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

Génomics

• De novo genome sequencing (Short & Long Read)
• Re-sequencing
• Bisulfite conversion
• Hi-C
• ChIP-Seq
• MedIP-Seq
• Metagenomics (Shotgun & Metabarcoding)
• Genotyping by sequencing
• Amplicon sequencing
• Methylation analysis on native DNA (PacBio)
• Ready-to-load libraries

Transcriptomics

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

Equipment

• Sequencing: 1 NovaSeq Illumina, 3 Miseq Illumina, 1 Sequel II Pac Bio, 2 MinION Oxford Nanopore Technology, 1 GridION Oxford Nanopore Technology, 1 GridION  Oxford Nanopore Technology, 1 PromethION Oxford Nanopore Technology.
• Robots: 3 EVO150 and 1 EVO200 Tecan
• Others: 1 Femto Pulse Agilent, 2 Fragment Analyser Agilent, Nanodrop, 2 QuantStudio 6 Life Technologies
• Other equipment available on GeT sites: 1 Ion S5 Ion Torrent, 1 Fragment Analyser Agilent, 1 robot BRAVO, 2 Drop Sense, 3 scanners Agilent, Innoscan 900 Innopsys, Roche MS200.

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

To meet the demands of research teams in the fields of agronomy and the environment, GeT-PlaGe and the bioinformatics core facility have obtained funding from the SeqOccIn project (FEDER Regional Project 2019-2022) for the development of new methodologies. The core facility also has adequate budgets to invest very quickly in new technologies when they reach the market. An extension of its current building should be completed within 3 years.

Eventually, new expertise will be available to the whole community, here is a non exhaustive list:

• Direct RNA sequencing via the ONT Long Read technology
• High molecular weight DNA extraction
• Epigenetics on native DNA and RNA
• Choice of technology combinations to obtain the best de novo genome assemblies
• EM-seq to replace bisulfite conversion
• TELL-seq to replace 10X Genomics’ linked-reads application
• New PromethION ONT to offer Q20+ technology
• Sparse-sequencing for lower cost genotyping
• Metagenomics (Shotgun & metabarcoding) long read

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 Nov 2021