Team BIOINFO is the GDEC bioinformatics platform. It also leads projects in the field of Triticeae genomics. We develop bioinformatics tools and pipelines to address the wheat genome complexity and we perform sequence analyses in order to improve of knowledge of wheat genome composition, organization, dynamics of transposable elements and their impact on wheat genome evolution and adaptation.

Platform activities

• Analyses of sequences and genomics data
•    Genome assembly, RNASeq, variant discovery
•    Annotation of genes and transposable elements
•    Comparative genomics, phylogeny
•    Molecular marker design
• Teaching and Formation to genome bioinformatics
•    Bioinformatics tools, NGS, BLAST, etc.
•    Bash and computing on HPC
•    Galaxy
• Information Technology
•    System administration, data storage and computing

Research projects

• Methodological development
•    Sequencing, assembly, and annotation of complex genomes
•    Exploring genomic variability
• Genome Dynamics
•    Dynamics of Transposable Elements and wheat genomic variability
•    Transposable elements and response to stress
•    Regulation of transposable element activity, impact of polyploidy and recent introgressions

Team Members (2023)

• Frédéric CHOULET, PhD, Group leader
• Hélène RIMBERT, Engineer
• Pauline LASSERRE-ZUBER, Engineer
• Vincent PAILLER, Engineer
• Fabien LELOUP, Assistant Engineer
• Philippe LEROY, Engineer (early retirement)

Former members

• Nathan PAPON, PhD st. (2019-2023)
• Jean-François CHARMET, Technician
• Romain DE OLIVEIRA, PhD Student (09/2016-12/2019)
• Cécile MONAT, postdoc (03/2019-02/2021)
• Students
  • Matthaus SIRVENT, Master1 UCA (2023)
  • Corentin BONHOMME, Master1 UCA (2023)
  • Nezha WATIL Master2 UCA (2022)
  • Alice BRICHET DIT FRANCE, Two-year degree UCA (2021)
  • Nolwenn PERARD, Three-year degree University Poitiers (2021)
  • Emilie GERARD-MARCHANT, Master2 UCA (2020)
  • Joris MORDIER, Master1 UCA (2019)

Recent Publications (5 years)

2023

Papon, N., Lasserre-Zuber, P., Rimbert, H., De Oliveira, R., Paux, E., and Choulet, F. (2023). All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity. Plant Genome 16, e20347. 10.1002/tpg2.20347

Zhang, J., Debernardi, J.M., Burguener, G.F., Choulet, F., Paux, E., O'Connor, L., Enk, J., and Dubcovsky, J. (2023). A second-generation capture panel for cost-effective sequencing of genome regulatory regions in wheat and relatives. Plant Genome 16, e20296. 10.1002/tpg2.20296

2022

Aury, J.M., Engelen, S., Istace, B., Monat, C., Lasserre-Zuber, P., Belser, C., Cruaud, C., Rimbert, H., Leroy, P., Arribat, S., Dufau, I., Bellec, A., Grimbichler, D., Papon, N., Paux, E., Ranoux, M., Alberti, A., Wincker, P., and Choulet, F. (2022). Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding. Gigascience 11. 10.1093/gigascience/giac034

Hussain, B., Akpınar, B.A., Alaux, M., Algharib, A.M., Sehgal, D., Ali, Z., Aradottir, G.I., Batley, J., Bellec, A., Bentley, A.R., Cagirici, H.B., Cattivelli, L., Choulet, F. […] Appels, R., and Budak, H. (2022). Capturing Wheat Phenotypes at the Genome Level. Front Plant Sci 13, 851079. 10.3389/fpls.2022.851079

Darrier, B., Colas, I., Rimbert, H., Choulet, F., Bazile, J., Sortais, A., Jenczewski, E., and Sourdille, P. (2022). Location and Identification on Chromosome 3B of Bread Wheat of Genes Affecting Chiasma Number. Plants (Basel) 11. 10.3390/plants11172281

2021

Juery, C., Concia, L., De Oliveira, R., Papon, N., Ramírez-González, R., Benhamed, M., Uauy, C., Choulet, F., and Paux, E. (2021). New insights into homoeologous copy number variations in the hexaploid wheat genome. Plant Genome 14, e20069. 10.1002/tpg2.20069

Zhu, T., Wang, L., Rimbert, H., Rodriguez, J.C., Deal, K.R., De Oliveira, R., Choulet, F., Keeble-Gagnère, G., Tibbits, J., Rogers, J., Eversole, K., Appels, R., Gu, Y.Q., Mascher, M., Dvorak, J., and Luo, M.C. (2021). Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly. Plant J 107, 303-314. 10.1111/tpj.15289

2020

De Oliveira, R., Rimbert, H., Balfourier, F., Kitt, J., Dynomant, E., Vrána, J., Doležel, J., Cattonaro, F., Paux, E., and Choulet, F. (2020). Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats. Front Genet 11, 891. 10.3389/fgene.2020.00891

Tahir, A., Kang, J., Choulet, F., Ravel, C., Romeuf, I., Rasouli, F., Nosheen, A., and Branlard, G. (2020). Deciphering carbohydrate metabolism during wheat grain development via integrated transcriptome and proteome dynamics. Mol Biol Rep 47, 5439-5449. 10.1007/s11033-020-05634-w

2019

Balfourier, F., Bouchet, S., Robert, S., De Oliveira, R., Rimbert, H., Kitt, J., Choulet, F., Paux, E., Consortium, I.W.G.S., and Consortium, B. (2019). Worldwide phylogeography and history of wheat genetic diversity. Sci Adv 5, eaav0536. 10.1126/sciadv.aav0536