My first internship at the University of Rennes 1 (France)
Over my master 1 Integrated Biology: Molecules, Population and Sustainable Development with a specialization in environmental genomics, I did a first internship at the university of Rennes 1 (3 months). I joined the Evolution Genome and Adaptation team at the ECOBIO lab, leaded by Prof. Malika Aïnouche.
You can download (in pdf) the french version of this page.
The subject of this internship was:
Reconstruction and assembly of ribosomal DNA (45S rDNA) in Spartines polyploidy
Polyploidy, NGS (Next-Generation-Sequencing), SNP (Single Nucleotide Polymorphism), 45S rDNA, Duplications
- Armel Salmon
- Malika Aïnouche
Partial or whole genome duplications are recurrent in the history of species. The whole genome duplication (polyploidy) characterize several groups (especially in plants) where it represents one major speciation mechanism, with a particular dynamic (fast evolution of duplicate genes by polyploidy, alteration of the epigenetic regulations and gene expression modifications), a source of phenotypic innovations and adaptative.
Within genomes, some genes thus find more or less numbers of copies, from tandem duplication which form duplicated gene clusters or duplicated genomic region more extended (such a chromosome arm or a whole chromosome) resulting in a dispersion of these duplicated genes in the genomes. Among the duplicated genes in tandem, genes encoding ribosomal DNA (45S rDNA) are particularly studied since their use in phylogeny and their tendency to a concerted evolution.
The aim of the internship consists to validate the 45S rDNA copies detected by the use of pyrosequencing technic and the detection of haplotypes with automatized bioinformatics tools in Spartina maritima (Poaceae; 2n=6x=60), native species from euro-african atlantic coast. This validation will allow in a second time the study of evolution of these copies inside the Spartines clade. S. maritima was recently hybridized (XIX century) with an american hexaploid species introduced (S. alterniflora) to give a new allododecaploid species which is strongly invasive, S. anglica. This one is a classic model of recent speciation by allopolyploidy, which result a research project in genomic in the host team.
The analyses will be performed with available datasets in the lab, from genome sequencing by pyrosequencing (Roche 454) and sequencing by synthesis (Illumina) done by the Environmental Genomic Platform (CAREN – Rennes) and at the Génoscope (Evry). It will be (i) amplify different region of 45S rDNA of Spartina maritima which contains SNPs (Single Nucleotide Polymorphism), which allow to distinguish the different copy of the gene, (ii) to clone the PCR products obtained by sequencing and (iii) assembling the different sequenced regions to reconstruct the different copies. This work inserts into a viewpoint to determine the evolutionary origin of these copies by distinguish the different duplicated copies (paralog: tandem duplication; and homeologous: duplicated by polyploidy).
Publication and communication
- A publication entitled Haplotype detection from next generation sequencing in high ploidy-level species: 45S rDNA genes copies in the hexaploid Spartina maritima was published in G3: Genes, Genomes, Genetics (2016).
- This experience was followed by a poster presented by Julien Boutte at the International Conference on Polyploidy, Hybridization, and Biodiversity (ICPHB) in Průhonice, Czech Republic (7th-10th May 2012). Julien won the first prize for this poster.
Letter of recommendation
Here you will find two letter of recommendations written by my advisor Armel Salmon (in french and in english).
- Wendel, J.F. (2000). Genome evolution in polyploids. Plant Mol. Biol., 42, 225–249
- Weider, L. J., Elser, J. J., Crease, T. J., Mateos, M., Cotner, J. B., and Markow, T. A. (2005). The functional significance of ribosomal (r)DNA variation: Impacts on the evolutionary ecology of organisms. Annu. Rev. Ecol. Evol. Syst. 36, 219–242
- Ainouche, M.L., Fortune, P.M., Salmon, A., Parisod, C., Grandbastien, M.-A., Fukunaga, K., et al. (2009). Hybridization, polyploidy and invasion: lessons from Spartina (Poaceae). Biol. Invasions, 11, 1159–1173
- Ainouche, M. (2008). Histoire évolutive et conquêtes de la spartine anglaise: contexte génomique de la naissance d’une espèce. Aestuaria, 35–52
- Jiao, Y., Wickett, N.J., Ayyampalayam, S., Chanderbali, A.S., Landherr, L., Ralph, P.E., et al. (2011). Ancestral polyploidy in seed plants and angiosperms. Nature, 473, 97–100
- Roa, F., and Guerra, M. (2012). Distribution of 45S rDNA sites in chromosomes of plants: structural and evolutionary implications. BMC Evol. Biol. 12, 225