umu.sePublications
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0003-2182-911X
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.ORCID iD: 0000-0002-9771-467X
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0002-3053-0796
Show others and affiliations
2020 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 12, no 1, p. 3586-3598Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Oxford University Press, 2020. Vol. 12, no 1, p. 3586-3598
Keywords [en]
mitogenome, repeats, recombination, rearrangement rates, structural variation
National Category
Earth and Related Environmental Sciences
Identifiers
URN: urn:nbn:se:umu:diva-168043DOI: 10.1093/gbe/evz263OAI: oai:DiVA.org:umu-168043DiVA, id: diva2:1392964
Available from: 2020-02-14 Created: 2020-02-14 Last updated: 2020-02-14Bibliographically approved
In thesis
1. A forest dark: an evolutionary history of Norway spruce
Open this publication in new window or tab >>A forest dark: an evolutionary history of Norway spruce
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Embedded within the relationships among species is a dense forest of gene trees, each with a potentially unique and discordant history. Such widespread genealogical heterogeneity is expected, but embracing this hierarchy of discordance while reconstructing the histories of populations and species remains a major challenge.

In this thesis, I studied the history of the genes and genomes contained within Norway spruce (Picea abies: Pinaceae), a forest tree distributed throughout boreal and montane Europe. I sequenced plastid genomes from all the commonly-recognized Picea species and developed a novel strategy to assemble the bacterial-sized mitochondrial genome of Norway spruce. Using multispecies coalescent network models, I reconstructed the relationships among populations of Norway spruce and the parapatric Siberian spruce (P. obovata) and distinguished between drift and hybridization as sources of phylogenetic discord.

Norway spruce holds heterogenous histories at multiple levels of organization. Although organelle genomes are expected to be clonal and uniparentally inherited, the chloroplast genome held by Norway spruce originated after sexual recombination between two divergent lineages. In the mitochondrial genome, recombination creates a diverse population of genome arrangements subjected to drift and selection within individuals and populations. Genetic diversity among populations is shaped in nearly equal measure by divergence and hybridization. Norway spruce is discordance distilled.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2020. p. 68
Keywords
phylogenetics, genome assembly, recombination, Picea, hybridization, mitogenome, Norway spruce, phylogeography, phylogenetic networks, plastome
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:umu:diva-168048 (URN)978-91-7855-211-5 (ISBN)
Public defence
2020-03-11, Carl Kempe salen (KB.E3.03), KBC-huset, Umeå, 13:00 (English)
Opponent
Supervisors
Available from: 2020-02-19 Created: 2020-02-14 Last updated: 2020-02-14Bibliographically approved

Open Access in DiVA

fulltext(1033 kB)19 downloads
File information
File name FULLTEXT01.pdfFile size 1033 kBChecksum SHA-512
e4a62bd3054489682106da0fbc57515f44165941188fa7f4460801aa3f721e634a7b17116ac086b6425a7379f7ec4df933e531e6fe153c6d91ea8eeaa55a348c
Type fulltextMimetype application/pdf

Other links

Publisher's full text

Authority records BETA

Sullivan, Alexis R.Schiffthaler, BastianDelhomme, NicolasKeech, OlivierStreet, NathanielWang, Xiao-Ru

Search in DiVA

By author/editor
Sullivan, Alexis R.Schiffthaler, BastianDelhomme, NicolasAsp, TorbenHebelstrup, Kim H.Keech, OlivierMøller, MaxArvestad, LarsStreet, NathanielWang, Xiao-Ru
By organisation
Department of Ecology and Environmental SciencesUmeå Plant Science Centre (UPSC)Department of Plant Physiology
In the same journal
Genome Biology and Evolution
Earth and Related Environmental Sciences

Search outside of DiVA

GoogleGoogle Scholar
Total: 19 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 43 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf