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The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).ORCID-id: 0000-0003-2182-911X
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.ORCID-id: 0000-0002-9771-467X
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).ORCID-id: 0000-0002-3053-0796
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2020 (Engelska)Ingår i: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 12, nr 1, s. 3586-3598Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
Oxford University Press, 2020. Vol. 12, nr 1, s. 3586-3598
Nyckelord [en]
mitogenome, repeats, recombination, rearrangement rates, structural variation
Nationell ämneskategori
Geovetenskap och miljövetenskap
Identifikatorer
URN: urn:nbn:se:umu:diva-168043DOI: 10.1093/gbe/evz263ISI: 000522860800005Scopus ID: 2-s2.0-85077489986OAI: oai:DiVA.org:umu-168043DiVA, id: diva2:1392964
Tillgänglig från: 2020-02-14 Skapad: 2020-02-14 Senast uppdaterad: 2023-09-05Bibliografiskt granskad
Ingår i avhandling
1. A forest dark: an evolutionary history of Norway spruce
Öppna denna publikation i ny flik eller fönster >>A forest dark: an evolutionary history of Norway spruce
2020 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
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.

Ort, förlag, år, upplaga, sidor
Umeå: Umeå University, 2020. s. 68
Nyckelord
phylogenetics, genome assembly, recombination, Picea, hybridization, mitogenome, Norway spruce, phylogeography, phylogenetic networks, plastome
Nationell ämneskategori
Evolutionsbiologi
Identifikatorer
urn:nbn:se:umu:diva-168048 (URN)978-91-7855-211-5 (ISBN)
Disputation
2020-03-11, Carl Kempe salen (KB.E3.03), KBC-huset, Umeå, 13:00 (Engelska)
Opponent
Handledare
Tillgänglig från: 2020-02-19 Skapad: 2020-02-14 Senast uppdaterad: 2020-02-14Bibliografiskt granskad

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

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Sullivan, Alexis R.Schiffthaler, BastianDelhomme, NicolasAsp, TorbenHebelstrup, Kim H.Keech, OlivierMøller, MaxArvestad, LarsStreet, NathanielWang, Xiao-Ru
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Institutionen för ekologi, miljö och geovetenskapUmeå Plant Science Centre (UPSC)Institutionen för fysiologisk botanik
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Genome Biology and Evolution
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