Introduction

GeT-PlaGe is a major player at regional and national level for genome analyses in the fields of agronomy, ecology, environment and microbiology.

The GeT core facility is a cutting-edge technology core facility located in Toulouse that provides the scientific community with tools and expertise in the fields of genomics and transcriptomics. Grouped together with the genomic core facilities of the Toulouse region, and forming part of GenoToul, they form the GeT core facility, which has the following missions :

• Acquire and maintain expertise in genomics, implement relevant developments
• Advise teams on the best genomic approaches (primarily high-throughput sequencing) to answer their research questions and support them throughout their projects in :

1. 1. Structural genomics: Reference genome (LR & HI-C), study of point or structural variations
   2. Functional genomics: Transcriptome and Epigenetics,

• Produce quality data
• Share our know-how

The core facility participates in research projects as a collaborator in the production of data for the development of new applications or technologies. It also offers to carry out certain bioinformatics analyses linked to NGS or microarray data produced on its sites.

GeT-PlaGe the main site is made up of 35 people including a team of 5 INRAE transfert staff dedicated to the service to private companies. The core facility produces data for 220 public projects per year (2020 figure). 50 companies have called on this service (2020).

Expertise

Genomics

• De novo genome sequencing (Short & Long Read)
• Re-sequencing
• Bisulfite conversion
• EM-seq
• Hi-C
• Metagenomics (Shotgun & Metabarcoding) – Short and long reads
• GBS – Low pass sequencing
• Amplicon sequencing
• Methylation analysis on native DNA (ONT/PacBio)
• Ready-to-load libraries

Transcriptomics

• RNAseq
• IsoSeq PacBio
• Quantitative PCR
• Direct RNAseq ONT
• Ready-to-load libraries

Equipment

• Sequencing:
  • Short Reads : 3 Aviti Element Biosciences, 1 NovaSeq6000 Illumina (début 2025), 2 Miseq Illumina
  • Long Reads : Sequel II PacBio, 1 GridION Oxford Nanopore Technology, 1 PromethION Oxford Nanopore Technology
• Other equipment available on GeT sites:
• • Sequencers : 1 automate Ion Chef et séquenceur Ion S5 Prime Thermofisher (GeT-Biopuces), 1 Miseq Illumina (GeT-Biopuces), 1 iSeq100 Illumina (GeT-TriX), 1 MinION Oxford Nanopore Technology (GeT-Biopuces), Chromium Controller (GeT-Santé)
  • Chips : 1 SPECTROstar Nano BMG labtech, Innoscan 900 Innopsys (GeT-Biopuces),  1 scanner de microarrays + four d’hybridation Agilent (GeT-TriX)

Bioinformatics analysis

The Toulouse genomic core facility, in partnership with the GenoToul bioinformatics core facility in Toulouse, has developed a site for making raw data available (nG6: https://ng6.toulouse.inra.fr/).  After sequencing, the following are available on the nG6 site:

• the raw sequences and associated qualities in fastq format, for 3 months on a backed up storage space
• the primary analysis (sequencing report and quality control (fastQC), search for contaminants)
• alignment of reads against a reference sequence (if applicable) and analysis of the alignment rate by position.

GeT-PlaGe then proposes to accompany research teams for the assembly of small genomes from long reads, from the definition of the project to the delivery of the result (assembly and metrics on the quality of the assembly). GeT-PlaGe also provides its users with computers equipped with software to analyze the data produced on its equipment (excluding NGS). The software allowing the analysis of NGS data is available on the infrastructure of the bioinformatics core facility.

The future at GeT-PlaGe

Drawing on the experience and expertise acquired over 24 years in connection with the scientific community, and in particular with the SeqOccIn project, the GeT-PlaGe platform supports you in 4 major areas:
• Knowledge of genomes: characterization of complete genomes and search for variations.
• Transcriptomics
• Epigenetics with, among other things, methylation research
• Metagenomics
We are committed to continuing to invest in the necessary tools and methods and to innovate in these areas to meet the expectations of research teams.
The platform also has adequate budgets allowing it to invest very quickly in new technologies when they arrive on the market. An extension to its current building should see the light of day within 3 years.

Main achievements

Medugorac et al. Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks. Nature Genetics, 2017. https://doi.org/10.1038/ng.3775

Badouin et al. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature, 2017. https://doi.org/10.1038/nature22380

Pecrix et al. Whole-genome landscape of Medicago truncatula symbiotic genes. Nature Plants, 2018. https://doi.org/10.1038/s41477-018-0286-7

Raymond et al. The Rosa genome provides new insights into the domestication of modern roses. Nature Genetics, 2018. https://doi.org/10.1038/s41588-018-0110-3

Groppi et al. Population genomics of apricots unravels domestication history and adaptive events. Nature Communications, 2021. https://doi.org/10.1038/s41467-021-24283-6

Last update Sept 2024