Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger

Macher, Jan‐Niklas; Macher, Till‐Hendrik; Leese, Florian

doi:10.3897/mbmg.1.22262

Cited by 22 publications

(26 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Users are often faced with the choice of using either BOLD or INSDC data for identification by creating custom COI databases to permit high-throughput identifications. The recently published BOLD_NCBI_MERGER script helps to combine records from BOLD with those in GenBank for use with BLAST and MEGAN lowest common ancestor taxonomic assignment [ 32 ]. The tool helps to combine high quality COI barcode records from BOLD with the broader taxonomic coverage of COI records from the NCBI nucleotide database.…”

Section: Discussionmentioning

confidence: 99%

“…First steps in allowing COI resources to be integrated with more general bioinformatics pipelines are being developed. The BOLD_NCBI_MERGER script discussed above allows this reference set to be used with microbiome analysis tool MEGAN Community Edition [ 32 , 46 ]. Recent work also provides a curated COI reference set that can be used with the RDP classifier [ 13 , 47 ].…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Over 2.5 million COI sequences in GenBank and growing

2018

View full text Add to dashboard Cite

The increasing popularity of cytochrome c oxidase subunit 1 (COI) DNA metabarcoding warrants a careful look at the underlying reference databases used to make high-throughput taxonomic assignments. The objectives of this study are to document trends and assess the future usability of COI records for metabarcode identification. The number of COI records deposited to the NCBI nucleotide database has increased by a geometric average of 51% per year, from 8,137 records deposited in 2003 to a cumulative total of ~ 2.5 million by the end of 2017. About half of these records are fully identified to the species rank, 92% are at least 500 bp in length, 74% have a country annotation, and 51% have latitude-longitude annotations. To ensure the future usability of COI records in GenBank we suggest: 1) Improving the geographic representation of COI records, 2) Improving the cross-referencing of COI records in the Barcode of Life Data System and GenBank to facilitate consolidation and incorporation into existing bioinformatic pipelines, 3) Adherence to the minimum information about a marker gene sequence guidelines, and 4) Integrating metabarcodes from eDNA and mixed community studies with existing reference sequences. The growth of COI reference records over the past 15 years has been substantial and is likely to be a resource across many fields for years to come.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Over 2.5 million COI sequences in GenBank and growing

2018

View full text Add to dashboard Cite

show abstract

“…There is a considerable overlap between these two large repositories; however, there remain sequences and metadata that are unique to both. Therefore, the compilation of a reference database for COI sequences for marine eukaryotes would ideally draw from both GenBank and BOLD 17,23 and would synonymize the species identities across sequences drawn from both repositories.…”

Section: Background and Summarymentioning

confidence: 99%

MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding

et al. 2020

View full text Add to dashboard Cite

the use of DNa metabarcoding to characterise the biodiversity of environmental and community samples has exploded in recent years. However, taxonomic inferences from these studies are contingent on the quality and completeness of the sequence reference database used to characterise sample species-composition. In response, studies often develop custom reference databases to improve species assignment. the disadvantage of this approach is that it limits the potential for database re-use, and the transferability of inferences across studies. Here, we present the MaRine Eukaryote Species (MaRES) reference database for use in marine metabarcoding studies, created using a transparent and reproducible pipeline. MaRES includes all COI sequences available in GenBank and BOLD for marine taxa, unified into a single taxonomy. Our pipeline facilitates the curation of sequences, synonymization of taxonomic identifiers used by different repositories, and formatting these data for use in taxonomic assignment tools. Overall, MaRES provides a benchmark COI reference database for marine eukaryotes, and a standardised pipeline for (re)producing reference databases enabling integration and fair comparison of marine DNa metabarcoding results.

show abstract

“…Making the merged reference data available in plain text formats would make it relatively straightforward to reformat so they can be used as the basis for alternative taxonomic assignment tools such as those that provide rank-flexible statistical measures of confidence. For example, the BOLD_NCBI_Merger script provides a means to combine data from BOLD and the NCBI nucleotide database for use with MEGAN (Huson et al, 2016;Macher et al, 2017). Our own approach has been to update the underlying reference sequence database used by the COI classifier v4 to combine data from BOLD and GenBank, and it is available from https://github.com/terrimporter/CO1Classifier (Wang et al, 2007;Porter and Hajibabaei, 2018a).…”

Section: How Can We Leverage Taxonomic Coverage Across Reference Datamentioning

confidence: 99%

Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis

Porter

Hajibabaei

2020

Front. Ecol. Evol.

View full text Add to dashboard Cite

DNA barcoding and metabarcoding are techniques that focus on signature genomic regions that in theory provide species level resolution, but in practice this is not always possible. We place animal-focused COI metabarcoding in context with respect to the use of marker gene sequencing in microbial and fungal ecology. We focus on three specific aspects of metabarcodes: (1) the process of metabarcode sequence clustering, (2) how metabarcode cluster types affect the results of biodiversity analyses, and (3) the current state of reference sequence databases used for metabarcode identification. Using examples from the arthropod COI metabarcode literature, we show that exact sequence variants (ESVs) detect more unique taxa than operational taxonomic units (OTUs) but with similar patterns in taxonomic resolution. We also show that the difference between ordinations based on ESVs or OTUs recover similar groupings. We compile a list of reference sequence databases useful for multi-marker metabarcoding and present a list of reference sequence databases specifically formatted for use with a naive Bayesian classifier for rigorous metabarcode taxonomic assignments. Sophisticated tools and reference databases are available for analyzing COI sequences, and these compare favorably with those available for other metabarcode markers such as the ribosomal RNA genes used to target microbes and fungi.

show abstract

Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger

Cited by 22 publications

References 33 publications

Over 2.5 million COI sequences in GenBank and growing

Over 2.5 million COI sequences in GenBank and growing

MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding

Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis

Contact Info

Product

Resources

About