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Related Experiment Video

Updated: Jul 26, 2025

High-Throughput Analysis of Optical Mapping Data Using ElectroMap

High-Throughput Analysis of Optical Mapping Data Using ElectroMap

Published on: June 4, 2019

Flow Sorting-Assisted Optical Mapping.

Hana Šimková¹, Zuzana Tulpová², Petr Cápal²

¹Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic. simkovah@ueb.cas.cz.

Methods in Molecular Biology (Clifton, N.J.)

|June 19, 2023

Summary

This summary is machine-generated.

Optical mapping requires ultra-long high-molecular-weight DNA (uHMW DNA). Flow cytometry effectively purifies plant nuclei for uHMW DNA isolation, enabling genome and chromosome optical maps.

Keywords:

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

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Area of Science:

Genomics
Molecular Biology
Biotechnology

Background:

Optical mapping is crucial for genome research, aiding sequence assembly and structural variation analysis.
Obtaining ultra-long high-molecular-weight DNA (uHMW DNA) from plants is difficult due to cell walls, chloroplasts, secondary metabolites, and nucleases.
Flow cytometry offers a solution for efficient purification of plant cell nuclei or chromosomes.

Purpose of the Study:

To present a detailed protocol for preparing uHMW DNA from plants using flow cytometry.
To enable the construction of whole-genome and chromosomal optical maps for diverse plant species.

Main Methods:

Utilizing flow cytometry for rapid and efficient purification of plant cell nuclei or metaphase chromosomes.
Embedding purified nuclei/chromosomes in agarose plugs for in situ isolation of uHMW DNA.
Applying the protocol to generate optical maps.

Main Results:

Successfully developed a flow sorting-assisted protocol for uHMW DNA preparation in plants.
Demonstrated the protocol's efficacy in constructing whole-genome and chromosomal optical maps.
Validated the method across 20 plant species from multiple families.

Conclusions:

Flow cytometry is a key enabling technology for overcoming plant-specific challenges in uHMW DNA isolation.
This protocol facilitates high-resolution optical mapping in a wide range of plant species.
The method supports advanced plant genome research, including assembly and structural variation studies.