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 ORCID: https://orcid.org/0000-0002-2115-0150; Hoffman, Joseph I. ORCID: https://orcid.org/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

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Abstract/Summary

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.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	https://doi.org/10.1093/gbe/evac104
ISSN:	1759-6653
Additional Keywords:	nuclear DNA sequences of mitochondrial origin (numts), genome evolution, mitochondrial DNA, pinniped, Antarctic fur seal, Arctocephalus gazella
Date made live:	14 Jul 2022 08:14 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/532911

Item Type:

Publication - Article

Digital Object Identifier (DOI):

https://doi.org/10.1093/gbe/evac104

ISSN:

1759-6653

Additional Keywords:

nuclear DNA sequences of mitochondrial origin (numts), genome evolution, mitochondrial DNA, pinniped, Antarctic fur seal, Arctocephalus gazella

Date made live:

14 Jul 2022 08:14 +0 (UTC)

URI:

https://nora.nerc.ac.uk/id/eprint/532911