Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA.
Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA.
BMC Genomics. 2018 Dec 10;19(1):896. doi: 10.1186/s12864-018-5253-1.
The application of genomic data and bioinformatics for the identification of restricted or illegally-sourced natural products is urgently needed. The taxonomic identity and geographic provenance of raw and processed materials have implications in sustainable-use commercial practices, and relevance to the enforcement of laws that regulate or restrict illegally harvested materials, such as timber. Improvements in genomics make it possible to capture and sequence partial-to-complete genomes from challenging tissues, such as wood and wood products.
In this paper, we report the success of an alignment-free genome comparison method, [Formula: see text] that differentiates different geographic sources of white oak (Quercus) species with a high level of accuracy with very small amount of genomic data. The method is robust to sequencing errors, different sequencing laboratories and sequencing platforms.
This method offers an approach based on genome-scale data, rather than panels of pre-selected markers for specific taxa. The method provides a generalizable platform for the identification and sourcing of materials using a unified next generation sequencing and analysis framework.
迫切需要将基因组数据和生物信息学应用于受限或非法来源的天然产物的鉴定。原材料和加工材料的分类学身份和地理来源对可持续利用的商业实践具有影响，并且与执行规范或限制非法采集材料的法律有关，例如木材。基因组学的进步使得从木材和木制品等具有挑战性的组织中捕获和测序部分到完整基因组成为可能。
在本文中，我们报告了一种无比对基因组比较方法[Formula: see text]的成功，该方法能够以非常少量的基因组数据高度准确地区分白橡木（Quercus）物种的不同地理来源。该方法对测序错误、不同的测序实验室和测序平台具有鲁棒性。
该方法提供了一种基于基因组规模数据的方法，而不是针对特定分类群的预选标记面板。该方法为使用统一的下一代测序和分析框架进行材料的鉴定和溯源提供了一个可推广的平台。
