Genome optical mapping

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Optical mapping is a technique that relies on the Saphyr system from Bionano Genomics to obtain the physical map, so called Optical Map, of a genome.

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The CNRGV is a certified service provider approved by Bionano Genomics for plant and animals genomes optical mapping.

This label recognizes the conformity of our process with guidelines and our expertise to providethe best possible data.

Based on in-silico assembly of large DNA molecules labelled at specific sites, the Optical Map provides long-distance information revealing the structure of studied genome.

The Optical Map is then combined with sequence information to provide a high quality scaffolded genome assembly called hybrid assembly. Figure 1a et 1b


figure 1a N50

Figure 1b chromosomes

1a - Increase of N50 values of the Hybrid Scaffolds (HS) after hybrid assembly compared to the sequence assembly N50 (NGS) and the Optical Maps N50 (OMAP).

1b -Scaffold number decrease in the hybrid assembly compared to the numbers of sequence contigs and the numbers of Optical Maps (OMAP). For each plant, the targeted scaffold numbers would be equal to chromosomes numbers indicated in yellow.

The CNRGV offer to build the Optical Map of your genome of interest from the extraction of the DNA to the combination of the data generated by the Saphyr system with your sequencing data.

Service workflow:

  • Isolation of High Molecular Weight DNA from plant tissues
  • Direct labeling of the DNA (DLE production)
  • Loading prepared DNA on a Saphyr Chip
  • Imaging of linearized DNA molecules by the Saphyr system
  • Data analysis using Access software to build the optical map of the genome

Optical Mapping with BioNano Genomics Technology General workflow

Optical maps are powerful tools for understanding the structures and functions of genomes. They are particularly useful for scaffolding de novo sequences and for detecting structural variations and repetitions within complex genomes.

Comparing several individual optical maps will allow you to highlight the structural variations and sequence copy number variation while providing positional information.

Since the installation of the first Bionano system in 2016, the CNRGV has carried out numerous projects to improve genome assembly or to analyse the structural variations between different genotypes. Figure 2


Optical map produced @CNRGV from 2016 to 2020

Figure 2: Number of optical maps produced at CNRGV per year and related species.


Example of Optical maps to improve the genome assembly quality :

  • Sunflower as part of the SUNRISE project: optical map with a 175Mb N50 and 25 maps for 17 chromosomes. Improvement of the genome scaffolds N50 by 350 times reaching chromosome size.
  • Tomato: optical maps with 60 Mbp N50 and only 30 maps for 30 chromosomes.
  • Maize as part of AMAIZING project : Validation of the NRGene maize assemblies with optical maps reaching N50 >100 Mb
  • Bread wheat, Renan genotype, as part of the WHEATomics project: optical maps will be combine with long reads produced by the third generation sequencing platform.

Example of Analysis of structural variations by comparing optical maps of several genotypes: 

  • Comparison of optical maps produced from wild and Landrace sunflower populations. Project in collaboration with B. Blackman, Berkley University, California.

Genome optical mapping equipment

The CNRGV is equipped with a complete equipment dedicated to the production and processing of DNA of ultra high molecular weight.

This UHMW DNA allows to obtain highly informative optical maps using the Bionano technology.

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