Nuclear Mitochondrial Sequences in Great Ape Telomere-to-Telomere Genomes

Mitochondrial sequences have integrated into the nuclear genome since the origin of eukaryotes. Recent insertions that retain homology to extant mitochondrial DNA (mtDNA), termed NUMTs, confound mtDNA sequence analysis. Here, we used great ape Telomere-to-Telomere (T2T) genomes to study NUMTs in bonobo, chimpanzee, human, gorilla, and Bornean and Sumatran orangutans. A phylogeny based on shared and lineage-specific NUMTs accurately recapitulated the great ape species tree topology. NUMTs were enriched at non-functional non-repetitive regions of the nuclear genome, and depleted within enhancers and coding sequences, suggesting negative selection. We validated the presence of a 76-kilobase-long heterozygous NUMT in chimpanzee, which was larger than any other NUMT observed in great apes, and found that dozens of NUMTs on the Pan Y chromosome expanded together with palindromes. Our study highlights NUMTs as a dynamic evolutionary force contributing to shaping ape genomes, and is valuable for characterizing mtDNA in great apes.