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Uvizl, Marek, Puechmaille, Sebastien J., Power, Sarahjane, Pippel, Martin, Carthy, Samuel, Haerty, Wilfried 
ORCID: https://orcid.org/0000-0003-0111-191X, Myers, Eugene W., Teeling, Emma C. and Huang, Zixia
(2024)
Comparative genome microsynteny illuminates the fast evolution of nuclear mitochondrial segments (NUMTs) in mammals.
Molecular Biology and Evolution, 41 (1).
ISSN 0737-4038
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Abstract
The escape of DNA from mitochondria into the nuclear genome (nuclear mitochondrial DNA, NUMT) is an ongoing process. Although pervasively observed in eukaryotic genomes, their evolutionary trajectories in a mammal-wide context are poorly understood. The main challenge lies in the orthology assignment of NUMTs across species due to their fast evolution and chromosomal rearrangements over the past 200 million years. To address this issue, we systematically investigated the characteristics of NUMT insertions in 45 mammalian genomes and established a novel, synteny-based method to accurately predict orthologous NUMTs and ascertain their evolution across mammals. With a series of comparative analyses across taxa, we revealed that NUMTs may originate from nonrandom regions in mtDNA, are likely found in transposon-rich and intergenic regions, and unlikely code for functional proteins. Using our synteny-based approach, we leveraged 630 pairwise comparisons of genome-wide microsynteny and predicted the NUMT orthology relationships across 36 mammals. With the phylogenetic patterns of NUMT presence-And-Absence across taxa, we constructed the ancestral state of NUMTs given the mammal tree using a coalescent method. We found support on the ancestral node of Fereuungulata within Laurasiatheria, whose subordinal relationships are still controversial. This study broadens our knowledge on NUMT insertion and evolution in mammalian genomes and highlights the merit of NUMTs as alternative genetic markers in phylogenetic inference.
| Item Type: | Article |
|---|---|
| Additional Information: | Data Availability Statement: The publicly available genome, mitogenome, and RNA-Seq data used in this study are documented in the supplementary tables S1 and S13, Supplementary Material online. The intermediate data supporting the conclusions can be available at the GitHub page (https://github.com/huangzixia/NUMT_evolution_in_mammals). Funding Information: This study is supported by the Irish Research Council Laureate Bursary Grant (No. 74725) and the UCD seed funding (No. 68674) to Z.H., the Irish Research Council Laureate Award IRCLA/2017/58 and Science Foundation Ireland Future Frontiers 19/FFP/6790 awarded to E.C.T., and the Junior Chair from the Institut Universitaire de France awarded to S.J.P. |
| Uncontrolled Keywords: | evolution,genome microsynteny,mammal,nuclear mitochondrial dna segment (numt),ecology, evolution, behavior and systematics,molecular biology,genetics ,/dk/atira/pure/subjectarea/asjc/1100/1105 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| UEA Research Groups: | Faculty of Medicine and Health Sciences > Research Centres > Norwich Institute for Healthy Aging |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 23 Oct 2024 15:30 |
| Last Modified: | 01 Nov 2024 12:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97152 |
| DOI: | 10.1093/molbev/msad278 |
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