Julie Ferreira de Carvalho
AgreenSkills session, year: 2nd session, 2016
Receiving laboratory: IGEPP Institute for Genetics, the Environment and Plant Protection, Rennes
Country of origin : The Netherlands
Immediate impact of polyploidy and of human selection on evolutionary dynamic of Brassica napus
Interspecific hybridization and genome doubling is a key factor of plant speciation and adaptation. These intriguing evolutionary processes entail extensive genome restructuring and reprogramming of functional regulatory pathways inherited from parental species. However, mechanisms responsible for genome stabilization and adaptation remain poorly understood. The aim of my project is to provide an interdisciplinary overview of the effects of polyploidy in a major crop. Brassica napus (oilseed rape) is an excellent system to unravel the immediate and long-term effects of polyploid speciation and adaptation under human selection. It has been made possible by the advent sequencing technologies and availability of Brassica complete genomes and transcriptomes. In my project, I will use a novel approach combining DNA Seq, RNA Seq and methylation variation levels in phenotypically contrasted polyploids. I will perform and implement in the host lab, cutting-edge methods to unravel the role of epigenetic regulation in genome stabilization. Altogether, my project will allow determining the effects of structural dynamic and epigenetic variation on (1) meiotic behaviour and fertility, (2) gene expression variation and (3) glucosinolate content. My expected findings will open a new avenue to better understand how to use genetic diversity and to modify agronomic traits through gene dosage and translocations in breeding programs.
Thanks to the rapidly evolving sequencing technologies, we are only just recently able to address questions in ecology of major importance and relevance using genomic approaches (even for non-model systems). More specifically, I am interested in unravelling molecular processes (transcriptomic, genomic and epigenetic) and building an integrative understanding (from genes to eco-agrosystems) of the main molecular mechanisms involved in plant genome evolution and adaptation. These fundamental mechanisms can help us predict the faith of biodiversity in a changing environmental context and improve its management.
My PhD research revealed the effects of divergent evolution on gene expression in two closely related species using the grass genus Spartina (Poaceae) as a model system. After building a de novo reference transcriptome for hexaploid Spartina species, I was able to identify many genes whose expression is altered following hybridization and genome doubling (Ferreira de Carvalho et al. 2013a in Heredity). Noticeably, I identified differential expression of ecologically relevant genes (conferring stress tolerance, growth and vigor involved in invasive abilities) within and between populations of Spartina species (hexaploids, F1 hybrids and allododecaploid) growing in natural populations (Ferreira de Carvalho et al. 2017 in Plant Systematics and Evolution). Since previous work in the laboratory showed that genome merger and duplication did not cause genomic alterations but induced epigenetic changes in regions flanking transposable elements, I decided to explore the genome of Spartina maritima using NGS data to enlighten our knowledge on transposable elements (Ferreira de Carvalho et al. 2013b in Plant Molecular Biology).
I was then keen to have more training in transgenerational epigenetic in plants and join Dr. Koen Verhoeven’s group at the Netherlands Institute of Ecology in Wageningen. I had the opportunity to develop my own research line on asexual genome evolution. More specifically, my postdoc project aims for one part to unravel gene expression differences within one apomictic lineage of Taraxacum officinale in the context of range expansion and plant adaptation using RNA-Seq data. This original study revealed that heritable transcriptomic changes are influenced mainly by regulatory sequences and transposable element protein domains (Ferreira de Carvalho et al. 2016a in BMC Genomics). Follow up experiments on gene promoter variation enlighten our knowledge on the potential role of epigenetic in the cis-regulation of gene expression and rapid phenotypic changes, notably in flowering time control (Ferreira de Carvalho et al. 2016b BMC Genomics and in prep). As the second part of my post-doc and in tight collaboration with Wageningen University, I was investigating the genomic footprints associated with apomixis, building and annotating the first reference genome for the common dandelion (Ferreira de Carvalho et al. in prep).
1. Preite V., Morgado L., Oplaat C., Anava S., Ferreira de Carvalho J., Rechavi O., Johannes F., and K.J.F. Verhoeven. Small RNAs reflect environment from grandparental generation in apomictic dandelions. Accepted in Molecular Biology and Evolution;
2. Ferreira de Carvalho J., Boutte J., Bourdau P., Chelaifa H., Ainouche K., Salmon A. and M. Ainouche. Gene expression variation in natural populations of hexaploid (parents and hybrids) and allododecaploid Spartina species (Poaceae). Accepted in Plant Systematics and Evolution;
3. Ferreira de Carvalho J., de Jager V., van Gurp T., Wagemaker N. and K.J.F. Verhoeven (2016). Recent and dynamic transposable elements contribute to genomic divergence under asexuality. BMC Genomics;
4. Boutte J., Ferreira de Carvalho J., Ainouche M. and Salmon A. Reference transcriptomes and detection of duplicated copies in hexaploid parents, hybrids and allododecaploid Spartina species (Poaceae) (2016). Genome Biology and Evolution;
5. Huska D., Leitch I., Ferreira de Carvalho J., Leitch A., Salmon A., Ainouche M. and A. Kovarik (2016). Persistence, dispersal and genetic evolution of recently formed Spartina homoploid hybrids and allopolyploids in Southern England. Biological Invasions 18(8):2137-51;
6. Ferreira de Carvalho J., Oplaat C., Pappas N., Derks M., de Ridder D. and K.J.F. Verhoeven (2016). Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants. BMC Genomics. 17: 203;
7. Boutte J., Aliaga B., Lima O., Ferreira de Carvalho J., Ainouche A., Macas J., Rousseau-Gueutin M., Coriton O., Ainouche M. and A. Salmon (2015). Haplotype Detection from Next Generation Sequencing in High Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima. G3 6(1):29-40;
8. Guillaume M., Rousseau-Gueutin M., Cordonnier S., Lima O., Michon-Coudouel S., Naquin D., Ferreira de Carvalho J., Ainouche M., Salmon A. and A. Ainouche (2014). The first complete chloroplast genome of Genistoid legume Lupinus lucteus: Evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family. Annals of Botany 113 (7): 1197-1210;
9. Ferreira de Carvalho J., Poulain J., Da Silva C., Wincker P., Michon-Coudouel S., Dheilly A., Naquin D., Boutte J., Salmon A. and M. Ainouche (2013a). Transcriptome de novo assembly from Next-Generation Sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae). Heredity 110: 181-93;
10. Ferreira de Carvalho J., Chelaifa H., Mangenot S., Couloux A., Wincker P., Bellec A., Fourment J., Berges H., Salmon A. and M. Aïnouche (2013b). Exploring the genome of the salt-marsh species Spartina maritima (Poaceae, Chloridoideae) through BAC End Sequence analysis. Plant Molecular Biology 83: 591-606.