Bell Karen L, Loeffler Virginia M, Brosi Berry J
Department of Environmental Science, Emory University, 400 Dowman Drive, Atlanta, Georgia 30322 USA.
Appl Plant Sci. 2017 Mar 10;5(3). doi: 10.3732/apps.1600110. eCollection 2017 Mar.
DNA metabarcoding has broad-ranging applications in ecology, aerobiology, biosecurity, and forensics. A bioinformatics pipeline has recently been published for identification using a comprehensive database of ITS2, one of the common plant DNA barcoding markers. There is, however, no corresponding database for , the other primary marker used in plants.
Using publicly available data, we compiled a reference library of sequences and trained databases for use with UTAX and RDP classifier algorithms. We used this reference library, along with the existing bioinformatics pipeline and ITS2 reference library, to identify species in an artificial mixture of nine species of pollen. We have made this database publicly available in multiple formats, to allow use with multiple bioinformatics pipelines, now and in the future.
Using the database, in addition to the ITS2 database, we succeeded in making species-level identifications for eight species and a family-level identification of the ninth species. This is an improvement on ITS2 sequence alone.
The reference library described here will assist with identification of plant species using . By making another gene region available for standard barcoding, this will increase the resolution and accuracy of identifications.
DNA 代谢条码技术在生态学、空气生物学、生物安全和法医学等领域有着广泛应用。最近发布了一种生物信息学流程，可利用常见植物 DNA 条形码标记之一 ITS2 的综合数据库进行物种鉴定。然而，对于植物中使用的另一个主要标记，却没有相应的数据库。
利用公开可用数据，我们编制了一个 序列参考文库，并针对 UTAX 和 RDP 分类器算法训练了数据库。我们使用这个参考文库，以及现有的生物信息学流程和 ITS2 参考文库，对九种花粉的人工混合物中的物种进行鉴定。我们已将该数据库以多种格式公开提供，以便现在及未来能与多种生物信息学流程配合使用。
除了 ITS2 数据库外，使用 数据库，我们成功地对八个物种进行了物种水平的鉴定，并对第九个物种进行了科级鉴定。这比仅使用 ITS2 序列有了改进。
这里描述的参考文库将有助于利用 鉴定植物物种。通过提供另一个用于标准条形码的基因区域，这将提高鉴定的分辨率和准确性。
