Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals
Abstract Nuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been characterized in many species. However, relatively little attention has been paid to understanding their evolutionary origins and to disentangling alternative sources of insertions. Numts conta...
Published in: | Genome Biology and Evolution |
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Language: | English |
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Oxford University Press (OUP)
2022
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Online Access: | http://dx.doi.org/10.1093/gbe/evac104 https://academic.oup.com/gbe/advance-article-pdf/doi/10.1093/gbe/evac104/44813031/evac104.pdf https://academic.oup.com/gbe/article-pdf/14/7/evac104/45193648/evac104.pdf |
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croxfordunivpr:10.1093/gbe/evac104 2024-10-20T14:04:41+00:00 Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals Vendrami, David L J Gossmann, Toni I Chakarov, Nayden Paijmans, Anneke J Litzke, Vivienne Eyre-Walker, Adam Forcada, Jaume Hoffman, Joseph I Betancourt, Andrea 2022 http://dx.doi.org/10.1093/gbe/evac104 https://academic.oup.com/gbe/advance-article-pdf/doi/10.1093/gbe/evac104/44813031/evac104.pdf https://academic.oup.com/gbe/article-pdf/14/7/evac104/45193648/evac104.pdf en eng Oxford University Press (OUP) https://creativecommons.org/licenses/by/4.0/ Genome Biology and Evolution volume 14, issue 7 ISSN 1759-6653 journal-article 2022 croxfordunivpr https://doi.org/10.1093/gbe/evac104 2024-09-24T04:05:51Z Abstract Nuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been characterized in many species. However, relatively little attention has been paid to understanding their evolutionary origins and to disentangling alternative sources of insertions. Numts containing genes with intact mitochondrial reading frames represent good candidates for this purpose. The sequences of the genes they contain can be compared with their mitochondrial homologs to characterize synonymous to nonsynonymous substitution rates, which can shed light on the selection pressures these genes have been subjected to. Here, we characterize 25 numts in the Antarctic fur seal (Arctocephalus gazella) genome. Among those containing genes with intact mitochondrial reading frames, three carry multiple substitutions in comparison to their mitochondrial homologs. Our analyses reveal that one represents a historic insertion subjected to strong purifying selection since it colonized the Otarioidea in a genomic region enriched in retrotransposons. By contrast, the other two numts appear to be more recent and their large number of substitutions can be attributed to noncanonical insertions, either the integration of heteroplasmic mtDNA or hybridization. Our study sheds new light on the evolutionary history of pinniped numts and uncovers the presence of hidden sources of mitonuclear variation. Article in Journal/Newspaper Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella Oxford University Press Antarctic The Antarctic Genome Biology and Evolution 14 7 |
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Open Polar |
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Oxford University Press |
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croxfordunivpr |
language |
English |
description |
Abstract Nuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been characterized in many species. However, relatively little attention has been paid to understanding their evolutionary origins and to disentangling alternative sources of insertions. Numts containing genes with intact mitochondrial reading frames represent good candidates for this purpose. The sequences of the genes they contain can be compared with their mitochondrial homologs to characterize synonymous to nonsynonymous substitution rates, which can shed light on the selection pressures these genes have been subjected to. Here, we characterize 25 numts in the Antarctic fur seal (Arctocephalus gazella) genome. Among those containing genes with intact mitochondrial reading frames, three carry multiple substitutions in comparison to their mitochondrial homologs. Our analyses reveal that one represents a historic insertion subjected to strong purifying selection since it colonized the Otarioidea in a genomic region enriched in retrotransposons. By contrast, the other two numts appear to be more recent and their large number of substitutions can be attributed to noncanonical insertions, either the integration of heteroplasmic mtDNA or hybridization. Our study sheds new light on the evolutionary history of pinniped numts and uncovers the presence of hidden sources of mitonuclear variation. |
author2 |
Betancourt, Andrea |
format |
Article in Journal/Newspaper |
author |
Vendrami, David L J Gossmann, Toni I Chakarov, Nayden Paijmans, Anneke J Litzke, Vivienne Eyre-Walker, Adam Forcada, Jaume Hoffman, Joseph I |
spellingShingle |
Vendrami, David L J Gossmann, Toni I Chakarov, Nayden Paijmans, Anneke J Litzke, Vivienne Eyre-Walker, Adam Forcada, Jaume Hoffman, Joseph I Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals |
author_facet |
Vendrami, David L J Gossmann, Toni I Chakarov, Nayden Paijmans, Anneke J Litzke, Vivienne Eyre-Walker, Adam Forcada, Jaume Hoffman, Joseph I |
author_sort |
Vendrami, David L J |
title |
Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals |
title_short |
Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals |
title_full |
Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals |
title_fullStr |
Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals |
title_full_unstemmed |
Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals |
title_sort |
signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals |
publisher |
Oxford University Press (OUP) |
publishDate |
2022 |
url |
http://dx.doi.org/10.1093/gbe/evac104 https://academic.oup.com/gbe/advance-article-pdf/doi/10.1093/gbe/evac104/44813031/evac104.pdf https://academic.oup.com/gbe/article-pdf/14/7/evac104/45193648/evac104.pdf |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
genre |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella |
genre_facet |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella |
op_source |
Genome Biology and Evolution volume 14, issue 7 ISSN 1759-6653 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1093/gbe/evac104 |
container_title |
Genome Biology and Evolution |
container_volume |
14 |
container_issue |
7 |
_version_ |
1813453501771022336 |