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Comparison of markers for the monitoring of freshwater benthic biodiversity through DNA metabarcoding
Molecular Ecology ( IF 4.9 ) Pub Date : 2020-09-13 , DOI: 10.1111/mec.15632
Gentile Francesco Ficetola 1, 2 , Frédéric Boyer 1 , Alice Valentini 3 , Aurélie Bonin 1, 2 , Albin Meyer 4 , Tony Dejean 3 , Coline Gaboriaud 3 , Philippe Usseglio-Polatera 4 , Pierre Taberlet 1, 5
Affiliation  

Metabarcoding of bulk or environmental DNA has great potential for biomonitoring of freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensive reference databases are essential to match the outcome of metabarcoding analyses with available taxonomy and biomonitoring indices. Benthic invertebrates, particularly insects, are key taxa for freshwater bioassessment. Nevertheless, few studies have so far assessed markers for metabarcoding of freshwater macrobenthos. Here we combined in silico and laboratory analyses to test the performance of different markers amplifying regions in the 18S rDNA (Euka02), 16S rDNA (Inse01) and COI (BF1_BR2-COI) genes, and developed an extensive database of benthic macroinvertebrates of France and Europe, with a particular focus on key insect orders (Ephemeroptera, Plecoptera and Trichoptera). Analyses on 1,514 individuals representing different taxa of benthic macroinvertebrates showed very different amplification success across primer combinations. The Euka02 marker showed the highest universality, while the Inse01 marker showed excellent performance for the amplification of insects. BF1_BR2-COI showed the highest resolution, while the resolution of Euka02 was often limited. By combining our data with GenBank information, we developed a curated database including sequences representing 822 genera. The heterogeneous performance of the different primers highlights the complexity in identifying the best markers, and advocates for the integration of multiple metabarcodes for a more comprehensive and accurate understanding of ecological impacts on freshwater biodiversity.

中文翻译:

DNA元条形码监测淡水底栖生物多样性标志物的比较

大量或环境 DNA 的元条形码在淡水环境的生物监测方面具有巨大的潜力。然而,元条形码在生物多样性监测中的成功应用需要具有高分类覆盖率的通用引物,以高分类分辨率放大高度可变的短元条形码。此外,可靠且广泛的参考数据库对于将元条形码分析的结果与可用的分类法和生物监测指数相匹配至关重要。底栖无脊椎动物,尤其是昆虫,是淡水生物评估的关键类群。然而,迄今为止,很少有研究评估淡水大型底栖动物元条形码的标记。在这里,我们结合计算机分析和实验室分析来测试 18S rDNA (Euka02) 中不同标记扩增区域的性能,16S rDNA (Inse01) 和 COI (BF1_BR2-COI) 基因,并开发了法国和欧洲底栖大型无脊椎动物的广泛数据库,特别关注关键昆虫目(蜉蝣目、鳞翅目和毛翅目)。对代表不同底栖大型无脊椎动物分类群的 1,514 个个体的分析表明,引物组合的扩增成功率非常不同。Euka02标记表现出最高的通用性,而Inse01标记表现出优异的昆虫扩增性能。BF1_BR2-COI 的分辨率最高,而 Euka02 的分辨率往往有限。通过将我们的数据与 GenBank 信息相结合,我们开发了一个包含代表 822 个属的序列的精选数据库。不同引物的异质性能突出了识别最佳标记的复杂性,
更新日期:2020-09-13
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