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Towards eradicating the nuisance of numts and noise in molecular biodiversity assessment
Molecular Ecology Resources ( IF 7.7 ) Pub Date : 2021-05-07 , DOI: 10.1111/1755-0998.13414
Natalie R Graham 1 , Rosemary G Gillespie 1 , Henrik Krehenwinkel 2
Affiliation  

DNA metabarcoding is a popular methodology for biodiversity assessment and increasingly used for community level analysis of intraspecific genetic diversity. The evolutionary history of hundreds of specimens can be captured in a single collection vial. However, the method is not without pitfalls, which may inflate or misrepresent recovered diversity metrics. Nuclear pseudogene copies of mitochondrial DNA (numts) have been particularly difficult to control because they can evolve rapidly and appear deceptively similar to true mitochondrial sequences. While the problem of numts has long been recognized for traditional sequencing approaches, the issues they create are particularly evident in metabarcoding in which the identity of individual specimens is generally not known. In this issue of Molecular Ecology Resources, Andújar et al. (2021) provide an easy to implement bioinformatic approach to reduce erroneous sequences due to numts and residual noise in metabarcoding data sets. The metaMATE software designates input sequences as authentic (mtDNA haplotypes) or nonauthentic (numts and erroneous sequences) by comparison to reference data and by analysing nucleotide substitution patterns. Filtering is applied over a range of abundance thresholds and the choice to proceed with a more rigid or less strict sequence removal strategy is at the researchers’ discretion. This is a valuable addition to a growing number of complementary tools for improving the reliability of modern biodiversity monitoring.

中文翻译:

在分子生物多样性评估中消除麻木和噪音的滋扰

DNA元条形码是一种流行的生物多样性评估方法,越来越多地用于种内遗传多样性的群落水平分析。数百个标本的进化历史可以在一个收集瓶中捕获。然而,该方法并非没有缺陷,这可能会夸大或歪曲恢复的多样性指标。线粒体 DNA (numts) 的核假基因拷贝特别难以控制,因为它们可以快速进化并且看起来与真正的线粒体序列看似相似。虽然长期以来人们已经认识到传统测序方法的 numts 问题,但它们造成的问题在元条形码中尤为明显,其中个体样本的身份通常是未知的。在本期分子生态资源,安杜哈尔等人。(2021) 提供了一种易于实施的生物信息学方法,以减少由于元条形码数据集中的 numts 和残余噪声而导致的错误序列。metaMATE 软件通过与参考数据进行比较和分析核苷酸替换模式,将输入序列指定为真实(mtDNA 单倍型)或非真实(numts 和错误序列)。过滤适用于一系列丰度阈值,研究人员可自行决定选择更严格或更不严格的序列去除策略。这是对越来越多的用于提高现代生物多样性监测可靠性的补充工具的宝贵补充。
更新日期:2021-05-07
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