DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match

@article{Deagle2014DNAMA,
  title={DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match},
  author={Bruce E. Deagle and Simon Neil Jarman and Eric Coissac and François Pompanon and Pierre Taberlet},
  journal={Biology Letters},
  year={2014},
  volume={10}
}
DNA metabarcoding enables efficient characterization of species composition in environmental DNA or bulk biodiversity samples, and this approach is making significant and unique contributions in the field of ecology. In metabarcoding of animals, the cytochrome c oxidase subunit I (COI) gene is frequently used as the marker of choice because no other genetic region can be found in taxonomically verified databases with sequences covering so many taxa. However, the accuracy of metabarcoding… 

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References

SHOWING 1-10 OF 15 REFERENCES

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

TLDR
The molecular analysis of gut contents targeting the 313 COI fragment using the newly designed mlCOIintF primer in combination with the jgHCO2198 primer offers enormous promise for metazoan metabarcoding studies.

Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all‐taxa biotic surveys

TLDR
The new primers, jgHCO2198 and jgLCO1490, are well suited for routine DNA barcoding, all‐taxon surveys and metazoan metagenomics.

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

TLDR
The ability of the new Illumina PCR-free pipeline for DNA metabarcoding to detect small arthropod specimens and its tendency to avoid most, if not all, false positives suggests its great potential in biodiversity-related surveillance, such as in biomonitoring programs.

An In silico approach for the evaluation of DNA barcodes

TLDR
A standard method for evaluating barcode quality is presented, based on the use of a new bioinformatic tool that performs in silico PCR over large databases, and shows a strong variation of taxonomic coverage: barcodes based on highly degenerated primers and those corresponding to the conserved region of the Cyt-b showed the highest coverage.

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

TLDR
The results of this study may be used as a guideline for selecting primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in PCR-based microbial diversity studies.

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding.

TLDR
Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution.

DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability

TLDR
A novel alignment–free sequence identification algorithm–BRONX–that accounts for observed within taxon variability and hierarchic relationships among taxa and performs better than all other methods when there is imperfect overlap between query and reference sequences.

Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces

TLDR
The pyrosequencing approach presented significantly expands the capabilities of DNA‐based methods of dietary analysis and is suitable for large‐scale diet investigations on a broad range of animals.

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

TLDR
Improved quality-filtering pipeline was applied to several benchmarking studies and observed that even with the stringent data curation pipeline, biases in the data generation pipeline and batch effects were observed that could potentially confound the interpretation of microbial community data.

Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens

TLDR
The potential application of next‐generation sequencing platforms for parallel acquisition of DNA barcode sequences from hundreds of specimens simultaneously is demonstrated and Wolbachia, nontarget species, and heteroplasmic sequences are detected.