The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants

Abstract Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their i...

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Veröffentlicht in:Genome biology and evolution 2020-01, Vol.12 (1), p.3586-3598
Hauptverfasser: Sullivan, Alexis R, Eldfjell, Yrin, Schiffthaler, Bastian, Delhomme, Nicolas, Asp, Torben, Hebelstrup, Kim H, Keech, Olivier, Öberg, Lisa, Møller, Ian Max, Arvestad, Lars, Street, Nathaniel R, Wang, Xiao-Ru
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container_issue 1
container_start_page 3586
container_title Genome biology and evolution
container_volume 12
creator Sullivan, Alexis R
Eldfjell, Yrin
Schiffthaler, Bastian
Delhomme, Nicolas
Asp, Torben
Hebelstrup, Kim H
Keech, Olivier
Öberg, Lisa
Møller, Ian Max
Arvestad, Lars
Street, Nathaniel R
Wang, Xiao-Ru
description Abstract Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.
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subjects Evolutionary Biology
Evolutionsbiologi
Genetics
Genetik
mitogenome
rearrangement rates
recombination
repeats
structural variation
title The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants
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