Use of rbcL and trnL-F as a two-locus DNA barcode for identification of NW-European ferns: an ecological perspective.
Use of rbcL and trnL-F as a two-locus DNA barcode for identification of NW-European ferns: an ecological perspective.
复制标题
DOI：
10.1371/journal.pone.0016371
复制
发表时间：
2011-01-26
期刊：
影响因子：
3.7
通讯作者：
Erkens RH
中科院分区：
文献类型：
--
作者：
de Groot GA;During HJ;Maas JW;Schneider H;Vogel JC;Erkens RH
虽然现在已经达成共识的一般两个位点的DNA条形码的陆地植物，选择的组合标记（rbcL + matK）是不适用于蕨类植物的时刻。然而，特别是蕨类植物，DNA条形码是潜在的巨大价值，因为蕨类植物配子体，而在蕨类植物的殖民和繁殖中发挥着重要作用，一般缺乏形态学为基础的识别的形态复杂性，因此在生态学研究中被低估。我们评估了rbcL与非编码质体标记，trnL-F，以获得蕨类植物的DNA鉴定的组合的潜力。通过建立西北欧洲野生同孢蕨类植物的可信rbcL和trnL-F序列参考数据库，采用了区域方法。进行简约性分析和基于距离的分析的组合以评估双区域条形码的区分能力。成功地从86个微小蕨类植物配子体中提取了DNA，并将其用作基于DNA的鉴定性能的测试案例。引物的通用性被证明是高的两个标记。基于rbcL + trnL-F组合数据集，所有属以及所有物种的叶绿体基因组不相等，形成自己的支持良好的单系分支，表明高的区分力。所有供试类群的种间距离均大于种内距离。对配子体的鉴定试验显示出相当的结果。所有供试样品均能在属的水平上进行鉴定，除非它们属于一对叶绿体基因组完全相同的鳞毛蕨属种，否则很可能进行种的鉴定。我们的研究结果表明，rbcL和trnL-F的组合使用作为一个两个位点的cpDNA条形码用于识别蕨类植物物种的高潜力。对于生态试验，最好采用区域办法。我们在这里提供了这样一个现成的蕨类植物条形码的方法，这开辟了一条道路，为回答整个范围的问题，以前没有解决蕨类植物配子体生态学。
Although consensus has now been reached on a general two-locus DNA barcode for land plants, the selected combination of markers (rbcL + matK) is not applicable for ferns at the moment. Yet especially for ferns, DNA barcoding is potentially of great value since fern gametophytes—while playing an essential role in fern colonization and reproduction—generally lack the morphological complexity for morphology-based identification and have therefore been underappreciated in ecological studies. We evaluated the potential of a combination of rbcL with a noncoding plastid marker, trnL-F, to obtain DNA-identifications for fern species. A regional approach was adopted, by creating a reference database of trusted rbcL and trnL-F sequences for the wild-occurring homosporous ferns of NW-Europe. A combination of parsimony analyses and distance-based analyses was performed to evaluate the discriminatory power of the two-region barcode. DNA was successfully extracted from 86 tiny fern gametophytes and was used as a test case for the performance of DNA-based identification. Primer universality proved high for both markers. Based on the combined rbcL + trnL-F dataset, all genera as well as all species with non-equal chloroplast genomes formed their own well supported monophyletic clade, indicating a high discriminatory power. Interspecific distances were larger than intraspecific distances for all tested taxa. Identification tests on gametophytes showed a comparable result. All test samples could be identified to genus level, species identification was well possible unless they belonged to a pair of Dryopteris species with completely identical chloroplast genomes. Our results suggest a high potential of the combined use of rbcL and trnL-F as a two-locus cpDNA barcode for identification of fern species. A regional approach may be preferred for ecological tests. We here offer such a ready-to-use barcoding approach for ferns, which opens the way for answering a whole range of questions previously unaddressed in fern gametophyte ecology.
登录
查看更多内容
影响因子：
3.9
作者：
Erkens, Roy H. J.;Maas, Jan W.;Couvreur, Thomas L. P.
通讯作者：
Couvreur, Thomas L. P.
影响因子：
4.1
作者：
Geiger, JMO;Ranker, TA
通讯作者：
Ranker, TA
影响因子：
2.8
作者：
Ishikawa, H;Watano, Y;Kurita, S
通讯作者：
Kurita, S
影响因子：
3
作者：
GASTONY, GJ;YATSKIEVYCH, G
通讯作者：
YATSKIEVYCH, G
DOI：
10.1017/cbo9780511541827.010
发表时间：
2008-01-01
期刊：
BIOLOGY AND EVOLUTION OF FERNS AND LYCOPHYTES
影响因子：
--
作者：
Farrar, Donald R.;Dassler, Cynthia;Skelton, Chanda
通讯作者：
Skelton, Chanda