The mitogenome of Norway spruce and a reappraisal of mitochondrial recombination in plants

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DOI

  • Alexis R Sullivan, Umeå Plant Science Center, Department of Ecology and Environmental Science, Umeå University, Sweden
  • Yrin Eldfjell, Department of Mathematics, Swedish e-Science Research Centre, Science for Life Laboratory, Stockholm University, Sweden
  • Bastian Schiffthaler, Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Sweden
  • Nicolas Delhomme, Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Sweden
  • Torben Asp
  • Kim Hebelstrup
  • Olivier Keech, Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Sweden
  • Lisa Öberg, oldTjikko Photo Art & Science, Sweden
  • Ian Max Møller
  • Lars Arvestad, Department of Mathematics, Swedish e-Science Research Centre, Science for Life Laboratory, Stockholm University, Sweden
  • Nathaniel R Street, Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Sweden
  • Xiao-Ru Wang, Umeå Plant Science Center, Department of Ecology and Environmental Science, Umeå University, Sweden
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 pre-genomic, 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 a 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.
Original languageEnglish
JournalGenome Biology and Evolution
Volume12
Issue1
Pages (from-to)3586-3598
Number of pages13
ISSN1759-6653
DOIs
Publication statusPublished - 1 Jan 2020

    Research areas

  • mitogenome, repeats, recombination, rearrangement rates, structural variation

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