MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences.

Bachir Balech, Anna Sandioniggi, Marinella Marzano, Graziano Pesole, Monica Santamaria

Database : the journal of biological databases and curation 2022 Feb 03

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Nucleotide sequences reference collections or databases are fundamental components in DNA barcoding and metabarcoding data analyses pipelines. In such analyses, the accurate taxonomic assignment is a crucial aspect, relying directly on the availability of comprehensive and curated reference sequence collection and its taxonomy information. The currently wide use of the mitochondrial cytochrome oxidase subunit-I (COXI) as a standard DNA barcode marker in metazoan biodiversity studies highlights the need to shed light on the availability of the related relevant information from different data sources and their eventual integration. To adequately address data integration process, many aspects should be markedly considered starting from DNA sequence curation followed by taxonomy alignment with solid reference backbone and metadata harmonization according to universal standards. Here, we present MetaCOXI, an integrated collection of curated metazoan COXI DNA sequences with their associated harmonized taxonomy and metadata. This collection was built on the two most extensive available data resources, namely the European Nucleotide Archive (ENA) and the Barcode of Life Data System (BOLD). The current release contains more than 5.6 million entries (39.1% unique to BOLD, 3.6% unique to ENA, and 57.2% shared between both), their related taxonomic classification based on NCBI reference taxonomy, and their available main metadata relevant to environmental DNA studies, such as geographical coordinates, sampling country and host species. MetaCOXI is available in standard universal formats ('fasta' for sequences & 'tsv' for taxonomy and metadata), which can be easily incorporated in standard or specific DNA barcoding and/or metabarcoding data analysis pipelines. Database URL: https://github.com/bachob5/MetaCOXI. © The Author(s) 2022. Published by Oxford University Press.

Citation

Bachir Balech, Anna Sandioniggi, Marinella Marzano, Graziano Pesole, Monica Santamaria. MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences. Database : the journal of biological databases and curation. 2022 Feb 03;2022