ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

Riaz, Tiayyba; Shehzad, Wasim; Viari, Alain; Pompanon, François; Taberlet, Pierre; Coissac, Éric

doi:10.1093/nar/gkr732

Cited by 505 publications

(522 citation statements)

References 36 publications

(60 reference statements)

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“…We used ecoPrimer (Riaz et al., 2011) to design new primers (Cop16SF and Cop16SR) based on 33 mitochondrial genomes from 11 copepod species. The ecoPrimer parameters used were a maximum of three mismatches between each primer and the target sequence with no mismatches allowed within two nucleotides of the 3′ end.…”

Section: Methodsmentioning

confidence: 99%

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

Clarke

Beard

Swadling

et al. 2017

Ecology and Evolution

163

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DNA metabarcoding is a promising approach for rapidly surveying biodiversity and is likely to become an important tool for measuring ecosystem responses to environmental change. Metabarcoding markers need sufficient taxonomic coverage to detect groups of interest, sufficient sequence divergence to resolve species, and will ideally indicate relative abundance of taxa present. We characterized zooplankton assemblages with three different metabarcoding markers (nuclear 18S rDNA, mitochondrial COI, and mitochondrial 16S rDNA) to compare their performance in terms of taxonomic coverage, taxonomic resolution, and correspondence between morphology‐ and DNA‐based identification. COI amplicons sequenced on separate runs showed that operational taxonomic units representing >0.1% of reads per sample were highly reproducible, although slightly more taxa were detected using a lower annealing temperature. Mitochondrial COI and nuclear 18S showed similar taxonomic coverage across zooplankton phyla. However, mitochondrial COI resolved up to threefold more taxa to species compared to 18S. All markers revealed similar patterns of beta‐diversity, although different taxa were identified as the greatest contributors to these patterns for 18S. For calanoid copepod families, all markers displayed a positive relationship between biomass and sequence reads, although the relationship was typically strongest for 18S. The use of COI for metabarcoding has been questioned due to lack of conserved primer‐binding sites. However, our results show the taxonomic coverage and resolution provided by degenerate COI primers, combined with a comparatively well‐developed reference sequence database, make them valuable metabarcoding markers for biodiversity assessment.

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Section: Methodsmentioning

confidence: 99%

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

Clarke

Beard

Swadling

et al. 2017

Ecology and Evolution

163

193

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“…Mammalian DNA was amplified using a new primer pair (MamP007F, 5 0 -CGAGAAGACCCTATGGAGCT-3 0 ; MamP007R, 5 0 -CCGAGGTCRCCCCAACC-3 0 ), which led to the amplification of a 60-to 84-bp fragment of the mitochondrial 16S gene. These primers were designed using the ecoPrimers program 43 (http://www.grenoble.prabi.fr/trac/ecoPrimers). Plant DNA was amplified using universal primers (g, 5 0 -GGGCAATCCTGAG CCAA-3 0 ; and h, 5 0 -CCATTGAGTCTCTGCACCTATC-3 0 ) that targeted the P6 loop region of the chloroplast trnL (UAA) intron 44 .…”

Section: Methodsmentioning

confidence: 99%

Long livestock farming history and human landscape shaping revealed by lake sediment DNA

et al. 2014

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The reconstruction of human-driven, Earth-shaping dynamics is important for understanding past human/environment interactions and for helping human societies that currently face global changes. However, it is often challenging to distinguish the effects of the climate from human activities on environmental changes. Here we evaluate an approach based on DNA metabarcoding used on lake sediments to provide the first high-resolution reconstruction of plant cover and livestock farming history since the Neolithic Period. By comparing these data with a previous reconstruction of erosive event frequency, we show that the most intense erosion period was caused by deforestation and overgrazing by sheep and cowherds during the Late Iron Age and Roman Period. Tracking plants and domestic mammals using lake sediment DNA (lake sedDNA) is a new, promising method for tracing past human practices, and it provides a new outlook of the effects of anthropogenic factors on landscape-scale changes.

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“…The forward and reverse 12S rRNA gene primers ( Table 1; Riaz et al, 2011) were modified by the addition of sample-specific nucleotide tags on the 5 ′ ends to allow for the assignment of sequence reads to the correct sample during bioinformatic processing (Valentini et al, 2009). Tags were designed using the OLIGOTAG program (Coissac, 2012) with a Hamming distance of at least three bases between tags.…”

Section: Vertebrates (12s Rrna Gene)mentioning

confidence: 99%

Evaluation of Filtration and DNA Extraction Methods for Environmental DNA Biodiversity Assessments across Multiple Trophic Levels

et al. 2017

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Metabarcoding of marine environmental DNA (eDNA), originating from tissue, cells, or extracellular DNA, offers the opportunity to survey the biological composition of communities across multiple trophic levels from a non-invasive seawater sample. Here we compare results of eDNA metabarcoding of multiple trophic levels from individual seawater samples collected from a kelp forest in Monterey Bay, California in order to establish methods for future cross-trophic level eDNA analysis. Triplicate 1 L water samples were filtered using five different 47 mm diameter membrane filters (PVDF, PES, GFF, PCTE, and NC) and DNA was extracted from triplicates of each filter-type using three widely-used extraction methods (the DNeasy Blood and Tissue kit, the MoBio PowerWater DNA Isolation kit, and standard phenol/chloroform methods) resulting in 45 individual eDNA samples prepared with 15 workflow combinations. Each DNA extract was amplified using PCR primers for the 16S rRNA gene (microorganisms; Bacteria and Archaea), 18S rRNA gene (phytoplankton), and the 12S rRNA gene (vertebrates), and PCR products were sequenced on an Illumina MiSeq platform. The richness and community composition of microbial, phytoplankton, and vertebrate OTUs were not significantly different between any of the 0.2 µm pore-size filter types extracted with the DNeasy or MoBio kits. However, phenol/chloroform extraction resulted in significantly different community structures. This study provides insight into multiple choices for extraction and filtration methods to use eDNA metabarcoding for biodiversity assessment of multiple trophic levels from a single sample. We recommend any combination of either DNeasy or MoBio with PES, PCTE, PVDF, or NC filters for a cross trophic level comparison.

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ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

Cited by 505 publications

References 36 publications

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

Long livestock farming history and human landscape shaping revealed by lake sediment DNA

Evaluation of Filtration and DNA Extraction Methods for Environmental DNA Biodiversity Assessments across Multiple Trophic Levels

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