A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod...

Area of Science:

• * Molecular Biology
• * Bioinformatics
• * Ecology

Background:

• * Metabarcoding relies on accurate sequence classification for reliable biodiversity assessments.
• * Hierarchical classification methods are crucial for maximizing barcoding inferences.
• * Existing databases often contain redundancy and may lack comprehensive representation of target taxa.

Purpose of the Study:

• * To construct and curate a high-quality database for hierarchical classification of the arthropod cytochrome c oxidase subunit I (COI) locus.
• * To address sequence redundancy in public databases and improve representation of arthropod diversity.
• * To evaluate the performance of the curated database with the Metaxa2 classifier and establish an optimal reliability score threshold.

Main Methods:

• * Generation of a comprehensive arthropod COI amplicon dataset from public archives and whole mitochondrion genomes.
• * Curation of the database to extract the target 157 bp COI region, focusing on low redundancy and broad taxonomic coverage.
• * Cross-validation analysis using the Metaxa2 classifier to assess the relationship between reliability scores and classification error, determining an optimal threshold.

Main Results:

• * A curated, low-redundancy arthropod COI database was created, encompassing major arthropod clades and key outgroups.
• * Approximately 81% of input sequences and 73% of genus-level diversity were successfully curated.
• * An optimal Metaxa2 reliability score threshold was identified, balancing classification confidence and error probability.

Conclusions:

• * The developed database significantly enhances the accuracy and reliability of arthropod metabarcoding.
• * The methods presented provide a framework for designing and evaluating reference databases for taxonomic classification.
• * This resource aids researchers in conducting more robust metabarcoding studies on arthropods and other taxa.