Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode.
Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode.
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DOI：
10.1371/journal.pone.0011533
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发表时间：
2010-07-13
期刊：
影响因子：
3.7
通讯作者：
Groff PA
中科院分区：
文献类型：
--
作者：
Whitlock BA;Hale AM;Groff PA
叶绿体trnH-psbA间隔区由于其高取代率而被认为是植物DNA条形码的主要候选者。然而，在被子植物的多个谱系中发现了与该区域回文序列相关的频繁反转，这可能使其作为条形码的使用复杂化，特别是如果它们发生在物种内。在这里，我们评估了trnH-psbA区域种内倒置对DNA条形码工作的影响。我们报告了6种龙胆科植物的多态性倒置，所有这些物种在形态学上都有狭窄的限制：海藻龙胆、fremontii龙胆、critinita龙胆、thermalis龙胆、macrantha龙胆和Frasera speciosa龙胆。我们将这些序列与其他15种龙胆科植物的序列进行了分析，结果表明，典型的简单序列比对方法可能导致同源性的错误分配和关系的错误评估。trnH-psbA区域的频繁反转，如果没有被正确识别和排列，可能会导致大量高估分离密切相关谱系的取代事件的数量，并将具有相同反转形式的远亲类群联合起来。因此，如果将trnH-psbA间隔区用作DNA条形码标记，则需要仔细注意其对齐。
The chloroplast trnH-psbA spacer region has been proposed as a prime candidate for use in DNA barcoding of plants because of its high substitution rate. However, frequent inversions associated with palindromic sequences within this region have been found in multiple lineages of Angiosperms and may complicate its use as a barcode, especially if they occur within species. Here, we evaluate the implications of intraspecific inversions in the trnH-psbA region for DNA barcoding efforts. We report polymorphic inversions within six species of Gentianaceae, all narrowly circumscribed morphologically: Gentiana algida, Gentiana fremontii, Gentianopsis crinita, Gentianopsis thermalis, Gentianopsis macrantha and Frasera speciosa. We analyze these sequences together with those from 15 other species of Gentianaceae and show that typical simple methods of sequence alignment can lead to misassignment of conspecifics and incorrect assessment of relationships. Frequent inversions in the trnH-psbA region, if not recognized and aligned appropriately, may lead to large overestimates of the number of substitution events separating closely related lineages and to uniting more distantly related taxa that share the same form of the inversion. Thus, alignment of the trnH-psbA spacer region will need careful attention if it is used as a marker for DNA barcoding.
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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：
2.5
作者：
Graham, SW;Olmstead, RG
通讯作者：
Olmstead, RG
影响因子：
5.8
作者：
Larkin, M. A.;Blackshields, G.;Higgins, D. G.
通讯作者：
Higgins, D. G.
影响因子：
14.9
作者：
Kim, CS;Lee, CH;Hyung, NI
通讯作者：
Hyung, NI
影响因子：
3.4
作者：
Cowan, Robyn S.;Chase, Mark W.;Savolainen, Vincent
通讯作者：
Savolainen, Vincent