NUMTsearcher: Advancing Detection and Evolutionary Insights of Nuclear Mitochondrial DNA Segments Across Human, Rabbit, and Fish Genomes

Nuclear mitochondrial DNA segments (Numts), which are mitochondrial DNA fragments integrated into the nuclear genome, serve as markers of evolutionary history. This study aims to enhance the detection and analysis of Numts by developing a script named NUMTsearcher. Utilizing the latest chromosome-level genome assemblies from various species, including human, rabbit, and six fish species, the study compares NUMTsearcher's performance against traditional methods such as LAST (Local Alignment Search Tool), BLAST (Basic Local Alignment Search Tool), BLAT (BLAST-Like Alignment Tool), and the pan-mitogenome approach, which integrates mitogenomes from diverse sources to identify fixed Numts in the nuclear genome. Simulation analyses indicate that false Numts significantly affect the detection capabilities of both NUMTsearcher and LAST, with NUMTsearcher mitigating false positives by increasing the hspthresh value (a threshold for sequence match sensitivity). In a comparative analysis with LAST on the rabbit genome, NUMTsearcher raised the hspthresh value to 11895, reporting only ten Numts as chromosomal inserts. A comparative analysis with the pan-mitogenome method identified 41 common Numts on chromosome 1 of the human genome and 22 previously unreported Numts. Our findings confirm the presence of Numts in <i>Danio rerio</i>, <i>Takifugu rubripes</i>, and <i>Tetraodon nigroviridis</i>. Neither BLAST nor BLAT detected Numts in <i>Megalobrama amblycephala </i>and <i>Chanodichthys erythropterus</i>, yet NUMTsearcher identified 13 in <i>M. amblycephala </i>and five in <i>C. erythropterus</i>. In<i> Culter alburnus</i>, while BLAST and BLAT each detected only one Numt, NUMTsearcher revealed three. The study suggests that the timing of Numt insertions is highly variable among species, indicating a significant randomness in these events, generally occurring around ten million years ago. These insights highlight Numts' potential to influence evolutionary interpretations, enhancing our understanding of Numt prevalence across diverse taxa.