Characterization of nuclear mitochondrial insertions in the whole genomes of primates
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 th...
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Published in | NAR genomics and bioinformatics Vol. 2; no. 4; p. lqaa089 |
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Main Authors | , , , , |
Format | Journal Article |
Language | English |
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Oxford University Press
01.12.2020
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Abstract | 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. |
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AbstractList | 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. 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. |
Author | Prado-Martinez, Javier Marques-Bonet, Tomas Zhou, Weichen Mills, Ryan E Dayama, Gargi |
Author_xml | – sequence: 1 givenname: Gargi orcidid: 0000-0003-1349-8998 surname: Dayama fullname: Dayama, Gargi – sequence: 2 givenname: Weichen orcidid: 0000-0003-4755-1072 surname: Zhou fullname: Zhou, Weichen – sequence: 3 givenname: Javier orcidid: 0000-0001-5402-2721 surname: Prado-Martinez fullname: Prado-Martinez, Javier – sequence: 4 givenname: Tomas surname: Marques-Bonet fullname: Marques-Bonet, Tomas – sequence: 5 givenname: Ryan E orcidid: 0000-0003-3425-6998 surname: Mills fullname: Mills, Ryan E email: remills@umich.edu |
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Cites_doi | 10.1093/molbev/msl149 10.1093/bioinformatics/btp324 10.1007/s00239-003-2485-7 10.1007/s00239-002-2390-5 10.1126/science.aar6343 10.1126/science.aae0344 10.1093/molbev/msq193 10.1073/pnas.1305904110 10.1002/ajp.20047 10.1093/nar/gkz1173 10.1038/nature11128 10.1093/oxfordjournals.molbev.a003971 10.1006/geno.2002.6798 10.1007/s00439-011-1125-3 10.1093/nar/gkv1275 10.1073/pnas.91.23.10771 10.1038/nature12228 10.1007/s00239-009-9243-4 10.1093/database/baw053 10.1371/journal.pbio.0020273 10.1371/journal.pgen.0030119 10.1101/gr.215087.116 10.1101/gr.092759.109 10.1093/nar/gku1038 10.1371/journal.pgen.1000834 10.1038/ng.806 10.1093/molbev/msp131 10.1093/nar/gks424 10.1038/s41598-017-16750-2 10.1038/378489a0 10.1371/journal.pgen.1000237 10.1007/s00239-012-9519-y 10.1093/gbe/evw124 10.1093/gbe/evz058 10.1186/1471-2105-13-S4-S15 10.1101/gr.9.9.868 |
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The transfer and integration of whole and partial mitochondrial genomes into the nuclear genomes of eukaryotes is an ongoing process that has... The transfer and integration of whole and partial mitochondrial genomes into the nuclear genomes of eukaryotes is an ongoing process that has facilitated the... |
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