Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals
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 gen...
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Oxford University Press
2022
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Online Access: | http://nora.nerc.ac.uk/id/eprint/532911/ https://nora.nerc.ac.uk/id/eprint/532911/1/evac104.pdf https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evac104/6637498 |
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ftnerc:oai:nora.nerc.ac.uk:532911 2023-05-15T13:41:46+02:00 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 Eyre-Walker, Adam Forcada, Jaume Hoffman, Joseph I. Betancourt, Andrea 2022-07-30 text http://nora.nerc.ac.uk/id/eprint/532911/ https://nora.nerc.ac.uk/id/eprint/532911/1/evac104.pdf https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evac104/6637498 en eng Oxford University Press https://nora.nerc.ac.uk/id/eprint/532911/1/evac104.pdf Vendrami, David L J; Gossmann, Toni I.; Chakarov, Nayden; Paijmans, Anneke J; Eyre-Walker, Adam; Forcada, Jaume orcid:0000-0002-2115-0150 Hoffman, Joseph I. orcid:0000-0001-5895-8949 Betancourt, Andrea. 2022 Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals. Genome Biology and Evolution, 14 (7), evac104. 12, pp. https://doi.org/10.1093/gbe/evac104 <https://doi.org/10.1093/gbe/evac104> cc_by_4 CC-BY Publication - Article PeerReviewed 2022 ftnerc https://doi.org/10.1093/gbe/evac104 2023-02-04T19:53:25Z 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 to their mitochondrial homologs to characterize synonymous to non-synonymous substitution rates, which can shed light on the selection pressures these genes have been subjected to. Here, we characterise 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 non-canonical 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 Natural Environment Research Council: NERC Open Research Archive Antarctic The Antarctic Genome Biology and Evolution 14 7 |
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Open Polar |
collection |
Natural Environment Research Council: NERC Open Research Archive |
op_collection_id |
ftnerc |
language |
English |
description |
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 to their mitochondrial homologs to characterize synonymous to non-synonymous substitution rates, which can shed light on the selection pressures these genes have been subjected to. Here, we characterise 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 non-canonical 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. |
format |
Article in Journal/Newspaper |
author |
Vendrami, David L J Gossmann, Toni I. Chakarov, Nayden Paijmans, Anneke J Eyre-Walker, Adam Forcada, Jaume Hoffman, Joseph I. Betancourt, Andrea |
spellingShingle |
Vendrami, David L J Gossmann, Toni I. Chakarov, Nayden Paijmans, Anneke J Eyre-Walker, Adam Forcada, Jaume Hoffman, Joseph I. Betancourt, Andrea 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 Eyre-Walker, Adam Forcada, Jaume Hoffman, Joseph I. Betancourt, Andrea |
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 |
publishDate |
2022 |
url |
http://nora.nerc.ac.uk/id/eprint/532911/ https://nora.nerc.ac.uk/id/eprint/532911/1/evac104.pdf https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evac104/6637498 |
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_relation |
https://nora.nerc.ac.uk/id/eprint/532911/1/evac104.pdf Vendrami, David L J; Gossmann, Toni I.; Chakarov, Nayden; Paijmans, Anneke J; Eyre-Walker, Adam; Forcada, Jaume orcid:0000-0002-2115-0150 Hoffman, Joseph I. orcid:0000-0001-5895-8949 Betancourt, Andrea. 2022 Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals. Genome Biology and Evolution, 14 (7), evac104. 12, pp. https://doi.org/10.1093/gbe/evac104 <https://doi.org/10.1093/gbe/evac104> |
op_rights |
cc_by_4 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1093/gbe/evac104 |
container_title |
Genome Biology and Evolution |
container_volume |
14 |
container_issue |
7 |
_version_ |
1766157928784461824 |