Data from: Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques

A well-covered reference library is crucial for successful identification of species by DNA barcoding. The biggest difficulty in building such a reference library is the lack of materials of organisms. Herbarium collections are potentially an enormous resource of materials. In this study, we demonstrate that it is likely to build such reference libraries using the reconstructed (self-primed PCR amplified) DNA from the herbarium specimens. We used 179 rosaceous specimens to test the effects of DNA reconstruction, 420 randomly sampled specimens to estimate the usable percentage and another 223 specimens of true cherries (Cerasus, Rosaceae) to test the coverage of usable specimens to the species. The barcode rbcLb (the central four-sevenths of rbcL gene) and matK was each amplified in two halves and sequenced on Roche GS 454 FLX+. DNA from the herbarium specimens was typically shorter than 300 bp. DNA reconstruction enabled amplification fragments of 400–500 bp without bringing or inducing any sequence errors. About one-third of specimens in the national herbarium of China (PE) were proven usable after DNA reconstruction. The specimens in PE cover all Chinese true cherry species and 91.5% of vascular species listed in Flora of China. It is very possible to build well-covered reference libraries for DNA barcoding of vascular species in China. As exemplified in this study, DNA reconstruction and DNA-labelled next-generation sequencing can accelerate the construction of local reference libraries. By putting the local reference libraries together, a global library for DNA barcoding becomes closer to reality.

覆盖全面的参考文库，对于通过DNA条形码（DNA barcoding）技术实现物种精准鉴定至关重要。构建此类参考文库的最大瓶颈在于生物样本材料的匮乏。标本馆（Herbarium）馆藏实则蕴藏着极为丰富的样本资源。本研究证实，可利用标本馆标本中提取的经重构（自引PCR扩增）的DNA来构建此类参考文库。我们选取179份蔷薇科（rosaceous）标本以验证DNA重构的效果，随机抽取420份标本以评估可用样本占比，另选取223份樱属（Cerasus，蔷薇科）真樱桃类标本以检测可用标本的物种覆盖度。本研究针对条形码基因rbcLb（rbcL基因的中央七分之四段）与matK基因，均采用分两段扩增的方式，并在Roche GS 454 FLX+测序平台上完成测序。标本馆标本提取的DNA片段长度通常短于300碱基对（base pair, bp）。通过DNA重构，可获得长度为400~500碱基对的扩增片段，且不会引入或产生任何序列误差。经DNA重构后，中国国家植物标本馆（National Herbarium of China, PE）中约三分之一的标本被证实可用。该馆馆藏标本涵盖了中国所有的真樱桃类物种，以及《中国植物志》（Flora of China）收录的91.5%的维管植物物种。由此可见，构建覆盖完备的中国维管植物DNA条形码参考文库具备极高可行性。正如本研究所示，DNA重构与DNA标记下一代测序技术可大幅加快本地参考文库的构建进程。将各地本地参考文库整合后，DNA条形码全球参考文库的实现将不再遥远。