从宏基因组样品中鉴定植物的快速可靠的分析方法在鉴定加工生物材料的复杂混合物的成分中起着重要作用,包括食物,草药产品,肠道内容物或环境样品。通常用于从宏基因组样品中鉴定植物的不同的基于PCR的方法通常由于DNA降解而不适用。低水平的成功扩增或缺乏检测能力。我们介绍了一种结合宏基因组测序和基于无比对k-mer的方法的方法,用于鉴定经处理的宏基因组样品中的植物DNA。我们的方法直接从宏基因组测序读取识别植物DNA,不需要定位或组装读取。我们从组装的叶绿体基因组序列中鉴定出超过31,000个羽扇豆特异性32聚体。我们证明了羽扇豆DNA可以从目标物种(不同的羽扇豆物种)和密切相关的非目标物种(Arachishypogaea,最大甘氨酸,Pisumsativum,维西娅·法巴,菜豆,Culinaris透镜,和Cicerarietinum)。此外,在以下加工样品中可以检测到这些32聚体:羽扇豆粉,保存的种子和烤饼干含有不同量的羽扇豆粉。在受控条件下,在小麦粉中含有至少0.05%羽扇豆粉的烤饼干中可检测到羽扇豆特异性成分。
Fast and reliable analytical methods for the identification of plants from metagenomic samples play an important role in identifying the components of complex mixtures of processed biological materials, including food, herbal products, gut contents or environmental samples. Different PCR-based methods that are commonly used for plant identification from metagenomic samples are often inapplicable due to DNA degradation, a low level of successful amplification or a lack of detection power. We introduce a method that combines metagenomic sequencing and an alignment-free k-mer based approach for the identification of plant DNA in processed metagenomic samples. Our method identifies plant DNA directly from metagenomic sequencing reads and does not require mapping or assembly of the reads. We identified more than 31,000 Lupinus-specific 32-mers from assembled chloroplast genome sequences. We demonstrate that lupin DNA can be detected from controlled mixtures of sequences from target species (different Lupinus species) and closely related non-target species (Arachis hypogaea, Glycine max, Pisum sativum, Vicia faba, Phaseolus vulgaris, Lens culinaris, and Cicer arietinum). Moreover, these 32-mers are detectable in the following processed samples: lupin flour, conserved seeds and baked cookies containing different amounts of lupin flour. Under controlled conditions, lupin-specific components are detectable in baked cookies containing a minimum of 0.05% of lupin flour in wheat flour.