Gene annotation errors are common in the mammalian mitochondrial genomes database.

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Animal mitochondrial DNA (mtDNA) evolves rapidly, but gene arrangements are typically conserved.
• Published mammalian mtDNA genomes in GenBank suggest significant rearrangements, questioning genome stability.
• Potential annotation errors in existing databases may lead to misinterpretations of mammalian mtDNA evolution.

Purpose of the Study:

• To perform a comparative genomic analysis of mammalian mitochondrial genomes.
• To verify potential annotation errors in published mammalian mitochondrial genome sequences.
• To clarify the true diversity of gene arrangements in mammalian mitochondrial genomes.

Main Methods:

• Comparative genomic analysis of 304 mammalian mitochondrial genomes from the NCBI database.
• Application of bioinformatics tools to examine mitochondrial gene arrangements.
• Verification of gene annotations and sequence completeness.

Main Results:

• Identified only two distinct mitochondrial genome arrangements across 304 mammalian species.
• One arrangement is specific to marsupials, while another is shared by monotremes and eutherians.
• All other reported gene rearrangements (68 cases) and numerous annotation errors were identified as mistakes.

Conclusions:

• The mammalian mitochondrial genome is more conserved in gene arrangement than previously suggested.
• Bioinformatic verification of gene annotations is crucial for accurate genome curation, especially for organelle genomes.
• Enhancing curation processes for databases like GenBank can prevent misleading interpretations of evolutionary data.