State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
Mol Ecol Resour. 2014 Mar;14(2):336-43. doi: 10.1111/1755-0998.12185. Epub 2013 Nov 22.
The ideal DNA barcode for plants remains to be discovered, and the candidate barcode rbcL has been met with considerable skepticism since its proposal. In fact, the variability within this gene has never been fully explored across all plant groups from algae to flowering plants, and its performance as a barcode has not been adequately tested. By analysing all of the rbcL sequences currently available in GenBank, we attempted to determine how well a region of rbcL performs as a barcode in species discrimination. We found that the rbcLb region was more variable than the frequently used rbcLa region. Both universal and plant group-specific primers were designed to amplify rbcLb, and the performance of rbcLa and rbcLb was tested in several ways. Using blast, both regions successfully identified all families and nearly all genera; however, the successful species identification rates varied significantly among plant groups, ranging from 24.58% to 85.50% for rbcLa and from 36.67% to 90.89% for rbcLb. Successful species discrimination ranged from 5.19% to 96.33% for rbcLa and from 22.09% to 98.43% for rbcLb in species-rich families, and from 0 to 88.73% for rbcLa and from 2.04% to 100% for rbcLb in species-rich genera. Both regions performed better for lower plants than for higher plants, although rbcLb performed significantly better than rbcLa overall, particularly for angiosperms. Considering the applicability across plants, easy and unambiguous alignment, high primer universality, high sequence quality and high species discrimination power for lower plants, we suggest rbcLb as a universal plant barcode.
植物的理想 DNA 条码仍有待发现，候选条码 rbcL 自提出以来一直受到相当大的怀疑。事实上，该基因的变异性从未在藻类到开花植物的所有植物群中得到充分探索，其作为条码的性能也没有得到充分测试。通过分析 GenBank 中目前可用的所有 rbcL 序列，我们试图确定 rbcL 作为物种鉴别条码的性能如何。我们发现 rbcLb 区域比常用的 rbcLa 区域更具变异性。设计了通用和植物群特异性引物来扩增 rbcLb，并以多种方式测试了 rbcLa 和 rbcLb 的性能。使用 blast，这两个区域都成功地识别了所有科和几乎所有属；然而，成功的物种鉴定率在植物群之间差异显著，rbcLa 的范围为 24.58%至 85.50%，rbcLb 的范围为 36.67%至 90.89%。rbcLa 的成功物种鉴别率从 5.19%到 96.33%，rbcLb 的从 22.09%到 98.43%，在物种丰富的科中，rbcLa 的从 0 到 88.73%，rbcLb 的从 2.04%到 100%。rbcLb 在低等植物中的表现优于高等植物，尽管 rbcLb 的总体表现明显优于 rbcLa，特别是对于被子植物。考虑到在植物中的适用性、易于明确的比对、高引物通用性、高质量序列和高低等植物的物种鉴别能力，我们建议 rbcLb 作为通用植物条码。
