Fugu genome does not contain mitochondrial pseudogenes

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Previous genome-wide surveys suggested the presence of nuclear mitochondrial DNA fragments (Numts) in fish genomes, including fugu (Takifugu rubripes), Tetraodon nigroviridis, and zebrafish (Danio rerio).
• These findings challenged the long-held view that fish nuclear genomes are devoid of such mitochondrial pseudogenes.

Purpose of the Study:

• To re-evaluate the presence of Numts in the fugu nuclear genome using the latest assembly (v4.0).
• To clarify the nature of previously identified Numts in fugu, Tetraodon, and zebrafish genomes.

Main Methods:

• Genome-wide analysis of the fugu (Takifugu rubripes) genome assembly v4.0.
• Comparison with previous fugu genome assemblies (v2.0).
• Assessment of potential artifacts in shotgun sequencing data.

Main Results:

• The latest fugu genome assembly (v4.0) does not contain mitochondrial pseudogenes.
• Previously identified "recent" Numts in fugu were found to be misassembled shotgun sequences of mitochondrial DNA.
• "Ancient" Numts appeared to be spurious matches, indicating artifacts.
• Similar artifacts are suspected in Tetraodon and zebrafish genomes.

Conclusions:

• The presence of Numts in fish genomes, as previously reported, is likely due to sequencing and assembly artifacts.
• Mitochondrial DNA fragments in nuclear genomes of fish may be rare or absent.
• Verification of Numts in shotgun genome assemblies using methods like Southern hybridization or PCR amplification is crucial.