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Analysis of institutional authors

Vilanova, SantiagoCorresponding AuthorAlonso, DavidAuthorGramazio, PietroAuthorPlazas, MariolaAuthorProhens, JaimeAuthor

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October 9, 2024
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Article

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

Publicated to: Plant Methods. 16 (1): 1-11 - 2020-01-01 16(1), DOI: 10.1186/s13007-020-00652-y

Authors:

Vilanova Navarro, Santiago; Alonso-Martín, David; Gramazio, Pietro; Plazas Ávila, María de la O; García-Fortea, Edgar; Ferrante, Paola; Schmidt, Maximilian; Díez Niclós, Mª José Teresa De Jesús; Usadel, Björn; Giuliano, Giovanni; Prohens Tomás, Jaime
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Affiliations

Forschungszentrum Julich, BG Bioinformat 4, D-52428 Julich, Germany - Author
Heinrich Heine Univ Dusseldorf, Inst Biol Data Sci, CEPLAS, D-40225 Dusseldorf, Germany - Author
Italian Natl Agcy New Technol Energy & Sustainabl, ENEA, Rome, Italy - Author
Univ Politecn Valencia, Inst Conservac & Mejora Agrodiversidad Valenciana, Camino Vera 14, Valencia 46022, Spain - Author
Univ Tsukuba, Fac Life & Environm Sci, 1-1-1 Tennodai, Tsukuba, Ibaraki 3058572, Japan - Author
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Abstract

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.
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Keywords

BuffeContaminant-free dnaCtab protocolDna extractionElaeagnifoliumHigh-molecular-weight dnaHigh-throughput genotypingNanoporNanoporeNext-generation sequencingPlasmidProtocolPurificationRecalcitrant speciesSilica matrixSpet

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Plant Methods due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2020, it was in position 24/235, thus managing to position itself as a Q1 (Primer Cuartil), in the category Plant Sciences. Notably, the journal is positioned above the 90th percentile.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 2.65. This indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 13, 2025)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Weighted Average of Normalized Impact by the Scopus agency: 2.82 (source consulted: FECYT Mar 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2026-04-03, the following number of citations:

  • WoS: 48
  • Scopus: 48
  • Europe PMC: 31
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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2026-04-03:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 138.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 138 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 30.
  • The number of mentions on the social network Facebook: 1 (Altmetric).
  • The number of mentions on the social network X (formerly Twitter): 53 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: http://hdl.handle.net/10251/176129
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Germany; Italy; Japan; United Kingdom.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Vilanova Navarro, Santiago) and Last Author (Prohens Tomás, Jaime).

the author responsible for correspondence tasks has been Vilanova Navarro, Santiago.

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Awards linked to the item

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).
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