A universal DNA mini-barcode for biodiversity analysis

By I. Meusnier, Gregory A. C. Singer, J. Landry, D. Hickey, Paul D. N. Hebert, Mehrdad Hajibabaei. BMC Genomics, 2008

672 citations recorded by the source corpus.

BackgroundThe goal of DNA barcoding is to develop a species-specific sequence library for all eukaryotes. A 650 bp fragment of the cytochrome c oxidase 1 (CO1) gene has been used successfully for species-level identification in several animal groups. It may be difficult in practice, however, to retrieve a 650 bp fragment from archival specimens, (because of DNA degradation) or from environmental samples (where universal primers are needed).ResultsWe used a bioinformatics analysis using all CO1 barcode sequences from GenBank and calculated the probability of having species-specific barcodes for varied size fragments. This analysis established the potential of much smaller fragments, mini-barcodes, for identifying unknown specimens. We then developed a universal primer set for the amplification of mini-barcodes. We further successfully tested the utility of this primer set on a comprehensive set of taxa from all major eukaryotic groups as well as archival specimens.ConclusionIn this study we address the important issue of minimum amount of sequence information required for identifying species in DNA barcoding. We establish a novel approach based on a much shorter barcode sequence and demonstrate its effectiveness in archival specimens. This approach will significantly broaden the application of DNA barcoding in biodiversity studies.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/20908f9b15942642488937b33be40ef50b627f95

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Citations in the corpus

Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all‐taxa biotic surveys (2013, background): “Meusnier et al. (2008) proposed ‘mini barcode’ primers that amplify an internal fragment of the standard barcode region from a broader swath of taxa at the cost of sequence length.”
ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis (2011, positive): “For these reasons the COI gene for animals (1) and rbcL and matK genes for plants (4) are recommended by CBoL.”
Tracking origins of invasive herbivores through herbaria and archival DNA: the case of the horse‐chestnut leaf miner (2011, background): “Thus, we attempted to amplify shorter fragments (“mini-barcodes”: Hajibabaei et al. 2006a, b; Meusnier et al. 2008) of 90–140 bp.”
Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment (2017, positive): “…been developed of which many are now used or could be suitable for metabarcoding studies (Figure 1, e.g., Folmer et al., 1994; Hebert et al., 2004; Meusnier et al., 2008; Van Houdt et al., 2010; Shokralla et al., 2011, 2015; Zeale et al., 2011; Geller et al., 2013; Leray et al., 2013; Gibson et…”
Comparison of morphological and DNA metabarcoding analyses of diets in exploited marine fishes (2015, methodology): “In part this results from the different phylogenetic breadth targeted by each marker, with the 16S Chord-cephA barcode in particular targeting Chordata and the COX1 Minibar and 18S Bilateria amplicons able to capture a broader taxonomic spectrum (Meusnier et al. 2008, Deagle et al. 2009).”
Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol (2015, background): “While the use of full COI barcodes targeting the classical primer regions might give the highest taxonomic resolution, mini barcodes might be sufficient to detect most species and are popular in environmental DNA barcoding [53].”
How will the ‘molecular revolution’ contribute to biological recording? (2015, background): “Mini-barcodes are typically a 90-250 bp long portion of the primary barcoding genes (e.g. for COI Hajibabaei et al., 2006; Meusnier et al., 2008 and rbcL Little, 2014).”
Next‐generation sequencing technologies for environmental DNA research (2012, background): “Here, we review the advantages and limitations of current next-generation sequencing technologies in regard to their application for environmental DNA analysis.”
Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring (2012, positive): “We remove sequences <100 bp, the length below which taxonomic information degrades rapidly (Meusnier et al. 2008).”
A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents (2013, methodology): “, < 400 bp) to maximize richness estimates [15,16] and increase the probability of recovering DNA templates that are more degraded (sheared), such as samples preserved for extended periods of time [17] or prey items in the gut and faecal contents of predators [18,19].”
Utility of Environmental DNA for Monitoring Rare and Indicator Macroinvertebrate Species (2014, background): “Detection with fragments that are too short (<100 bp for COI) may hinder adequate species identification and probably depends on the genetic region used for identification (Meusnier et al. 2008).”
Unveiling cryptic species of the bumblebee subgenus Bombus s. str. worldwide with COI barcodes (Hymenoptera: Apidae) (2012, background): “…even the short COI-barcode region of 658 nucleotides can be used to identify the most closely related taxa (Hebert et al., 2003; Baker et al., 2009), and indeed COI-barcode sequences as short as 100 nucleotides can be diagnostic for 90% of the species in other animal groups (Meusnier et al., 2008).”
An In silico approach for the evaluation of DNA barcodes (2010, methodology): “[20] can be obtained using ecoPCR by allowing a large number of mismatches (up to eight) (Figure 4).”