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Metabarcoding of zooplankton diversity within the Chukchi Borderland, Arctic Ocean: improved resolution from multi-gene markers and region-specific DNA databases
Marine Biodiversity ( IF 1.6 ) Pub Date : 2021-01-09 , DOI: 10.1007/s12526-020-01136-x
Jennifer M. Questel , Russell R. Hopcroft , Hayley M. DeHart , Caitlin A. Smoot , Ksenia N. Kosobokova , Ann Bucklin

DNA-based analyses have become powerful tools for characterizing the metazoan biodiversity of diverse marine ecosystems. Metabarcoding (i.e., large-scale taxonomic identification of complex samples via high-throughput sequencing of a DNA barcode region) frequently uses hypervariable regions of the nuclear eukaryotic 18S ribosomal RNA (rRNA) gene. However, species-level taxonomic identification is hampered by the conservative nature of the 18S gene in comparison to the mitochondrial cytochrome oxidase I (COI) barcode gene. Additionally, metabarcoding relies on reference DNA sequence databases for classification of millions of unknown sequence reads and molecular operational taxonomic units (OTUs); databases that are at present depauperate for marine zooplankton taxa. Here, we characterized the mesozooplankton community for the Chukchi Borderland (CBL) region, western Arctic Ocean, through metabarcoding analysis of the V4 and V9 hypervariable regions of 18S rRNA and a portion of COI. Characterization of zooplankton diversity for the epipelagic and upper mesopelagic layers (0–500 m) was based upon 17 metazoan taxonomic categories encompassing 24 orders in 14 classes. Taxonomic classification using the V4 and V9 markers was most reliable for orders, with copepods dominating OTU counts. To increase taxonomic resolution and allow detection of species, V4, V9, and COI OTUs were classified against DNA sequence databases for the Arctic Ocean for the subclass Copepoda. The geographic region-specific databases for 18S rRNA and COI resulted in the detection and identification of 6 genera and 49 species of copepods representing 23 families, a marked increase in the taxonomic classification of the 18S rRNA markers. The greatest copepod species diversity was captured with V4 (34 species) followed by COI (28 species) with the least copepod diversity detected by V9 (5 species). Our results demonstrate the power of using multiple gene markers, with DNA reference databases that are specific to the geographic region of interest, providing more accurate metabarcoding biodiversity measures for the copepod assemblages compared to universal metazoan sequence reference databases. Results from this study highlight the need for continued DNA barcode sequencing to increase species representation in the reference sequence databases that are crucial for accurate characterization of mesozooplankton communities.



中文翻译:

北冰洋楚科奇边疆地区浮游动物多样性的元条形码:来自多基因标记和区域特定DNA数据库的高分辨率

基于DNA的分析已成为表征多种海洋生态系统后生生物多样性的有力工具。元条形码(即通过DNA条形码区域的高通量测序对复杂样品进行大规模分类学鉴定)经常使用核真核18S核糖体RNA(rRNA)基因的高变区。但是,与线粒体细胞色素氧化酶I(COI)条形码基因相比,物种级别的分类学鉴定受到18S基因保守性的阻碍。此外,元条形码技术依靠参考DNA序列数据库对数百万个未知序列读数和分子操作分类单位(OTU)进行分类。目前正在减少海洋浮游生物类群的数据库。这里,通过对18S rRNA的V4和V9高变区和部分COI进行元条形码分析,我们为北冰洋西部楚科奇边疆(CBL)地区的中游浮游动物群落定了特征。表层上层和中中上层(0-500 m)的浮游动物多样性的表征是基于17个后生动物分类学类别的,涵盖14个类别的24个阶。对于订单,使用V4和V9标记的分类学分类最为可靠,而pe足类动物占主导地位。为了提高分类学分辨率并允许检测物种,V4,V9和COI OTU相对于北冰洋的DNA足类亚类的DNA序列数据库进行了分类。针对18S rRNA和COI的地理区域特定数据库导致检测和鉴定了代表23个科的6属和49种pe足类动物,这大大增加了18S rRNA标记的分类学分类。V4(34种)捕获的V足类物种多样性最大,其次是COI(28种),而V9(5种)检测到的diversity足类多样性最少。我们的结果证明,使用多种基因标记以及特定于感兴趣地理区域的DNA参考数据库的功能,与通用后生动物序列参考数据库相比,可以为the足类提供更准确的元条形码生物多样性度量。

更新日期:2021-01-10
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