Ecological genomics of invasive polyploids: Case study from hexaploid and allo-dodecaploid Spartina species colonizing salt marshes

Julie Ferreira de Carvalho , Julie Poulain , Corinne da Silva , Patrick Wincker , Sophie Coudouel
International Conference of Ployploidy, Hybridization and Biodiversity (ICPHB), May 2012, Pruhonice, Czech Republic
Conference papers hal-01108907v1

Vers la caractérisation des compartiments codant et répété du génome des spartines polyploïdes par séquençage en masse

Julie Ferreira de Carvalho , Houda Chelaifa , Jiri Macas , Oscar Lima , Sophie Coudouel
Colloque « Biodiversité, Histoire des Espèces, Evolution des Génomes », Jun 2011, Rennes, France
Conference papers hal-01108953v1

Ecological genomics of the recent Spartina hybrids and allopolyploid invading salt-marshes

Malika L. Aïnouche , Houda Chelaifa , Julie Ferreira de Carvalho , Sidonie Bellot , Armel Salmon
13th Congress of the European Society for Evolutionary Biology, European Society for Evolutionary Biology, Aug 2011, Tübingen, Germany
Conference papers hal-01108929v1

Functional consequences of transposable elements on duplicated gene transcription and retention in polyploid Brassica species

Julie Ferreira de Carvalho , Julien Boutte , Loeiz Maillet , Thomas Chaussepied , Sébastien Letort
International Conference on Polyploidy, Jun 2019, Ghent, Belgium
Conference poster hal-03318194v1

Shift to self-compatibility in synthetic allopolyploid Brassica napus

Thanina Azibi , Mathieu Rousseau-Gueutin , Gwenn Trotoux , Maryse Lodé-Taburel , Julie Ferreira de Carvalho
21st Crucifer Genetics Conference on Brassica - Brassica 2018, Jul 2018, Saint-Malo, France
Conference poster hal-03318239v1

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
International Conference on Invasive Spartina 2014, Jul 2014, Rennes, France. , 1 p., 2014
Conference poster hal-01109652v1

The hexaploid Spartina maritime (Poaceae, Chloridoidea) genome: Composition and evolution in the grass family

Julie Ferreira de Carvalho , Carine Charron , Houda Chelaifa , Julien Boutte , Mathieu Rousseau-Gueutin
Plant Genome Evolution Meeting, Sep 2013, Amsterdam, Netherlands. , 2013
Conference poster hal-01110188v1

Genome and transcriptome analyses in hexaploid Spartina species (Poaceae) colonizing salt marshes

Julie Ferreira de Carvalho , Julie Poulain , Corinne da Silva , Patrick Wincker , Sophie Coudouel
PAG XIX Plant and Animal Genome Conference, Jan 2012, San Diego, United States
Conference poster hal-01110212v1

Automatized detection of duplicated copies from NGS data: Application to 45S rDNA and coding genes in hexaploid Spartina species (Poaceae)

Julien Boutte , Benoit Aliaga , Julie Ferreira de Carvalho , Oscar Lima , Sophie Coudouel
International Conference of Ployploidy, Hybridization and Biodiversity (ICPHB), May 2012, Prague, Czech Republic
Conference poster hal-01110201v1