Replacing Sanger with Next Generation Sequencing to improve coverage and quality of reference DNA barcodes for plants.
Replacing Sanger with Next Generation Sequencing to improve coverage and quality of reference DNA barcodes for plants.
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DOI：
10.1038/srep46040
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发表时间：
2017-04-12
影响因子：
4.6
通讯作者：
Gooding P
中科院分区：
文献类型：
--
作者：
Wilkinson MJ;Szabo C;Ford CS;Yarom Y;Croxford AE;Camp A;Gooding P
我们估计全球BOLD系统数据库拥有约15%的陆地植物物种的核心DNA条形码（rbcL + matK），全面的物种覆盖仍需数十年。资源的临时性能受到可变序列重叠和每个条形码内适度信息内容的影响。我们的模型预测，随着数据库的增长，物种独特条形码的比例会降低，并且在数据库几乎完成之前，“假”物种独特条形码的比例仍保持在>5%。我们得出结论，目前的rbcL + matK条形码不适合目的。基因组略读和补充条形码可以提高诊断能力，但会减缓新条形码的获取。因此，我们提出了两种新的下一代测序方案（免费软件），能够准确，大规模并行从头组装>1400 bp的高质量DNA条形码。我们将探讨这些能力如何在未来几十年内增强物种诊断。
We estimate the global BOLD Systems database holds core DNA barcodes (rbcL + matK) for about 15% of land plant species and that comprehensive species coverage is still many decades away. Interim performance of the resource is compromised by variable sequence overlap and modest information content within each barcode. Our model predicts that the proportion of species-unique barcodes reduces as the database grows and that ‘false’ species-unique barcodes remain >5% until the database is almost complete. We conclude the current rbcL + matK barcode is unfit for purpose. Genome skimming and supplementary barcodes could improve diagnostic power but would slow new barcode acquisition. We therefore present two novel Next Generation Sequencing protocols (with freeware) capable of accurate, massively parallel de novo assembly of high quality DNA barcodes of >1400 bp. We explore how these capabilities could enhance species diagnosis in the coming decades.