Whole Genome Characterization

"From the seed to the genome"

The CNRGV is a partner for plant genome characterization projects, from DNA extraction to genome assembly at the chromosomal level.

With 15 years of expertise in plant genomics, particularly in high molecular weight DNA extraction, we propose strategies adapted to the specificities of the plants studied and the scientific objectives pursued.

We carry out the extraction, qualification, and preparation of DNA from plant material either from seedlings that we produce or collected in situ.

For the sequencing step, we work closely with several sequencing platforms, including platforms from the " INRAE Genomics" infrastructure, to access the PacBio HiFi sequencing technology. The reads produced by the PacBio Sequel II system are high quality, so-called high fidelity (HiFi) reads, with average sizes between 17 and 20 kb.

Our bioinformatics team validates these data and then assembles them into sequence contigs.

We then combine the contigs with complementary data to organize them at the chromosomal level, such as  optical maps and Hi-C data. We can also integrate other available resources (close reference genome, genetic map) to validate and finalize the genomes.

We manage the storage and transfer of the data in a fully secure manner.

We are currently validating the use of  EuGene software for annotation of assembled genomes.  Thus, we propose annotation proposed as a service in development.