利用节肢动物模拟样本和爱尔兰蝙蝠饮食特征评价牛津纳米孔技术MinION测序仪作为一种新型短扩增子元条形码工具

IF 2.3 2区 生物学 Q2 ECOLOGY
James M. Nolan, Ilze Skujina, Gwenaëlle Hurpy, Andrew J. Tighe, Conor Whelan, Emma C. Teeling
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引用次数: 0

摘要

元条形码生物多样性监测作为一种常规的环境管理手段已得到广泛应用。然而,尽管第三代高通量测序平台发展迅速,但评估最适合环境元条形码研究的工具和方法的研究有限。我们测试了Oxford Nanopore Technologies MinION测序对已知节肢动物物种组成的线粒体COI迷你条形码的短读扩增子测序的实用性,并将其性能与更常用的Illumina NovaSeq测序进行了比较。模拟节肢动物物种组合使我们能够优化生物信息学过滤管道,利用MinION长读取来识别节肢动物物种。利用这一方法,我们通过对5只爱尔兰棕色长耳蝙蝠(Plecotus auritus)栖息地的粪便进行测序,确定了寄主种类和饮食组成。我们发现MinION数据提供了与NovaSeq相似的分类分配,但前提是参考物种条形码数据库准确而全面。根据先前的形态学和Illumina元条形码研究,推断出的auritus饮食与预期一致。研究结果表明,MinION的完整物种组成检测需要较少的测序深度和较多的生物样品。一种相对简单的生物信息过滤工具,如纳米管道,可以充分检索宿主物种和饮食组成。最大的挑战是参考数据库格式的可移植性和全面性。该管道可用于指导未来使用纳米孔测序的元条形码研究,以最大限度地降低成本和努力,同时优化结果。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Evaluation of Oxford Nanopore Technologies MinION Sequencer as a Novel Short Amplicon Metabarcoding Tool Using Arthropod Mock Sample and Irish Bat Diet Characterisation

Evaluation of Oxford Nanopore Technologies MinION Sequencer as a Novel Short Amplicon Metabarcoding Tool Using Arthropod Mock Sample and Irish Bat Diet Characterisation

Biodiversity monitoring using metabarcoding is now widely used as a routine environmental management tool. However, despite the rapid advancement of third-generation high-throughput sequencing platforms, there are limited studies assessing the most suitable tools and approaches for environmental metabarcoding studies. We tested the utility of Oxford Nanopore Technologies MinION sequencing for short-read amplicon sequencing of mitochondrial COI mini-barcodes from a known composition of arthropod species and compared its performance with more commonly used Illumina NovaSeq sequencing. The mock arthropod species assemblage allowed us to optimise a bioinformatic filtering pipeline to identify arthropod species using MinION long reads. Using this pipeline, we identified host species and diet composition by sequencing droppings collected from five individual Irish brown long-eared bats (Plecotus auritus) roosts. We showed that MinION data provided a similar taxonomic assignment to NovaSeq but only if the reference species barcode database was accurate and comprehensive. The P. auritus diet inferred was as expected based on previous morphological and Illumina metabarcoding studies. We showed that less sequencing depth, but a higher number of biological samples were necessary for complete species composition detection by MinION. A relatively simple bioinformatic filtering tool such as NanoPipe could adequately retrieve both host species and diet composition. The biggest standing challenge was the reference database format transferability and comprehensiveness. This pipeline can be used to guide future metabarcoding studies using nanopore sequencing to minimise the cost and effort while optimising results.

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来源期刊
CiteScore
4.40
自引率
3.80%
发文量
1027
审稿时长
3-6 weeks
期刊介绍: Ecology and Evolution is the peer reviewed journal for rapid dissemination of research in all areas of ecology, evolution and conservation science. The journal gives priority to quality research reports, theoretical or empirical, that develop our understanding of organisms and their diversity, interactions between them, and the natural environment. Ecology and Evolution gives prompt and equal consideration to papers reporting theoretical, experimental, applied and descriptive work in terrestrial and aquatic environments. The journal will consider submissions across taxa in areas including but not limited to micro and macro ecological and evolutionary processes, characteristics of and interactions between individuals, populations, communities and the environment, physiological responses to environmental change, population genetics and phylogenetics, relatedness and kin selection, life histories, systematics and taxonomy, conservation genetics, extinction, speciation, adaption, behaviour, biodiversity, species abundance, macroecology, population and ecosystem dynamics, and conservation policy.
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