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 affect the detection capabilities of both NUMTsearcher and LAST, with NUMTsearcher mitigating false positives by increasing the hspthresh value (also known as the K value), which sets the score threshold for high-scoring segment pairs (HSPs). In a comparative analysis with LAST on the rabbit genome, following optimization of the hspthresh value, NUMTsearcher reported 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 Danio rerio, Takifugu rubripes, Tetraodon nigroviridis, Megalobrama amblycephala, Culter alburnus, and Chanodichthys erythropterus. The study further reveals that NUMT insertion timing varies across the six fish species, suggesting a significant degree of randomness. These results underscore the potential of NUMTs to influence evolutionary interpretations and deepen our understanding of their prevalence across diverse taxa.