Genome optical mapping
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 Irys 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 Irys system:
- Isolation of High Molecular Weight DNA from frozen or fresh tissues of your plant of interest
- Nicking, labeling, repairing and staining of the DNA (NLRS production)
- Loading prepared DNA on an IrysChip chip
- Irys images of DNA molecules linearized in the nanochannels
- Data analysis using Irysview software to build the optical map of the genome
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.
Irys 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 are finished and / or are currently being carried out at the CNRGV:
- Sunflower genome assembly improvement using optical maps (in the frame of SUNRISE project): optical map with 2Mb N50 with BspQ1 and 1 Mb N50 with BssS1. Improvement of the genome scaffold assembly N50 by 12 fold
- Tomato genome assembly: optical map with 3.6 Mb N50 with BspQ1 and 2.7 Mb N50 with BssS1. Improvement of the genome scaffolds N50 by 10 fold (N50 genome scaffolds = 34 Mb)
- Cherry tree genome assembly: optical map of 1.8Mb N50 with BssS1
- Genomic structural variation analysis of maize variety in the frame of AMAIZING project
And several other projects have been carried out or are in progress (orobanch, passiflore, Medicago, oak, lupine...)