Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.
Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.
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DOI：
10.1371/journal.pone.0002802
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发表时间：
2008-07-30
期刊：
影响因子：
3.7
通讯作者：
Barrett SC
中科院分区：
文献类型：
--
作者：
Fazekas AJ;Burgess KS;Kesanakurti PR;Graham SW;Newmaster SG;Husband BC;Percy DM;Hajibabaei M;Barrett SC
陆地植物的通用条形码系统将是一种宝贵的资源，在生态学、植物学、执法和工业等领域具有潜在的用途。然而，植物条形码的应用一直受到关于最可变和技术上实用的dna区域缺乏共识的限制(S)。我们比较了来自质体体的8个候选植物条形码区域和来自线粒体基因组的一个候选植物条形码区域对32个不同属的92个物种的单系区分能力(N = 251个样本)。叶绿体标记包括5个编码区(rpoB、rpoC1、rbcL、matK和23S rDNA)和3个非编码区(trnH-PSBA、atpF-atpH和psbK-PSBI)。我们的调查包括几个分类上复杂的类群，在所有情况下，我们都检查了多个种群和物种。就扩增和测序成功而言，这些区域在区分物种的能力和检索的便利性方面存在差异。单基因座分辨率为7%(23S RDNA)到59%(trnH-PSBA)，具有良好的单系支持。序列回收率主要与扩增成功率有关(叶绿体基因座为85%-100%)，其中matK需要最大的努力才能实现合理的回收(使用10对引物时为88%)。有几个基因座(matK、psbK-PSBI、trnH-PSBA)对产生全双向序列有问题。撇开与扩增和测序相关的技术问题不谈，结合更具变异性的叶绿体标记对分辨物种提供了明显的好处，尽管回报递减，因为使用四到七个区域评估的所有组合的成功率仅略有不同(69-71%；几个两区域和三区域组合接近的值)。这一性能平台期可能表明物种识别精度的基本上限，这可能是包括适中数量的叶绿体标记的DNA条形码系统所可能的。因此，解决关于植物条形码的有争议的争论应该涉及更多地关注与多位点植物DNA条形码系统中的序列恢复的简易性、全局比对和标记冗余相关的实际问题。
A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s). We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (N = 251 samples). The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA) and three non-coding (trnH-psbA, atpF–atpH, and psbK–psbI) loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA) to 59% (trnH-psbA) of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85–100% for plastid loci), with matK requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs). Several loci (matK, psbK–psbI, trnH-psbA) were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69–71%; values that were approached by several two- and three-region combinations). This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the contentious debate on plant barcoding should therefore involve increased attention to practical issues related to the ease of sequence recovery, global alignability, and marker redundancy in multilocus plant DNA barcoding systems.
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DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
影响因子：
3.4
作者：
Cowan, Robyn S.;Chase, Mark W.;Savolainen, Vincent
通讯作者：
Savolainen, Vincent
影响因子：
3.4
作者：
Mower JP;Touzet P;Gummow JS;Delph LF;Palmer JD
通讯作者：
Palmer JD
影响因子：
6.5
作者：
Maddison, WP
通讯作者：
Maddison, WP
影响因子：
2.1
作者：
Ivanova, Natalia V.;Fazekas, Aron J.;Hebert, Paul D. N.
通讯作者：
Hebert, Paul D. N.