Characterization of nuclear mitochondrial insertions in the whole genomes of primates.

Tomas Marques-Bonet,Gargi Dayama,Javier Prado-Martinez,Ryan E Mills,Weichen Zhou

doi:10.1093/nargab/lqaa089

Tomas Marques-Bonet, Gargi Dayama + Show 3 more

Open Access

https://doi.org/10.1093/nargab/lqaa089

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Abstract

The transfer and integration of whole and partial mitochondrial genomes into the nuclear genomes of eukaryotes is an ongoing process that has facilitated the transfer of genes and contributed to the evolution of various cellular pathways. Many previous studies have explored the impact of these insertions, referred to as NumtS, but have focused primarily on older events that have become fixed and are therefore present in all individual genomes for a given species. We previously developed an approach to identify novel Numt polymorphisms from next-generation sequence data and applied it to thousands of human genomes. Here, we extend this analysis to 79 individuals of other great ape species including chimpanzee, bonobo, gorilla, orang-utan and also an old world monkey, macaque. We show that recent Numt insertions are prevalent in each species though at different apparent rates, with chimpanzees exhibiting a significant increase in both polymorphic and fixed Numt sequences as compared to other great apes. We further assessed positional effects in each species in terms of evolutionary time and rate of insertion and identified putative hotspots on chromosome 5 for Numt integration, providing insight into both recent polymorphic and older fixed reference NumtS in great apes in comparison to human events.

Highlights

Polymorphic Nuclear Mitochondrial Insertions (NumtS) are fragments of mitochondrial DNA that have been transferred and integrated into the nuclear genome of an organism
Chimpanzee was observed to encompass the largest number of polymorphic Nuclear insertions of mitochondrial origin (Numt) insertions with a total of 187 events discovered in 24 samples across four different subgroups at an observed rate of 20.8 average per sample
We are reporting a total of 4274 reference NumtS in great apes and macaque (Additional file 2)

Summary

Introduction

Polymorphic Nuclear Mitochondrial Insertions (NumtS) are fragments of mitochondrial DNA (mtDNA) that have been transferred and integrated into the nuclear genome of an organism. NumtS vary in size from smaller fragments to full length mitochondrial integrations and can share varying degree of homology with the genome of their parent mitochondria, depending on the age and time of insertion. Once these pieces of mtDNA have inserted themselves, their mutation rate decreases by an order of magnitude to the background rate of the organisms nuclear genome, essentially fossilizing the fragment and providing a snapshot of the ancestral mitochondria from when it was inserted[1,2,3]. The majority of prior studies have focused on older, fixed insertions, recent efforts have begun to explore the impact of segregating Numt alleles within human populations[2, 7]

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