Identification of species in the angiosperm family Apiaceae using DNA barcodes
Identification of species in the angiosperm family Apiaceae using DNA barcodes
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DOI：
10.1111/1755-0998.12262
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发表时间：
2014-11-01
影响因子：
7.7
通讯作者：
Downie, Stephen R.
中科院分区：
文献类型：
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作者：
Liu, Jinxin;Shi, Linchun;Downie, Stephen R.
伞形科（Apiaceae）是被子植物的一个大科，包括许多药用重要物种。识别这些物种及其掺杂物的能力很重要，但由于其微妙的果实形态差异以及保存标本中通常缺乏诊断特征而难以做到。此外，干燥的根通常是官方的医疗器官，使视觉识别物种几乎不可能。DNA条形码已被认为是一种强有力的物种鉴定工具。生命条形码联盟（CBOL）植物工作组建议将rbcL+matK的组合作为核心植物条形码。最近，中国植物BOL组提出，核核糖体DNA内转录间隔区（ITS），以及该标记的一个子集（ITS 2），与rbcL+matK一起纳入种子植物，特别是被子植物的核心条形码。在这项研究中，我们评估了这四个标记加上psbA-trnH作为伞形科条形码的有效性。共获得6032条序列，代表385属1957种，其中211条为新获得序列，代表7种50个个体。在这5个标记中，ITS和ITS 2在种内和种间差异和DNA条形码缺口评估中显示出上级结果。在匹配的数据集（173个样本，代表5属45个物种）中，ITS位点的识别效率最高（73.3%），而ITS 2的识别效率也相对较高（66.7%）。ITS+psbA-trnH标记组合（ITS 2 +psbA-trnH为80%）的鉴定效率显著高于rbcL+matK标记组合（40%）。对3052个ITS序列、3732个ITS 2序列、1011个psbA-trnH序列、567个matK序列和566个rbcL序列的全样本数据集，ITS、ITS 2、psbA-trnH、matK和rbcL的区分能力分别为70.0%、64.3%、49.5%、38.6%和32.1%。这些结果证实了ITS或其子集ITS 2可以整合到伞形科的核心条形码中，并且ITS/ITS 2 +psbA-trnH的组合作为伞形科鉴定的强大的标准DNA条形码具有很大的潜在价值。
Apiaceae (Umbelliferae) is a large angiosperm family that includes many medicinally important species. The ability to identify these species and their adulterants is important, yet difficult to do so because of their subtle fruit morphological differences and often lack of diagnostic features in preserved specimens. Moreover, dried roots are often the official medical organs, making visual identification to species almost impossible. DNA barcoding has been proposed as a powerful taxonomic tool for species identification. The Consortium for the Barcode of Life (CBOL) Plant Working Group has recommended the combination of rbcL+matK as the core plant barcode. Recently, the China Plant BOL Group proposed that the nuclear ribosomal DNA internal transcribed spacer (ITS), as well as a subset of this marker (ITS2), be incorporated alongside rbcL+matK into the core barcode for seed plants, particularly angiosperms. In this study, we assess the effectiveness of these four markers plus psbA-trnH as Apiaceae barcodes. A total of 6032 sequences representing 1957 species in 385 diverse genera were sampled, of which 211 sequences from 50 individuals (representing seven species) were newly obtained. Of these five markers, ITS and ITS2 showed superior results in intra- and interspecific divergence and DNA barcoding gap assessments. For the matched data set (173 samples representing 45 species in five genera), the ITS locus had the highest identification efficiency (73.3%), yet ITS2 also performed relatively well with 66.7% identification efficiency. The identification efficiency increased to 82.2% when using an ITS+psbA-trnH marker combination (ITS2+psbA-trnH was 80%), which was significantly higher than that of rbcL+matK (40%). For the full sample data set (3052 ITS sequences, 3732 ITS2 sequences, 1011 psbA-trnH sequences, 567 matK sequences and 566 rbcL sequences), ITS, ITS2, psbA-trnH, matK and rbcL had 70.0%, 64.3%, 49.5%, 38.6% and 32.1% discrimination abilities, respectively. These results confirm that ITS or its subset ITS2 be incorporated into the core barcode for Apiaceae and that the combination of ITS/ITS2+psbA-trnH has much potential value as a powerful, standard DNA barcode for Apiaceae identification.