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Updated: Apr 18, 2026

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Navigating Cetacean Mitochondrial Genome Data: Identifying Coverage and Deficiencies in Public Repositories.

Luís Afonso1,2,3, Alessandro Lagrotteria1,4,5, Ana Sofia Lavrador1

  • 1Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIIMAR-LA), University of Porto, Matosinhos, Portugal.

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|April 17, 2026
PubMed
Summary
This summary is machine-generated.

Genetic reference databases for cetacean biodiversity are incomplete and lack taxonomic accuracy. Improving data quality and geographic representation is crucial for effective environmental DNA (eDNA) monitoring.

Keywords:
BOLDGenBankdata repositoriesenvironmental DNAgap analysismarine mammalsmitogenome

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Area of Science:

  • Marine Biology
  • Genomics
  • Bioinformatics

Background:

  • Genetic reference databases are vital for cetacean biodiversity studies, including environmental DNA (eDNA) analysis.
  • Database reliability hinges on data completeness, taxonomic accuracy, and metadata quality.

Purpose of the Study:

  • To conduct the first global assessment of mitochondrial sequence availability for cetaceans.
  • To evaluate taxonomic coverage, geographic representation, and metadata completeness.
  • To analyze the distribution of five common mitochondrial markers.

Main Methods:

  • Retrieved 17,569 cetacean accessions from NCBI Nucleotide and 259 COI-only records from BOLD Systems.
  • Assessed sequence availability, taxonomic accuracy, geographic metadata, and marker distribution.
  • Compared database records against current cetacean taxonomy.

Main Results:

  • Sequence availability is biased towards Delphinidae and Balaenopteridae, with underrepresentation in families like Ziphiidae.
  • Discrepancies were found between database records and accepted cetacean taxonomy.
  • The D-loop marker is most represented, often as standalone sequences.
  • Only 38% of accessions included geographic metadata, with significant regional gaps (e.g., Africa).

Conclusions:

  • Critical deficiencies exist in mitochondrial reference databases for cetaceans.
  • There is a need for improved metadata standards and targeted sequencing of underrepresented taxa and regions.
  • Enhanced data sharing is essential for global eDNA-based cetacean monitoring.