Genome optical mapping

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Next Generation Sequencing (NGS) has become a significant tool for genomic research. However, the short reads generated do not make it possible to organize the very repeated zones. Even the long reads of 3rd generation sequencing leave unknown zones in genome assemblies.

Optical mapping is a technique used to obtain a physical map of a genome through the production of specific fingerprints left by large labeled DNA molecules. Bionano’s Saphyr provides long-distance information to reveal the true structure of the genome.

At the CNRGV, we offer the possibility to build a physical map of your genome of interest from plant tissue DNA extraction until the establishment of an optical map with the Saphyr system and the new chemistry that labels directly the DNA:

  • Isolation of High Molecular Weight DNA from frozen or fresh tissues  of your plant of interest
  • Direct labeling of the DNA (DLE production)
  • Loading prepared DNA on a Saphyr Chip
  • Saphyr images of DNA molecules linearized in the nanochannels
  • 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.

Saphyr technology can also be used to develop other applications involving the detection of specific DNA markers. We are always ready to help you with your scientific projects.

Several projects have been carried out and others are currently in progress at the CNRGV. Their objective is to improve genome assembly or to analyze the structural variations between different genotypes.


Example of Optical maps to improve the genome assembly quality :

  • Sunflower as part of the SUNRISE project: optical map with a 175Mb N50 and only 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.


Many other projects have been realized (orobanch, melon, medicago, lupine, vanilla, rapeseed, ragweed...) or are in progress (beech, aphid, sunflower ...)


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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