Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects

PeerJ

article

Vasco Elbrecht¹  Pierre Taberlet³  Tony Dejean⁴  Alice Valentini⁴  Philippe Usseglio-Polatera⁵  Jean-Nicolas Beisel⁶  Eric Coissac³  Frederic Boyer³  Florian Leese² 

[1] Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum;Aquatic Ecosystem Research, University of Duisburg-Essen;Laboratoire d’Ecologie Alpine;SPYGEN;Lab Interdisciplinaire des Environnements Continentaux ,(LIEC), Université de Lorraine;Ecole Nationale du Génie de l’Eau et de l’Environnement de Strasbourg;UMR CNRS 7362—LIVE, Université de Strasbourg;Centre for Water and Environmental Research ,(ZWU) Essen, University of Duisburg-Essen

关键词: Biodiversity assessment;    Stream monitoring;    Small ribosomal subunit;    High throughput sequencing;    DNA metabarcoding;    Method testing;    Freshwater invertebrates;    Stream ecosystems;    Primer bias;    Illumina sequencing;   

DOI  :  10.7717/peerj.1966

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate.

【 授权许可】

CC BY