Cargando…

Characterization of nuclear mitochondrial insertions in the whole genomes of primates

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 inser...

Descripción completa

Detalles Bibliográficos
Autores principales: Dayama, Gargi, Zhou, Weichen, Prado-Martinez, Javier, Marques-Bonet, Tomas, Mills, Ryan E
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671390/
https://www.ncbi.nlm.nih.gov/pubmed/33575633
http://dx.doi.org/10.1093/nargab/lqaa089
_version_ 1783610920227831808
author Dayama, Gargi
Zhou, Weichen
Prado-Martinez, Javier
Marques-Bonet, Tomas
Mills, Ryan E
author_facet Dayama, Gargi
Zhou, Weichen
Prado-Martinez, Javier
Marques-Bonet, Tomas
Mills, Ryan E
author_sort Dayama, Gargi
collection PubMed
description 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.
format Online
Article
Text
id pubmed-7671390
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-76713902021-02-10 Characterization of nuclear mitochondrial insertions in the whole genomes of primates Dayama, Gargi Zhou, Weichen Prado-Martinez, Javier Marques-Bonet, Tomas Mills, Ryan E NAR Genom Bioinform Standard Article 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. Oxford University Press 2020-11-16 /pmc/articles/PMC7671390/ /pubmed/33575633 http://dx.doi.org/10.1093/nargab/lqaa089 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Standard Article
Dayama, Gargi
Zhou, Weichen
Prado-Martinez, Javier
Marques-Bonet, Tomas
Mills, Ryan E
Characterization of nuclear mitochondrial insertions in the whole genomes of primates
title Characterization of nuclear mitochondrial insertions in the whole genomes of primates
title_full Characterization of nuclear mitochondrial insertions in the whole genomes of primates
title_fullStr Characterization of nuclear mitochondrial insertions in the whole genomes of primates
title_full_unstemmed Characterization of nuclear mitochondrial insertions in the whole genomes of primates
title_short Characterization of nuclear mitochondrial insertions in the whole genomes of primates
title_sort characterization of nuclear mitochondrial insertions in the whole genomes of primates
topic Standard Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671390/
https://www.ncbi.nlm.nih.gov/pubmed/33575633
http://dx.doi.org/10.1093/nargab/lqaa089
work_keys_str_mv AT dayamagargi characterizationofnuclearmitochondrialinsertionsinthewholegenomesofprimates
AT zhouweichen characterizationofnuclearmitochondrialinsertionsinthewholegenomesofprimates
AT pradomartinezjavier characterizationofnuclearmitochondrialinsertionsinthewholegenomesofprimates
AT marquesbonettomas characterizationofnuclearmitochondrialinsertionsinthewholegenomesofprimates
AT millsryane characterizationofnuclearmitochondrialinsertionsinthewholegenomesofprimates