Nuclear Mitochondrial Sequences in Great Ape Telomere-to-Telomere Genomes
Jul 7, 2026·
E Torres-González, MA Cremona, JM Storer, M Ventura, RJ O’Neill, KD Makova
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0 min read
Abstract
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.
Type
Publication
Genome Research
Authors
Ph.D. student
Before starting his PhD in the Makova lab, Edmundo worked on regional human variation as an undergraduate in Puerto Rico and on translational cancer genomics as a postdoc in NIH. As part of this thesis work, he focuses on mitochondrial genomics that cover its evolution, and
relation to complex phenotypes.
Authors
Visiting Research Professor
Marzia develops statistical techniques for the analysis of large, high-dimensional and complex data – in particular functional data. An important aspect of her research is its collaborative and multidisciplinary nature. Indeed, much of her work is at the interface between statistics and computational biology, and her main application area is in the “Omics” sciences.
Authors
Professor
Kateryna is interested in genomics, evolution, and human genetics.
Her lab studies mutations using both computational and experimental
approaches. Additional topics of interest include sex chromosome
evolution and genomics of childhood obesity.