Flow Sorting–Assisted Optical Mapping

Hana Šimková*, Zuzana Tulpová, Petr Cápal

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


Optical mapping—a technique that visualizes short sequence motives along DNA molecules of hundred kilobases to megabase in size—has found an important place in genome research. It is widely used to facilitate genome sequence assemblies and analyses of genome structural variations. Application of the technique is conditional on availability of highly pure ultra-long high-molecular-weight DNA (uHMW DNA), which is challenging to achieve in plants due to the presence of the cell wall, chloroplasts, and secondary metabolites, just as a high content of polysaccharides and DNA nucleases in some species. These obstacles can be overcome by employment of flow cytometry, enabling a fast and highly efficient purification of cell nuclei or metaphase chromosomes, which are afterward embedded in agarose plugs and used to isolate the uHMW DNA in situ. Here, we provide a detailed protocol for the flow sorting–assisted uHMW DNA preparation that has been successfully used to construct whole-genome as well as chromosomal optical maps for 20 plant species from several plant families.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages19
StatePublished - 2023
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Bionano genome map
  • Chromosomes
  • Flow cytometry and sorting
  • HMW DNA preparation
  • Nuclei
  • Optical mapping
  • ultralong high-molecular-weight DNA


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