Naturalis Biodiversity Center, Darwinweg 4, 2333 CR Leiden, The Netherlands.
BMC Bioinformatics. 2014 Feb 6;15:44. doi: 10.1186/1471-2105-15-44.
Mixtures of internationally traded organic substances can contain parts of species protected by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). These mixtures often raise the suspicion of border control and customs offices, which can lead to confiscation, for example in the case of Traditional Chinese medicines (TCMs). High-throughput sequencing of DNA barcoding markers obtained from such samples provides insight into species constituents of mixtures, but manual cross-referencing of results against the CITES appendices is labor intensive. Matching DNA barcodes against NCBI GenBank using BLAST may yield misleading results both as false positives, due to incorrectly annotated sequences, and false negatives, due to spurious taxonomic re-assignment. Incongruence between the taxonomies of CITES and NCBI GenBank can result in erroneous estimates of illegal trade.
The HTS barcode checker pipeline is an application for automated processing of sets of 'next generation' barcode sequences to determine whether these contain DNA barcodes obtained from species listed on the CITES appendices. This analytical pipeline builds upon and extends existing open-source applications for BLAST matching against the NCBI GenBank reference database and for taxonomic name reconciliation. In a single operation, reads are converted into taxonomic identifications matched with names on the CITES appendices. By inclusion of a blacklist and additional names databases, the HTS barcode checker pipeline prevents false positives and resolves taxonomic heterogeneity.
The HTS barcode checker pipeline can detect and correctly identify DNA barcodes of CITES-protected species from reads obtained from TCM samples in just a few minutes. The pipeline facilitates and improves molecular monitoring of trade in endangered species, and can aid in safeguarding these species from extinction in the wild. The HTS barcode checker pipeline is available at https://github.com/naturalis/HTS-barcode-checker.
国际贸易中的混合有机物质可能包含受《濒危野生动植物种国际贸易公约》（CITES）保护的物种的一部分。这些混合物经常引起边境管制和海关办公室的怀疑，可能导致没收，例如在传统中药（TCM）的情况下。从这些样本中获得的 DNA 条形码标记的高通量测序提供了对混合物中物种成分的深入了解，但手动将结果交叉引用 CITES 附录是劳动密集型的。使用 BLAST 将 DNA 条形码与 NCBI GenBank 进行匹配可能会产生误导性结果，既可能出现假阳性（由于注释序列不正确），也可能出现假阴性（由于虚假的分类重新分配）。CITES 和 NCBI GenBank 的分类学之间的不一致可能导致对非法贸易的错误估计。
HTS 条形码检查器管道是一种用于自动处理“下一代”条形码序列集的应用程序，以确定这些序列是否包含来自 CITES 附录中列出的物种的 DNA 条形码。该分析管道建立在现有的用于针对 NCBI GenBank 参考数据库进行 BLAST 匹配和分类名称协调的开源应用程序之上，并进行了扩展。在单个操作中，读取内容会转换为与 CITES 附录中的名称匹配的分类鉴定。通过包含黑名单和其他名称数据库，HTS 条形码检查器管道可以防止假阳性并解决分类异质性。
HTS 条形码检查器管道可以在短短几分钟内从 TCM 样本中获得的读取内容中检测并正确识别 CITES 保护物种的 DNA 条形码。该管道有助于并改善对濒危物种贸易的分子监测，并有助于保护这些物种免受野外灭绝。HTS 条形码检查器管道可在 https://github.com/naturalis/HTS-barcode-checker 上获得。
