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. 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 €/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 from Solanum elaeagnifolium using 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. 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.

中文翻译：

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SILEX：一种快速、廉价的高质量 DNA 提取方法，适用于多个测序平台和顽固植物物种。

测序和基因分型平台的使用已经发生了巨大的改进，能够生成大量的基因组信息。尽管取得了这些进展，但足够浓度的高质量基因组 DNA (gDNA) 的可用性通常是一个主要限制，特别是对于第三代测序平台而言。有多种 DNA 提取方法和商业试剂盒可供选择。然而，其中许多方法成本高昂，并且常常产生低产量或低质量的 DNA，不适合下一代测序 (NGS) 平台。在这里，我们描述了一种快速且廉价的 DNA 提取方法 (SILEX)，适用于多种植物物种和组织。SILEX 是一种高通量 DNA 提取方案，基于标准 CTAB 方法和 DNA 硅胶基质回收，可获取 NGS 质量的高分子量植物基因组 DNA，不含抑制化合物。将 SILEX 与标准 CTAB 提取方案和常见的商业提取试剂盒在多种物种（包括来自不同科的顽固物种）中进行了比较。与其他方法相比，SILEX 产生的 DNA 浓度更高、质量更高。一人可在 96 分钟内手动提取 48 个样品，试剂和耗材成本为 0.12 欧元/样品。使用 SILEX 或商业试剂盒获得的数百个番茄 gDNA 样本均通过 Illumina HiSeq 2500 平台的单引物富集技术 (SPET) 成功进行了基因分型。此外，使用该方案从茄叶中提取的 DNA 通过脉冲场凝胶电泳 (PFGE) 进行评估，获得适合大多数需要高分子量 DNA（例如 Nanopore 或 PacBio）的测序平台的合适大小范围。针对多种植物和组织开发并验证了高通量、快速且廉价的 DNA 提取方案。SILEX 提供了一种简单、可扩展、高效且廉价的方法来提取 DNA，用于各种下一代测序应用，包括 SPET 和 Nanopore 等。