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@ARTICLE{Vilanova:878413,
      author       = {Vilanova, Santiago and Alonso, David and Gramazio, Pietro
                      and Plazas, Mariola and García-Fortea, Edgar and Ferrante,
                      Paola and Schmidt, Maximilian and Díez, María José and
                      Usadel, Björn and Giuliano, Giovanni and Prohens, Jaime},
      title        = {{SILEX}: a fast and inexpensive high-quality {DNA}
                      extraction method suitable for multiple sequencing platforms
                      and recalcitrant plant species},
      journal      = {Plant methods},
      volume       = {16},
      number       = {1},
      issn         = {1746-4811},
      address      = {London},
      publisher    = {BioMed Central},
      reportid     = {FZJ-2020-02843},
      pages        = {110},
      year         = {2020},
      abstract     = {Background: The use of sequencing and genotyping platforms
                      has undergone dramatic improvements, enablingthe generation
                      of a wealth of genomic information. Despite this progress,
                      the availability of high-quality genomicDNA (gDNA) in
                      sufcient concentrations is often a main limitation,
                      especially for third-generation sequencing plat‑forms. A
                      variety of DNA extraction methods and commercial kits are
                      available. However, many of these are costly andfrequently
                      give either low yield or low-quality DNA, inappropriate for
                      next generation sequencing (NGS) platforms.Here, we describe
                      a fast and inexpensive DNA extraction method (SILEX)
                      applicable to a wide range of plant speciesand
                      tissues.Results: SILEX is a high-throughput DNA extraction
                      protocol, based on the standard CTAB method with a DNA
                      silicamatrix recovery, which allows obtaining NGS-quality
                      high molecular weight genomic plant DNA free of
                      inhibitorycompounds. SILEX was compared with a standard CTAB
                      extraction protocol and a common commercial extraction kitin
                      a variety of species, including recalcitrant ones, from
                      diferent families. In comparison with the other methods,
                      SILEXyielded DNA in higher concentrations and of higher
                      quality. Manual extraction of 48 samples can be done in 96
                      minby one person at a cost of 0.12 €/sample of reagents
                      and consumables. Hundreds of tomato gDNA samples
                      obtainedwith either SILEX or the commercial kit were
                      successfully genotyped with Single Primer Enrichment
                      Technology(SPET) with the Illumina HiSeq 2500 platform.
                      Furthermore, DNA extracted from Solanum elaeagnifolium using
                      thisprotocol was assessed by Pulsed-feld gel electrophoresis
                      (PFGE), obtaining a suitable size ranges for most
                      sequencingplatforms that required high-molecular-weight DNA
                      such as Nanopore or PacBio.Conclusions: A high-throughput,
                      fast and inexpensive DNA extraction protocol was developed
                      and validated for awide variety of plants and tissues. SILEX
                      ofers an easy, scalable, efcient and inexpensive way to
                      extract DNA for vari‑ous next-generation sequencing
                      applications including SPET and Nanopore among
                      others.Keywords: DNA extraction, CTAB protocol, Silica
                      matrix, Contaminant-free DNA, High-molecular-weight DNA,
                      Nextgeneration sequencing, High-throughput genotyping,
                      Recalcitrant species, SPET, Nanopore},
      cin          = {IBG-4},
      ddc          = {570},
      cid          = {I:(DE-Juel1)IBG-4-20200403},
      pnm          = {582 - Plant Science (POF3-582) / 583 - Innovative
                      Synergisms (POF3-583)},
      pid          = {G:(DE-HGF)POF3-582 / G:(DE-HGF)POF3-583},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:32793297},
      UT           = {WOS:000561439100002},
      doi          = {10.1186/s13007-020-00652-y},
      url          = {https://juser.fz-juelich.de/record/878413},
}