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, 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 six fish 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.

核线粒体DNA片段（nuclear mitochondrial DNA segments, NUMTs），即整合至核基因组的线粒体DNA片段，可作为进化历史的分子标记。本研究旨在通过开发一款名为NUMTsearcher的脚本工具，提升对NUMTs的检测与分析能力。本研究采用来自人类、家兔以及6种鱼类的最新染色体级基因组组装数据，将NUMTsearcher的性能与传统方法进行对比，这些传统方法包括LAST（局部联配搜索工具，Local Alignment Search Tool）、BLAST（基础局部联配搜索工具，Basic Local Alignment Search Tool）、BLAT（类BLAST联配工具，BLAST-Like Alignment Tool），以及泛线粒体基因组方法——该方法通过整合不同来源的线粒体基因组，以鉴定核基因组中的固定NUMTs。模拟分析结果显示，假阳性NUMTs会对NUMTsearcher与LAST的检测性能造成干扰，而NUMTsearcher可通过提高hspthresh值（亦称K值，该值用于设定高分片段对（high-scoring segment pairs, HSPs）的得分阈值）来降低假阳性率。在针对家兔基因组与LAST的对比分析中，NUMTsearcher将hspthresh值调整至11895，仅鉴定出10个作为染色体插入片段的NUMTs。与泛线粒体基因组方法的对比分析则发现，人类基因组1号染色体上存在41个共有NUMTs，以及22个此前未被报道的NUMTs。本研究证实了斑马鱼（Danio rerio）、红鳍东方鲀（Takifugu rubripes）以及暗纹东方鲀（Tetraodon nigroviridis）中均存在NUMTs。BLAST与BLAT均未在团头鲂（Megalobrama amblycephala）和翘嘴红鲌（Chanodichthys erythropterus）中检测到NUMTs，而NUMTsearcher则在团头鲂中鉴定出13个NUMTs，在翘嘴红鲌中鉴定出5个。在翘嘴鲌（Culter alburnus）中，BLAST与BLAT各仅检测到1个NUMT，而NUMTsearcher则发现了3个。研究表明，6种鱼类的NUMT插入事件发生时间差异极大，说明此类事件具有显著的随机性，通常发生于约1000万年前。上述研究结果凸显了NUMTs对进化解读的潜在影响，有助于加深我们对不同类群中NUMTs流行情况的认知。