| 1. |
- Ament-Velásquez, Sandra Lorena, M.Sc. 1988-
(författare)
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Drivers of evolutionary change in Podospora anserina
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Genomic diversity is shaped by a myriad of forces acting in different directions. Some genes work in concert with the interests of the organism, often shaped by natural selection, while others follow their own interests. The latter genes are considered “selfish”, behaving either neutrally to the host, or causing it harm. In this thesis, I focused on genes that have substantial fitness effects on the fungus Podospora anserina and relatives, but whose effects are very contrasting. In Papers I and II, I explored the evolution of a particular type of selfish genetic elements that cause meiotic drive. Meiotic drivers manipulate the outcome of meiosis to achieve overrepresentation in the progeny, thus increasing their likelihood of invading and propagating in a population. In P. anserina there are multiple meiotic drivers but their genetic basis was previously unknown. In Paper I, we demonstrated that drive is caused by members of the Spok gene family. We discovered two new Spok genes, Spok3 and Spok4, which locate in different chromosomes in different strains. In Paper II, we showed that Spok3 and Spok4 are found on a gigantic (up to 247 Kb long) variant of Enterprise, a Crypton-like transposable element. Enterprise likely mobilize through the action of a putative tyrosine-recombinase that we call Kirc. When carrying the Spoks, this element has double selfish properties: transposition and meiotic drive. In addition, we found that homologs of the Spoks (Paper I) and of Kirc (Paper II) are widespread in fungi but their phylogenies are discordant with that of the species, suggesting that they have undergone horizontal gene transfer. In Papers III and IV, I turned the focus into genes that have an adaptive function. In fungi, the het genes control conspecific self/non-self recognition. Such genes are expected to evolve under frequency-dependent balancing selection. In Paper III, we found evidence of balancing selection acting on some het genes across the P. anserina species complex. Unexpectedly, we also discovered that het genes of the HNWD gene family are duplicated in a transposon-like manner, broadening our understanding of their potential fitness effects. Finally, in Paper IV we show how het genes with pleiotropic effects on sexual recognition lead to the evolution of strong reproductive isolation, and hence speciation. Overall, the results of my thesis highlight the functional intersection between mobile selfish genetic elements and other genes, either selfish or adaptive, and their effects on genome architecture and population structure.
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| 2. |
- Ament-Velásquez, Sandra Lorena, M.Sc. 1988-, et al.
(författare)
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The evolution of the allorecognition gene repertoire in the Podospora anserina species complex
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Across the Tree of Life, self/non-self recognition is typically achieved through highly polymorphic loci under balancing selection. In fungi, vegetative conspecific recognition, or allorecognition, is defined by the compatibility interactions between loci known as het genes. In this study we explore the evolution of the het genes in the model fungus Podospora anserina and its closest relatives (the Podospora anserina species complex). First, we used chromosome-level genome assemblies to resolve their phylogenetic relationships. We found that the species in the complex are well defined but diversified recently and rapidly, leading to high degrees of conflict at deep branches of the phylogeny. Unlike typical orthologous genes from the complex, some allorecognition genes (het-z and het-s) show trans-species polymorphism, a hallmark of long-term balancing selection. By contrast, the het genes belonging to the HNWD family exhibit a high turn-over, with losses and duplications happening often. In particular, the species P. pseudocomata has a considerable increase of HNWD genes. Unexpectedly, we show that the HNWD paralogs have clean defined boundaries flanked by a target site duplication (TSD), implicating a DNA transposon-like mechanism in the genesis of new duplicates. Overall, our data highlights the diversity of evolutionary histories behind individual self/non-self recognition genes at short evolutionary timescales.
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| 3. |
- Ament-Velásquez, Sandra Lorena, M.Sc. 1988-, et al.
(författare)
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The taxonomy of the model filamentous fungus Podospora anserina
- 2020
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :75, s. 51-69
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Tidskriftsartikel (refereegranskat)abstract
- The filamentous fungus Podospora anserina has been used as a model organism for more than 100 years and has proved to be an invaluable resource in numerous areas of research. Throughout this period, P. anserina has been embroiled in a number of taxonomic controversies regarding the proper name under which it should be called. The most recent taxonomic treatment proposed to change the name of this important species to Triangularia anserina. The results of past name changes of this species indicate that the broader research community is unlikely to accept this change, which will lead to nomenclatural instability and confusion in literature. Here, we review the phylogeny of the species closely related to P. anserina and provide evidence that currently available marker information is insufficient to resolve the relationships amongst many of the lineages. We argue that it is not only premature to propose a new name for P. anserina based on current data, but also that every effort should be made to retain P. anserina as the current name to ensure stability and to minimise confusion in scientific literature. Therefore, we synonymise Triangularia with Podospora and suggest that either the type species of Podospora be moved to P. anserina from P. fimiseda or that all species within the Podosporaceae be placed in the genus Podospora.
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| 4. |
- Hiltunen, Markus, et al.
(författare)
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Dynamics of transposon activity and genomic rearrangements in natural and cultured isolates of the fairy-ring fungus Marasmius oreades
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In fungi, genetic variability can be generated by an array of different mechanisms, many of which are not restricted to the sexual part of the life cycle. Many fungal species have an extended vegetative phase of the life cycle, raising the question of how important this phase is for generating diversity in fungal populations. Recent findings have revealed remarkable genome stability at the nucleotide level in mushroom-forming fungi, but if this pattern extends to include other types of genotypic changes, e.g. mitotic recombination, structural rearrangements and transposon mobilization, is still an open question. Here we used a Marasmius oreades fairy ring that had grown for an estimated 12 years in nature as a dikaryon, with two different haploid nuclei per cell, to look into this question. By separating the two nuclear genotypes from four fruiting bodies through non-meiotic techniques and generating nearly finished genome assemblies of them, we unlocked full genomic access to find and analyze changes to the genotype of any size. We found that during dikaryotic growth in nature, the genome stays intact, but after separating the nuclear genotypes through protoplasts, a considerable amount of structural variation had started to accumulate. In particular, activity of an autonomous and associated non-autonomous hAT transposons was triggered, and translocations up to several hundred kilobases were found near the telomeres. Our study adds to a growing pool of evidence that long-lived fungi are able to suppress the rise or spread of genotypic changes during dikaryotic growth. Furthermore, our results reveal that genome integrity can be interrupted if the two nuclei of the dikaryon are divorced through laboratory means, leading to genomic rearrangements and sparking the activity of transposable elements.
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| 5. |
- Hiltunen, Markus, et al.
(författare)
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The assembled and annotated genome of the fairy-ring fungus Marasmius oreades
- 2021
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653 .- 1759-6653. ; 13:7
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Tidskriftsartikel (refereegranskat)abstract
- Marasmius oreades is a basidiomycete fungus that grows in so called “fairy rings”, which are circular, underground mycelia common in lawns across temperate areas of the world. Fairy rings can be thought of as natural, long-term evolutionary experiments. As each ring has a common origin and expands radially outwards over many years, different sectors will independently accumulate mutations during growth. The genotype can be followed to the next generation, as mushrooms producing the sexual spores are formed seasonally at the edge of the ring. Here we present new genomic data from 95 single-spore isolates of the species, which we used to construct a genetic linkage map and an updated version of the genome assembly. The 44 Mb assembly was anchored to 11 linkage groups, producing chromosome-length scaffolds. Gene annotation revealed 13,891 genes, 55% of which contained a pfam domain. The repetitive fraction of the genome was 22%, and dominated by retrotransposons and DNA elements of the KDZ and Plavaka groups. The level of assembly contiguity we present is so far rare in mushroom-forming fungi, and we expect studies of genomics, transposons, phylogenetics, and evolution to be facilitated by the data we present here of the iconic fairy-ring mushroom.
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