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The effect of genomic conflict on genome evolution in Neurospora intermedia
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Genomic conflicts are predicted to have a major influence on genome evolution, but empirical data is needed in order to confirm or refute this prediction. In this study, we used a genomic approach to address the influence of genomic conflicts, caused by selfish genetic elements, on genome evolution in the model fungus Neurospora intermedia. We gathered high-quality genomic data from sixteen strains of Neurospora by using the PacBio RSII long-read sequencing platform. Six of these strains carry the meiotic drive element Sk-2 or Sk-3, which are multigene systems of killer and resistance loci linked together in haplotypes. We show that in the N. intermedia genomes, in which an array of protective mechanisms act to limit the negative effects of selfish DNA, both the Sk-2 and Sk-3 haplotypes have accumulated a dense set of inversions that are interspersed with transposable elements. The inversions are unique for each killer type, showing that they have a long separated evolutionary history and likely have established themselves as meiotic drivers independently. For the Sk-2 haplotype, for which we have polymorphism-data, we see signs of relaxed selection, which is consistent with the hypothesis that recombination suppression reduces the efficacy of selection in this region. Thus, our data indicates that albeit N. intermedia possesses an active genome defence system, selfish genetic elements have worked in concert and significantly affected the evolutionary trajectory of chromosome 3 in this species.

Keywords [en]
Genomics, genomic conflict, mieotic drive, spore killer, Neurospora
National Category
Evolutionary Biology
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
URN: urn:nbn:se:uu:diva-329493OAI: oai:DiVA.org:uu-329493DiVA, id: diva2:1141854
Available from: 2017-09-17 Created: 2017-09-17 Last updated: 2017-09-17
In thesis
1. Catching the Spore killers: Genomic conflict and genome evolution in Neurospora
Open this publication in new window or tab >>Catching the Spore killers: Genomic conflict and genome evolution in Neurospora
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

A genome is shaped by many different forces. Recombination can for instance both create and maintain genetic diversity, but the need to locally reduce recombination rates will also leave specific signatures. Genetic elements can act selfishly and spreading at the expense of the rest of the genome can leave marks of their activity, as can mechanisms that suppresses them, in a phenomenon known as genomic conflict. In this thesis, I have studied the forces driving genome evolution, using modern genome sequencing techniques and with a special focus on a class of selfish genetic elements known as Spore killers found in the fungus Neurospora. First, we show novel findings on large-scale suppression of recombination by non-structural means in the N. tetrasperma genomes. In contrary, in the genomic region harbouring the spore killer elements Sk-2 and Sk-3 of N. intermedia, a dense set of inversions that are interspersed with transposable elements have accumulated. The inversions are unique for each killer type, showing that they have a long separated evolutionary history and likely have established themselves independently. For the Sk-2 haplotype, where we have polymorphism data, we see signs of relaxed selection, which is consistent with the hypothesis that recombination suppression reduces the efficacy of selection in this region. These results show the strong effects the divergent selective forces of genomic conflicts can have on chromosome architecture. Furthermore, we investigate the hypothesis that spore killing can drive reproductive isolation, by comparing the fertility of crosses between N. metzenbergii and either killer or non-killer N. intermedia strains. We show that crosses with spore killer strains have lower fertility, which cannot be explained by the killing itself, but is potentially caused by an incompatibility gene captured in the non-recombining region. Finally, we identified the genetic element responsible for causing spore killing in the Sk-1 spore killer strains found in N. sitophila. Unlike the Sk-2 and Sk-3 elements, Sk-1 is not connected to a large, non-recombining region, but is caused by a single locus, and we also find indications that this locus was introgressed from N. hispaniola.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2017. p. 51
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1561
Keywords
Genomics, genomic conflict, genome evolution, meiotic drive, spore killer, suppression of recombination, inversions, fungi, Neurospora
National Category
Evolutionary Biology
Research subject
Biology
Identifiers
urn:nbn:se:uu:diva-329498 (URN)978-91-513-0074-0 (ISBN)
Public defence
2017-11-03, Lindahlsalen, Norbyvägen 18A, Uppsala, 09:00
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Available from: 2017-10-13 Created: 2017-09-17 Last updated: 2017-10-18

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