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

Sullivan, Alexis R. and Eldfjell, Yrin and Schiffthaler, Bastian and Delhomme, Nicolas and Asp, Torben and Hebelstrup, Kim H. and Keech, Olivier and Oberg, Lisa and Moller, Ian Max and Arvestad, Lars and Street, Nathaniel R. and Wang, Xiao-Ru (2020). The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants. Genome Biology and Evolution. 12 , 3586-3598
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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.

Authors/Creators:Sullivan, Alexis R. and Eldfjell, Yrin and Schiffthaler, Bastian and Delhomme, Nicolas and Asp, Torben and Hebelstrup, Kim H. and Keech, Olivier and Oberg, Lisa and Moller, Ian Max and Arvestad, Lars and Street, Nathaniel R. and Wang, Xiao-Ru
Title:The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants
Year of publishing :2020
Volume:12
Page range:3586-3598
Number of Pages:13
Publisher:Oxford University Press, The Society for Molecular Biology and Evolution
ISSN:1759-6653
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution-Noncommercial 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Evolutionary Biology
Keywords:mitogenome, repeats, recombination, rearrangement rates, structural variation
URN:NBN:urn:nbn:se:slu:epsilon-p-105334
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-105334
Additional ID:
Type of IDID
DOI10.1093/gbe/evz263
Web of Science (WoS)000522860800005
ID Code:16955
Faculty:S - Faculty of Forest Sciences
Department:(S) > Dept. of Forest Genetics and Plant Physiology
Deposited By: SLUpub Connector
Deposited On:05 May 2020 08:43
Metadata Last Modified:05 May 2020 08:43

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