Intact DNA purified from flow-sorted nuclei unlocks the potential of next-generation genome mapping and assembly in Solanum species

Paola Gaiero, Hana Šimková, Jan Vrána, Federico F. Santiñaque, Beatriz López-Carro, Gustavo A. Folle, José van de Belt, Sander A. Peters, Jaroslav Doležel, Hans de Jong

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Next-generation genome mapping through nanochannels (Bionano optical mapping) of plant genomes brings genome assemblies to the ‘nearly-finished’ level for reliable and detailed gene annotations and assessment of structural variations. Despite the recent progress in its development, researchers face the technical challenges of obtaining sufficient high molecular weight (HMW) nuclear DNA due to cell walls which are difficult to disrupt and to the presence of cytoplasmic polyphenols and polysaccharides that co-precipitate or are covalently bound to DNA and might cause oxidation and/or affect the access of nicking enzymes to DNA, preventing downstream applications. Here we describe important improvements for obtaining HMW DNA that we tested on Solanum crops and wild relatives. The methods that we further elaborated and refined focus on • Improving flexibility of using different tissues as source materials, like fast-growing root tips and young leaves from seedlings or in vitro plantlets.• Obtaining nuclei suspensions through either lab homogenizers or by chopping.• Increasing flow sorting efficiency using DAPI (4′,6-diamidino-2-phenylindole) and PI (propidium iodide) DNA stains, with different lasers (UV or 488 nm) and sorting platforms such as the FACSAria and FACSVantage flow sorters, thus making it appropriate for more laboratories working on plant genomics.The obtained nuclei are embedded into agarose plugs for processing and isolating uncontaminated HMW DNA, which is a prerequisite for nanochannel-based next-generation optical mapping strategies.
LanguageEnglish
Pages328-336
JournalMethodsX
Volume5
DOIs
Publication statusPublished - 1 Jan 2018

Fingerprint

Solanum
Chromosome Mapping
Genes
DNA
Molecular Weight
Molecular weight
Sorting
Plant Genome
Molecular Sequence Annotation
Meristem
Propidium
Deoxyribonuclease I
Polyphenols
Genomics
Seedlings
Sepharose
Cell Wall
Polysaccharides
Suspensions
Lasers

Keywords

  • BioNano genome mapping
  • Flow sorting
  • Genome finishing
  • HMW DNA isolation

Cite this

Gaiero, Paola ; Šimková, Hana ; Vrána, Jan ; Santiñaque, Federico F. ; López-Carro, Beatriz ; Folle, Gustavo A. ; van de Belt, José ; Peters, Sander A. ; Doležel, Jaroslav ; de Jong, Hans. / Intact DNA purified from flow-sorted nuclei unlocks the potential of next-generation genome mapping and assembly in Solanum species. In: MethodsX. 2018 ; Vol. 5. pp. 328-336.
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Intact DNA purified from flow-sorted nuclei unlocks the potential of next-generation genome mapping and assembly in Solanum species. / Gaiero, Paola; Šimková, Hana; Vrána, Jan; Santiñaque, Federico F.; López-Carro, Beatriz; Folle, Gustavo A.; van de Belt, José; Peters, Sander A.; Doležel, Jaroslav; de Jong, Hans.

In: MethodsX, Vol. 5, 01.01.2018, p. 328-336.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Folle, Gustavo A.

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