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

By Tiayyba Riaz, W. Shehzad, A. Viari, F. Pompanon, P. Taberlet, É. Coissac. Nucleic Acids Research, 2011

679 citations recorded by the source corpus.

Using non-conventional markers, DNA metabarcoding allows biodiversity assessment from complex substrates. In this article, we present ecoPrimers, a software for identifying new barcode markers and their associated PCR primers. ecoPrimers scans whole genomes to find such markers without a priori knowledge. ecoPrimers optimizes two quality indices measuring taxonomical range and discrimination to select the most efficient markers from a set of reference sequences, according to specific experimental constraints such as marker length or specifically targeted taxa. The key step of the algorithm is the identification of conserved regions among reference sequences for anchoring primers. We propose an efficient algorithm based on data mining, that allows the analysis of huge sets of sequences. We evaluate the efficiency of ecoPrimers by running it on three different sequence sets: mitochondrial, chloroplast and bacterial genomes. Identified barcode markers correspond either to barcode regions already in use for plants or animals, or to new potential barcodes. Results from empirical experiments carried out on a promising new barcode for analyzing vertebrate diversity fully agree with expectations based on bioinformatics analysis. These tests demonstrate the efficiency of ecoPrimers for inferring new barcodes fitting with diverse experimental contexts. ecoPrimers is available as an open source project at: http://www.grenoble.prabi.fr/trac/ecoPrimers.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/09717a349d5e739b260eab843465d0819bf3fd50

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Molecular Biology

Citations in the corpus

Trawl and eDNA assessment of marine fish diversity, seasonality, and relative abundance in coastal New Jersey, USA (2021, methodology): “Briefly, amplifications were carried out in 25 ll of total volume with TaKaRa High Yield PCR EcoDry Premix, 5 ll of DNA sample or 5 ll of molecular biology grade water, and 200 lM Illumina-tailed “ecoPrimers” (IDT) that target an 106-bp segment of vertebrate mitochondrial 12S V5 region (Riaz et al.,”
Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity (2015, background): “This will in turn limit the results to species with best primer affinity or to species, which is already known to be locally present so specific-primers can be designed (Riaz et al., 2011; Wilcox et al., 2013).”
Insights into global diatom distribution and diversity in the world’s ocean (2016, background): “The choice of variable DNA regions to be barcoded needs to be evaluated carefully (33).”
Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea (2019, background): “, 2012a, 2012b), we set out to develop species-specific primers and probes for a short mitochondrial gene fragment (around 100 bp), targeting gene regions that vary among sympatric species (Riaz et al., 2011).”
Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals (2019, neutral): “ACTGGGATTAGATACCCC-3’) and 12S-V5-R (5’-TAGAACAGGCTCCTCTAG-3’) (Riaz et al., 2011).”
Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies (2017, methodology): “Software programs such as ecoPrimers (Riaz et al., 2011), ecoPCR (Ficetola et al.”
Non‐specific amplification compromises environmental DNA metabarcoding with COI (2019, background): “Various regions of 12S have been proposed as metabarcoding markers, including a ca. 63 bp fragment (Valentini et al., 2016), a ca. 106 bp fragment (Kelly et al., 2014a; Riaz et al., 2011), and a ca. 171 bp fragment (Miya et al., 2015).”
A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish (2020, background): “…group, broad intra-group coverage and even amplification across species, in addition to high discriminatory power (i.e. sufficient sequence variation between amplicons from different species) to ensure comprehensive and accurate species identification (Coissac et al., 2012; Riaz et al., 2011).”
Environmental DNA (2012, background): “…describe the PCR-based approach for simultaneously identifying multiple taxa: ecometagenetics (Porazinska et al. 2010), ecogenomics (Chariton et al. 2010), environmental barcoding (Hajibabaei et al. 2011) or DNA metabarcoding (Pompanon et al. 2011; Riaz et al. 2011; plus 11 papers in this issue).”
MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species (2015, methodology): “The latter study [12] employed PCR primers that have been developed using the computer software ‘ECOPRIMERS’ [14] and that are supposedly universal among vertebrates.”
Who is eating what: diet assessment using next generation sequencing (2012, background): “Based on this approach, designing the best-suited barcodes and associated primers for a given range of food species is now possible (Riaz et al. 2011).”
DNA-based methods in paleolimnology: new opportunities for investigating long-term dynamics of lacustrine biodiversity (2017, background): “metabarcoding, and for testing their characteristics in silico (Ficetola et al. 2010; Riaz et al. 2011; Elbrecht and Leese 2015).”
Comparing local‐ and regional‐scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods (2018, background): “At present, there are a few universal primer sets for eDNA 68 metabarcoding of fishes (12S-V5: Riaz et al., 2011; Kelly et al., 2014b; Mifish-U/E: Miya et 69 al., 2015; Ac12s and Ac16s: Evans et al. 2016; teleo: Valentini et al., 2016).”