Molecular Biology technical platform

SCIENTIFIC BACKGROUND AND OBJECTIVES

The aim of this technical platform is to pool technologies and skills in molecular biology to support the unit’s research programmes.

The methods used generate the genetic data needed to characterise biodiversity and study phylogeny and population genetics, as well as genome structure, organism adaptation and gene function for species or communities of interest.

The site has 11 permanent staff and welcomes a large number of students.

Anne-Laure CLAMENS

Technician, INRAE

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Anne-Laure CLAMENS

Technician, INRAE

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Laure SAUNE

Technician, INRAE

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Laure SAUNE

Technician, INRAE

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Guillaume CASTEL

Research manager, INRAE

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Guillaume CASTEL

Research manager, INRAE

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See the platform permanent members

Activities and main facilities available

The platform has 200 m² of laboratories dedicated to the various activities based on the principle of forward progress. The main activities are as follows:

High-throughput purification of nucleic acids (RNA and DNA)
Main equipment: Sigma 4K15 centrifuge, Eppendorf epMotion 5075 robot
PCR amplification for genotyping (microsatellites, RFLP, AFLP) and sequencing (conventional and high-throughput)
Main equipment: 96 Eppendorf block thermocyclers (Mastercycler, epGradient and Nexus) and 384 TProfessional (Biometra)
Quantitative PCR: measurement of gene expression, pathogen detection, target quantification
Main equipment: LightCycler 480 (Roche), 96- and 384-well blocks
Preparation of libraries for high-throughput sequencing: AmpliconSeq (metabarcoding, 16S metagenomics, MHC genotyping, etc.), RADseq, RNAseq, Shotgun, etc.
Quality control of nucleic acids, PCR products and genomic libraries
Main equipment: electrophoresis tanks (Mupid), Bioanalyzer 2100 (Agilent), NanoDrop ND8000 spectrophotometer (Thermo), Qubit fluorometer (Invitrogen)
Cytogenetics: karyotyping, PRINS, FISH of repeated probes, BAC-FISH, chromosome painting, Zoo-FISH
Main equipment: fluorescence microscope (Zeiss) coupled to an image analysis system (Genus, Cytovision)

As CBGP is part of the LabEx CeMEB (Centre Méditerranéen Environnement et Biodiversité) and the LabEx Agro, users of our technical platform also benefit from access to shared equipment on partner platforms (Applied Biosystems capillary sequencers, Illumina MiSeq sequencer, Thermofisher KingFisher automated extraction system, Covaris S220 sonicator):

CeMEB labelled platforms

Grand Regional Genotyping Technical Platform

Sow A., Seye D., Faye E., Benoit L., Galan M., Haran J. & Brévault T. 2020. Birds and bats contribute to natural regulation of the millet head miner in tree-crop agroforestry systems. Crop Protection 132 : 105127. (https://dx.doi.org/10.1016/j.cropro.2020.105127)

Sow A., Haran J., Benoit L., Galan M. & Brévault T. 2020. DNA Metabarcoding as a tool for disentangling food webs in agroecosystems. Insects 11 : 294. (https://dx.doi.org/10.3390/insects11050294)

Villette P., Afonso E., Couval G., Levret A., Galan M., Goydadin A.-C., Cosson J.-F. & Giraudoux P. 2020. Spatio-temporal trends in richness and persistence of bacterial communities in decline-phase water vole populations. Scientific Reports 10 : 9506. (https://dx.doi.org/10.1038/s41598-020-66107-5)

Stragier C., Piry S., Loiseau A., Kane M., Sow A., Niang Y., Diallo M., Ndiaye A., Gauthier P., Borderon M., Granjon L., Brouat C. & Berthier K. 2020. Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa). PCI Ecology bioRxiv 557066, ver 4 : peer-reviewed and recommended by PCI Ecology. ((http://dx.doi.org/10.1101/557066)

Tournayre O., Leuchtmann M., Filippi-Codaccioni O., Trillat M., Piry S., Pontier D., Charbonnel N. & Galan M. 2020. In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses. Ecology and Evolution 10 : 6310-6332. (https://dx.doi.org/10.1002/ece3.6362)

Rasplus J.-Y., Blaimer B.B., Brady S.G., Burks R.A., Delvare G., Fisher N., Gates M., Gauthier N., Gumovsky A.V., Hansson C., Heraty J.M., Fusu L., Nidelet S., Pereira R.A.S., Sauné L., Ubaidillah R. & Cruaud A. 2020. A first phylogenomic hypothesis for Eulophidae (Hymenoptera, Chalcidoidea). Journal of Natural History 54 : 597-609. (https://dx.doi.org/10.1080/00222933.2020.1762941)