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SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

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SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

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dc.contributor.author Vilanova Navarro, Santiago es_ES
dc.contributor.author Alonso-Martín, David es_ES
dc.contributor.author Gramazio, Pietro es_ES
dc.contributor.author Plazas Ávila, María de la O es_ES
dc.contributor.author García-Fortea, Edgar es_ES
dc.contributor.author Ferrante, Paola es_ES
dc.contributor.author Schmidt, Maximilian es_ES
dc.contributor.author Díez Niclós, Mª José Teresa De Jesús es_ES
dc.contributor.author Usadel, Björn es_ES
dc.contributor.author Giuliano, Giovanni es_ES
dc.contributor.author Prohens Tomás, Jaime es_ES
dc.date.accessioned 2021-11-05T12:37:14Z
dc.date.available 2021-11-05T12:37:14Z
dc.date.issued 2020-08-10 es_ES
dc.identifier.issn 1746-4811 es_ES
dc.identifier.uri http://hdl.handle.net/10251/176129
dc.description.abstract [EN] Background The use of sequencing and genotyping platforms has undergone dramatic improvements, enabling the generation of a wealth of genomic information. Despite this progress, the availability of high-quality genomic DNA (gDNA) in sufficient concentrations is often a main limitation, especially for third-generation sequencing platforms. A variety of DNA extraction methods and commercial kits are available. However, many of these are costly and frequently 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 species and tissues. Results SILEX is a high-throughput DNA extraction protocol, based on the standard CTAB method with a DNA silica matrix recovery, which allows obtaining NGS-quality high molecular weight genomic plant DNA free of inhibitory compounds. SILEX was compared with a standard CTAB extraction protocol and a common commercial extraction kit in a variety of species, including recalcitrant ones, from different families. In comparison with the other methods, SILEX yielded DNA in higher concentrations and of higher quality. Manual extraction of 48 samples can be done in 96 min by one person at a cost of 0.12 euro/sample of reagents and consumables. Hundreds of tomato gDNA samples obtained with either SILEX or the commercial kit were successfully genotyped with Single Primer Enrichment Technology (SPET) with the Illumina HiSeq 2500 platform. Furthermore, DNA extracted fromSolanum elaeagnifoliumusing this protocol was assessed by Pulsed-field gel electrophoresis (PFGE), obtaining a suitable size ranges for most sequencing platforms 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 a wide variety of plants and tissues. SILEX offers an easy, scalable, efficient and inexpensive way to extract DNA for various next-generation sequencing applications including SPET and Nanopore among others. es_ES
dc.description.sponsorship This research has been funded by the European Union's Horizon 2020 research and innovation programme under grant agreement No 677379 (Linking genetic resources, genomes and phenotypes of Solanaceous crops; G2P-SOL). David Alonso is grateful to Universitat Politecnica de Valencia for a predoctoral (PAID-01-16) contract under the Programa de Ayudas de Investigacion y Desarrollo initiative. Mariola Plazas is grateful to Generalitat Valenciana and Fondo Social Europeo for a postdoctoral grant (APOSTD/2018/014). Pietro Gramazio is grateful to Japan Society for the Promotion of Science for a Postdoctoral Grant (P19105, FY2019 JSPS Postdoctoral Fellowship for Research in Japan (Standard)). The Spanish Ministerio de Educacion, Cultura y Deporte funded a predoctoral fellowship granted to Edgar Garcia-Fortea (FPU17/02389). es_ES
dc.language Inglés es_ES
dc.publisher Springer (Biomed Central Ltd.) es_ES
dc.relation.ispartof Plant Methods es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject DNA extraction es_ES
dc.subject CTAB protocol es_ES
dc.subject Silica matrix es_ES
dc.subject Contaminant-free DNA es_ES
dc.subject High-molecular-weight DNA es_ES
dc.subject Next-generation sequencing es_ES
dc.subject High-throughput genotyping es_ES
dc.subject Recalcitrant species es_ES
dc.subject SPET es_ES
dc.subject Nanopore es_ES
dc.subject.classification GENETICA es_ES
dc.title SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/s13007-020-00652-y es_ES
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/677379/EU/Linking genetic resources, genomes and phenotypes of Solanaceous crops/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/UPV//PAID-01-16/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/JSPS//P19105/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/GVA//APOSTD%2F2018%2F014//Contratación investigador postdoctoral GVA-Plazas Avila. Proyecto: Desarrollo de materiales de berenjena con introgresiones silv/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MECD//FPU17%2F02389//AYUDA CONTRATO PREDOCTORAL FPU-GARCIA FORTEA. PROYECTO: UTILIZACION DE ESPECIES SILVESTRES RELACIONADAS PARA LA MEJORA GENETICA DE LA BERENJENA/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana - Institut Universitari de Conservació i Millora de l'Agrodiversitat Valenciana es_ES
dc.description.bibliographicCitation Vilanova Navarro, S.; Alonso-Martín, D.; Gramazio, P.; Plazas Ávila, MDLO.; García-Fortea, E.; Ferrante, P.; Schmidt, M.... (2020). SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species. Plant Methods. 16(1):1-11. https://doi.org/10.1186/s13007-020-00652-y es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1186/s13007-020-00652-y es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 11 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 16 es_ES
dc.description.issue 1 es_ES
dc.identifier.pmid 32793297 es_ES
dc.identifier.pmcid PMC7419208 es_ES
dc.relation.pasarela S\431061 es_ES
dc.contributor.funder Generalitat Valenciana es_ES
dc.contributor.funder COMISION DE LAS COMUNIDADES EUROPEA es_ES
dc.contributor.funder Universitat Politècnica de València es_ES
dc.contributor.funder Japan Society for the Promotion of Science es_ES
dc.contributor.funder Ministerio de Educación, Cultura y Deporte es_ES
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