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Research article - Peer-reviewed, 2020

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

Sullivan, Alexis R.; Eldfjell, Yrin; Schiffthaler, Bastian; Delhomme, Nicolas; Asp, Torben; Hebelstrup, Kim H.; Keech, Olivier; Oberg, Lisa; Moller, Ian Max; Arvestad, Lars; Street, Nathaniel R.; Wang, Xiao-Ru

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.

Keywords

mitogenome; repeats; recombination; rearrangement rates; structural variation

Published in

Genome Biology and Evolution
2020, volume: 12, number: 1, pages: 3586-3598
Publisher: OXFORD UNIV PRESS

Authors' information

Sullivan, Alexis R.
Umea Univ
Eldfjell, Yrin
Stockholm Univ
Schiffthaler, Bastian
Umea Univ
Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology
Asp, Torben
Aarhus Univ
Hebelstrup, Kim H.
Aarhus Univ
Keech, Olivier
Umea Univ
Oberg, Lisa
Oldtjikko Photo Art and Sci
Moller, Ian Max
Aarhus Univ
Arvestad, Lars
Stockholm Univ
Street, Nathaniel R.
Umea Univ
Wang, Xiao-Ru
Umea Univ

UKÄ Subject classification

Genetics
Evolutionary Biology

Publication Identifiers

DOI: https://doi.org/10.1093/gbe/evz263

URI (permanent link to this page)

https://res.slu.se/id/publ/105334