Genome optical mapping

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Optical mapping is a technique that relies on the Saphyr system from Bionano 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 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.


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 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.


Example of Optical maps to improve the assembly quality of genome:


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  • Genome size: 3.2G
  • Genome Optical map results: 43 maps with N50=155Mb
  • Sequence assembly results: 552 contigs with N50=140 Mb
  • Hybrid assembly results combining of data assembly from optical map and sequencing: 1 scaffold by chromosome (2n = 34) with N50=178Mb


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Polyploid wheat

  • Genome size: 15Gb
  • Genome optical map results obtained thanks to roots DNA extraction: 968 maps with N50=51Mb
  • Sequence assembly results: 5055 contigs with N50=30.22 Mb
  • Hybrid assembly results combining of data assembly from optical map and sequencing: 324 scaffolds with N50=204.3 Mb

The longest hybrid scaffold was 627.2 Mb and covered 99% of chromosome 3D.

Publication:  Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning


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Apricot tree

  • Genome size: 0.24Gb
  • Genome optical map results: 30 maps with N50=14Mb
  • Sequence assembly results: 301 contigs with N50=1.7 Mb
  • Hybrid assembly results combining of data assembly from optical map and sequencing: 19 scaffolds with N50=14.6Mb

In this project, this apricot genome was the reference to be compared with three other genomes, produced using the same assembly strategy at various levels.We used OMAP to produce a catalog of large SV (insertion/deletion, duplication and inversion) for the 3 genomes compared to the reference. This approach is complementary to genome comparison through sequences alignments, bringing validation of SV detected through contigs comparison.

Publication: Population genomics of apricots unravels domestication history and adaptive events

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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