| 1. |
- Rhoades, Nicholas A., et al.
(författare)
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Identification of rfk-1, a Meiotic Driver Undergoing RNA Editing in Neurospora
- 2019
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Ingår i: Genetics. - : GENETICS SOCIETY AMERICA. - 0016-6731 .- 1943-2631. ; 212:1, s. 93-110
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Tidskriftsartikel (refereegranskat)abstract
- Sk-2 is a meiotic drive element that was discovered in wild populations of Neurospora fungi over 40 years ago. While early studies quickly determined that Sk-2 transmits itself through sexual reproduction in a biased manner via spore killing, the genetic factors responsible for this phenomenon have remained mostly unknown. Here, we identify and characterize rfk-1, a gene required for Sk-2-based spore killing. The rfk-1 gene contains four exons, three introns, and two stop codons, the first of which undergoes RNA editing to a tryptophan codon during sexual development. Translation of an unedited rfk-1 transcript in vegetative tissue is expected to produce a 102-amino acid protein, whereas translation of an edited rfk-1 transcript in sexual tissue is expected to produce a protein with 130 amino acids. These findings indicate that unedited and edited rfk-1 transcripts exist and that these transcripts could have different roles with respect to the mechanism of meiotic drive by spore killing. Regardless of RNA editing, spore killing only succeeds if rfk-1 transcripts avoid silencing caused by a genome defense process called meiotic silencing by unpaired DNA (MSUD). We show that rfk-1's MSUD avoidance mechanism is linked to the genomic landscape surrounding the rfk-1 gene, which is located near the Sk-2 border on the right arm of chromosome III. In addition to demonstrating that the location of rfk-1 is critical to spore-killing success, our results add to accumulating evidence that MSUD helps protect Neurospora genomes from complex meiotic drive elements.
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| 2. |
- Svedberg, Jesper, et al.
(författare)
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Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements
- 2018
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Meiotic drive is widespread in nature. The conflict it generates is expected to be an important motor for evolutionary change and innovation. In this study, we investigated the genomic consequences of two large multi-gene meiotic drive elements, Sk-2 and Sk-3, found in the filamentous ascomycete Neurospora intermedia. Using long-read sequencing, we generated the first complete and well-annotated genome assemblies of large, highly diverged, non-recombining regions associated with meiotic drive elements. Phylogenetic analysis shows that, even though Sk-2 and Sk-3 are located in the same chromosomal region, they do not form sister clades, suggesting independent origins or at least a long evolutionary separation. We conclude that they have in a convergent manner accumulated similar patterns of tandem inversions and dense repeat clusters, presumably in response to similar needs to create linkage between genes causing drive and resistance.
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| 3. |
- Svedberg, Jesper, 1981-, et al.
(författare)
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The effect of genomic conflict on genome evolution in Neurospora intermedia
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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