Know your limits; miniCOI metabarcoding fails with key marine zooplankton taxa.

IF 1.9 3区 环境科学与生态学 Q2 MARINE & FRESHWATER BIOLOGY Journal of Plankton Research Pub Date : 2024-11-02 eCollection Date: 2024-11-01 DOI:10.1093/plankt/fbae057
Aitor Albaina, Rade Garić, Lidia Yebra
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Abstract

Eleven years after the publication of the first work applying deoxyribonucleic acid (DNA) metabarcoding to zooplankton communities, the commonly known "miniCOI" barcode is widely used, becoming the marker of choice. However, several primer combinations co-exist for this barcode and a critical evaluation of their performance is needed. This article reviews the misperformance of miniCOI metabarcoding with marine zooplankton communities, comparing them to microscopy and/or other universal markers. In total, misperformances were reported for 26 zooplankton taxa, including 18 copepods and five tunicates. We report a detection failure with Class Appendicularia and contrasting performances for Oithona similis (from good correspondence to detection failure), two worldwide abundant taxa with a crucial role in the marine pelagic realm. A combination of forward primer mismatches, the presence of long poly-T inserts and a low number of reference sequences would explain the failure to detect appendicularians. However, the contrasting performance with O. similis would correspond to distinct numbers of mismatches in the forward primer in different lineages within this cryptic taxon. This is reinforced by the report of similar patterns with other locally abundant zooplankton taxa. Therefore, we strongly call for the use of miniCOI in combination with alternative methods capable of addressing these limitations.

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了解自己的极限;miniCOI元条形码在关键的海洋浮游动物分类中失败。
在首次将脱氧核糖核酸(DNA)元条形码应用于浮游动物群落的工作发表11年后,俗称的“miniCOI”条形码被广泛使用,成为首选的标记。然而,该条形码的几种引物组合共存,需要对其性能进行严格的评估。本文回顾了miniCOI元条形码在海洋浮游动物群落中的错误表现,并将其与显微镜和/或其他通用标记进行了比较。总共有26个浮游动物类群,包括18个桡足类和5个被囊动物。本文报道了阑尾纲(Appendicularia)的检测失败,并对比了在海洋中上层领域中具有重要作用的两个世界范围内丰富的分类群Oithona similis的性能(从良好对应到检测失败)。前引物不匹配、长poly-T插入和低参考序列的存在可能解释了尾状虫检测失败的原因。然而,与O. similis的对比表现可能对应于该隐分类单元中不同谱系的前引物中不同数量的错配。在其他当地丰富的浮游动物类群中也发现了类似的模式,这进一步证实了这一点。因此,我们强烈要求将miniCOI与能够解决这些限制的其他方法结合使用。
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来源期刊
Journal of Plankton Research
Journal of Plankton Research 生物-海洋学
CiteScore
3.50
自引率
9.50%
发文量
65
审稿时长
1 months
期刊介绍: Journal of Plankton Research publishes innovative papers that significantly advance the field of plankton research, and in particular, our understanding of plankton dynamics.
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