The Genoscope (French National Sequencing Centre at the CEA) is equipped with an Argus® system (Figure 1), available from OpGenen (www.opgen.com), which can be used to generate optical mapping data for a genome. This technology is made available to the scientific community via the France Génomique infrastructure.
Figure 1 : The “ArgusTM Optical Mapping System” enables the contruction of whole genome restriction maps of microbial genomes
The principle of optical mapping data involves establishing an enzyme profile from genomic DNA molecules (gDNA), based on the size and order of the fragments obtained after digestion. Compiling several profiles from several molecules enables the construction of a whole genome restriction map, called an optical map. Currently, it is only possible to obtain a whole genome map for genomes of less than 50 Mb in size. For organisms with larger genomes, the optical mapping data can be combined with sequence data to improve assembly and in particular the N50 of the scaffolds.
Construction of whole genome restriction maps of cultivable bacteria (rarely more than 7 Mb in size) is a routine application in laboratories that have the Argus® system (14 such machines exist in the world), on condition that the necessary precautions are undertaken for preparation of the starting material. In fact, the degree of difficulty of the experiment is dependent on the quality of the material (genomic DNA) that is used. The desired size of the gDNA molecules, generally obtained after extraction, must be of high molecular weight, around 200-400 Kb. For organisms with a genome larger than 7 Mb, it is recommended to extract the gDNA from the lysed cells trapped in the agarose plugs.
Optical mapping has multiple applications.
Figure 2 : The ordered restriction map of a whole genome enables typing of strains (A), application of comparative genomics (B) and assembly improvements (C).
In the case of bacterial genomes, the most frequent uses are typing (Figure 2A) and comparative genomics of strains (Figure 2B), in addition to validation and improvement of sequence assembly (Figure 2C).
Thus, Genoscope offers the scientific community access to this equipment and expertise through scientific collaborations for the construction and analysis of optical maps for microbial genomes of interest. As for sequencing projects, requests for optical mapping can be made via the France Génomique web portal.
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