Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals
Vendrami D, Goßmann T, Chakarov N, et al. Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals. Genome Biology and Evolution . 2022;14(7): evac104. Nuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been c...
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Oxford University Press
2022
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Online Access: | https://nbn-resolving.org/urn:nbn:de:0070-pub-29645127 https://pub.uni-bielefeld.de/record/2964512 https://pub.uni-bielefeld.de/download/2964512/2966651 |
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ftubbiepub:oai:pub.uni-bielefeld.de:2964512 2023-05-15T13:49:13+02:00 Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals Vendrami, David Goßmann, Toni Chakarov, Nayden Paijmans, Anneke Eyre-Walker, Adam Forcada, Jaume Hoffman, Joseph 2022 https://nbn-resolving.org/urn:nbn:de:0070-pub-29645127 https://pub.uni-bielefeld.de/record/2964512 https://pub.uni-bielefeld.de/download/2964512/2966651 eng eng Oxford University Press info:eu-repo/semantics/altIdentifier/doi/10.1093/gbe/evac104 info:eu-repo/semantics/altIdentifier/issn/1759-6653 info:eu-repo/semantics/altIdentifier/wos/000833077400001 info:eu-repo/semantics/altIdentifier/pmid/35809042 https://nbn-resolving.org/urn:nbn:de:0070-pub-29645127 https://pub.uni-bielefeld.de/record/2964512 https://pub.uni-bielefeld.de/download/2964512/2966651 https://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess CC-BY nuclear DNA sequences of mitochondrial origin (numts) genome evolution mitochondrial DNA pinniped Antarctic fur seal Arctocephalus gazella ddc:570 http://purl.org/coar/resource_type/c_6501 info:eu-repo/semantics/article doc-type:article text 2022 ftubbiepub https://doi.org/10.1093/gbe/evac104 2023-01-30T00:00:22Z Vendrami D, Goßmann T, Chakarov N, et al. Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals. Genome Biology and Evolution . 2022;14(7): evac104. 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 PUB - Publications at Bielefeld University Antarctic The Antarctic Genome Biology and Evolution 14 7 |
institution |
Open Polar |
collection |
PUB - Publications at Bielefeld University |
op_collection_id |
ftubbiepub |
language |
English |
topic |
nuclear DNA sequences of mitochondrial origin (numts) genome evolution mitochondrial DNA pinniped Antarctic fur seal Arctocephalus gazella ddc:570 |
spellingShingle |
nuclear DNA sequences of mitochondrial origin (numts) genome evolution mitochondrial DNA pinniped Antarctic fur seal Arctocephalus gazella ddc:570 Vendrami, David Goßmann, Toni Chakarov, Nayden Paijmans, Anneke Eyre-Walker, Adam Forcada, Jaume Hoffman, Joseph Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals |
topic_facet |
nuclear DNA sequences of mitochondrial origin (numts) genome evolution mitochondrial DNA pinniped Antarctic fur seal Arctocephalus gazella ddc:570 |
description |
Vendrami D, Goßmann T, Chakarov N, et al. Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals. Genome Biology and Evolution . 2022;14(7): evac104. 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. |
format |
Article in Journal/Newspaper |
author |
Vendrami, David Goßmann, Toni Chakarov, Nayden Paijmans, Anneke Eyre-Walker, Adam Forcada, Jaume Hoffman, Joseph |
author_facet |
Vendrami, David Goßmann, Toni Chakarov, Nayden Paijmans, Anneke Eyre-Walker, Adam Forcada, Jaume Hoffman, Joseph |
author_sort |
Vendrami, David |
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 |
https://nbn-resolving.org/urn:nbn:de:0070-pub-29645127 https://pub.uni-bielefeld.de/record/2964512 https://pub.uni-bielefeld.de/download/2964512/2966651 |
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 |
info:eu-repo/semantics/altIdentifier/doi/10.1093/gbe/evac104 info:eu-repo/semantics/altIdentifier/issn/1759-6653 info:eu-repo/semantics/altIdentifier/wos/000833077400001 info:eu-repo/semantics/altIdentifier/pmid/35809042 https://nbn-resolving.org/urn:nbn:de:0070-pub-29645127 https://pub.uni-bielefeld.de/record/2964512 https://pub.uni-bielefeld.de/download/2964512/2966651 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess |
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_ |
1766251003724693504 |