Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys
Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys
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DOI：
10.1111/1755-0998.12138
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发表时间：
2013-09-01
影响因子：
7.7
通讯作者：
Hawk, H.
中科院分区：
文献类型：
--
作者：
Geller, J.;Meyer, C.;Hawk, H.
DNA条形码是物种检测、鉴定和发现的有力工具。后生动物DNA条形码主要基于细胞色素C氧化酶I亚单位基因的特定区域，该基因由Folmer等人设计的引物HCO2198和LCO1490(Folmer Primer‘)进行聚合酶链式反应(PCR)扩增。(《分子海洋生物学与生物技术》，3,1994,294)。对1994年以来发表的序列的分析表明，Folmer引物与许多后生动物不匹配。这些序列还表明，在更新的Folmer引物中需要极高水平的简并性，以保持广泛的分类学用途。在引物jgHCO2198和jgLCO1490中，我们用补充所有四种天然核苷酸的肌苷核苷酸取代了大多数完全退化的位点，并修改了其他位点，以更好地匹配主要的海洋无脊椎动物群体。对来自法属波利尼西亚莫雷亚和美国加利福尼亚州旧金山湾的9105份标本的细胞色素C氧化酶亚基I进行了扩增和测序，分别代表23门、42纲、121目。新的引物jgHCO2198和jgLCO1490非常适合于常规DNA条形码、全分类群调查和后生动物元基因组学。
DNA barcoding is a powerful tool for species detection, identification and discovery. Metazoan DNA barcoding is primarily based upon a specific region of the cytochrome c oxidase subunit I gene that is PCR amplified by primers HCO2198 and LCO1490 (Folmer primers') designed by Folmer etal. (Molecular Marine Biology and Biotechnology, 3, 1994, 294). Analysis of sequences published since 1994 has revealed mismatches in the Folmer primers to many metazoans. These sequences also show that an extremely high level of degeneracy would be necessary in updated Folmer primers to maintain broad taxonomic utility. In primers jgHCO2198 and jgLCO1490, we replaced most fully degenerated sites with inosine nucleotides that complement all four natural nucleotides and modified other sites to better match major marine invertebrate groups. The modified primers were used to amplify and sequence cytochrome c oxidase subunit I from 9105 specimens from Moorea, French Polynesia and San Francisco Bay, California, USA representing 23 phyla, 42 classes and 121 orders. The new primers, jgHCO2198 and jgLCO1490, are well suited for routine DNA barcoding, all-taxon surveys and metazoan metagenomics.