Periodic Reporting for period 4 - SpoKiGen (Spore killer genomics: elucidating causes and consequences of a fungal meiotic drive element)
Reporting period: 2019-11-01 to 2020-04-30
Selfish genetic elements skew sexual transmission in their own favor, at the expense of other genes in the genome. Although meiotic drive is widespread in nature and has been identified in a wide range of eukaryotes, there is a profound lack of empirical insight into the evolutionary causes and consequences of this class of genetic element. This lack of knowledge is largely due to the difficulties in studying these elements and a lack of appropriate and tractable genetic models.
In this project, we use the filamentous ascomycetes as a novel system for the study of the evolutionary causes and consequences of meiotic drive. This sexual eukaryote model system is a carrier of the meiotic drive element Spore killer. The phenomenon of spore killing in fungi has been investigated for several decades, with research primarily focusing on its cytological properties and natural distribution. Data on the distribution of Spore killers in fungi suggest that it is an important driver of both genome evolution and higher-order processes such as speciation and mating-system transitions. Hence, the existing knowledge and resources of this system provided a foundation for the SpoKiGen research program, which combined experimental and state-of-the-art genomic approaches and I) identified and characterize the gene(s) encoding Spore killer elements, II) assessed the strength of Spore killer as a meiotic driver, III) unravelled the evolutionary history of the Spore killer complex in Neurospora, IV) investigated the association between Spore killer and genome evolution, and V) analyzed the role of Spore killer as a driver of speciation and mating system transitions.
In this project, we use the filamentous ascomycetes as a novel system for the study of the evolutionary causes and consequences of meiotic drive. This sexual eukaryote model system is a carrier of the meiotic drive element Spore killer. The phenomenon of spore killing in fungi has been investigated for several decades, with research primarily focusing on its cytological properties and natural distribution. Data on the distribution of Spore killers in fungi suggest that it is an important driver of both genome evolution and higher-order processes such as speciation and mating-system transitions. Hence, the existing knowledge and resources of this system provided a foundation for the SpoKiGen research program, which combined experimental and state-of-the-art genomic approaches and I) identified and characterize the gene(s) encoding Spore killer elements, II) assessed the strength of Spore killer as a meiotic driver, III) unravelled the evolutionary history of the Spore killer complex in Neurospora, IV) investigated the association between Spore killer and genome evolution, and V) analyzed the role of Spore killer as a driver of speciation and mating system transitions.
We have published one paper (Meunier, C., et al (2018)) in which we address the concept and evolutionary consequences of intragenomic conflict in Neurospora. This study confirms conflict (or avoidance of such) as a driver of evolutionary change, and the suitability of the model system for addressing this issue.
Another study was recently published (Hosseini, S., et al (2020)), in which we show the evolutionary rate of genome defense mechanisms in this group of fungi.
Furthermore, we have generated a large genomic dataset of species and populations of fungi, focusing on the genus Neurospora but also included close relatives such as strains and species of Podospora, for comparative purposes. We have used that to create high quality assemblies from multiple strains, and to confirm how diversity is distributed in populations and species. Thereby, we have gotten far into building a platform for the study of meiotic drive elements in natural fungal populations and their consequences over evolutionary time, as specifically outlined below.
First, we have used our achieved skills of genome assembly to generate a scaffolder that we are now in the pipeline of publishing (under review in the journal Bioinformatics, and posted on bioRxiv: Hiltunen, M., et al (2020). ARBitR: An overlap-aware genome assembly scaffolder for linked reads.)
We have also used our generated datasets to identify the meiotic drive elements. Specifically, following the Aim I of the SpoKiGen project we have used genomic data and genome-wise association, together with functional verification, to identify the Spore killer of N. sitophila, N. intermedia, and in Podospora. This work is published in the two listed papers:
* Vogan, A. A., et al (2019). Combinations of Spok genes create multiple meiotic drivers in Podospora. eLife 8:e46454
* Svedberg, J.,et al (2018) Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements. Nature Communications 9: 4242
In our effort to asses the strength of the spore killers as meiotic drivers (Aim II of the SpoKiGen project), we have estimated fitness effects of carrying the spore killers and their persistence in populations over generations, data that we have included into the following two publications by Vogan et al (2019 and 2020) and integrated into a theoretical study (by Martinossi et al, (2020)) on the dynamics of drive in natural populations.
Aim III of the project has been fulfilled. A general (and to us surprising) pattern we see is that the spore killer genes is likely to be introgressed between species, data that can be found in Vogan et al., 2019 and in Svedberg, J., et al (2020). An introgressed gene causes meiotic drive in Neurospora sitophila. bioRxiv
Aim IV of the SpoKiGen project is to understand the influence of Spore killer on genome evolution. Here, we have published a paper showing the general conservation of chromosomal synteny in Neurospora and the development of a method for detection of structural variants:
* Sun, Y., et al (2017). Large-scale suppression of recombination predates genomic rearrangements in Neurospora tetrasperma. Nature Communications 8:1140.
Furthermore, in Svedberg, J.,et al (2018) we have detected multiple inversions in the spore killer haplotypes, and we also see that recombination suppression has resulted in the accumulation of transposable elements and non-beneficial mutations over a relatively short evolutionary time.
Finally, in Vogan, A.A. et al (2020) we have one study deposited to bioRxiv and under review for publication in Genome Research, in which we find that spore killers in Podospora are associated with massive transposable blocks of DNA, hence affect genome architecture significantly.
Aim V was formulated as “The role of Spore killer as a driver of speciation and mating system transition”. For this part of the SpoKiGen project we have verified by crosses and that reproductive isolation between populations of N. intermedia is linked to the spore killer haplotype. The results are currently put together into a manuscript, which was included in the PhD-thesis of Jesper Svedberg. And, we see association between spore killers and speciation in Podospora, which is put together in a manuscript that will soon be submitted, and was included in the PhD-thesis of Sandra Lorena Ament-Velasquez. We have explored, but not been able to confirm, a link between spore killers and mating systems transitions.
Another study was recently published (Hosseini, S., et al (2020)), in which we show the evolutionary rate of genome defense mechanisms in this group of fungi.
Furthermore, we have generated a large genomic dataset of species and populations of fungi, focusing on the genus Neurospora but also included close relatives such as strains and species of Podospora, for comparative purposes. We have used that to create high quality assemblies from multiple strains, and to confirm how diversity is distributed in populations and species. Thereby, we have gotten far into building a platform for the study of meiotic drive elements in natural fungal populations and their consequences over evolutionary time, as specifically outlined below.
First, we have used our achieved skills of genome assembly to generate a scaffolder that we are now in the pipeline of publishing (under review in the journal Bioinformatics, and posted on bioRxiv: Hiltunen, M., et al (2020). ARBitR: An overlap-aware genome assembly scaffolder for linked reads.)
We have also used our generated datasets to identify the meiotic drive elements. Specifically, following the Aim I of the SpoKiGen project we have used genomic data and genome-wise association, together with functional verification, to identify the Spore killer of N. sitophila, N. intermedia, and in Podospora. This work is published in the two listed papers:
* Vogan, A. A., et al (2019). Combinations of Spok genes create multiple meiotic drivers in Podospora. eLife 8:e46454
* Svedberg, J.,et al (2018) Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements. Nature Communications 9: 4242
In our effort to asses the strength of the spore killers as meiotic drivers (Aim II of the SpoKiGen project), we have estimated fitness effects of carrying the spore killers and their persistence in populations over generations, data that we have included into the following two publications by Vogan et al (2019 and 2020) and integrated into a theoretical study (by Martinossi et al, (2020)) on the dynamics of drive in natural populations.
Aim III of the project has been fulfilled. A general (and to us surprising) pattern we see is that the spore killer genes is likely to be introgressed between species, data that can be found in Vogan et al., 2019 and in Svedberg, J., et al (2020). An introgressed gene causes meiotic drive in Neurospora sitophila. bioRxiv
Aim IV of the SpoKiGen project is to understand the influence of Spore killer on genome evolution. Here, we have published a paper showing the general conservation of chromosomal synteny in Neurospora and the development of a method for detection of structural variants:
* Sun, Y., et al (2017). Large-scale suppression of recombination predates genomic rearrangements in Neurospora tetrasperma. Nature Communications 8:1140.
Furthermore, in Svedberg, J.,et al (2018) we have detected multiple inversions in the spore killer haplotypes, and we also see that recombination suppression has resulted in the accumulation of transposable elements and non-beneficial mutations over a relatively short evolutionary time.
Finally, in Vogan, A.A. et al (2020) we have one study deposited to bioRxiv and under review for publication in Genome Research, in which we find that spore killers in Podospora are associated with massive transposable blocks of DNA, hence affect genome architecture significantly.
Aim V was formulated as “The role of Spore killer as a driver of speciation and mating system transition”. For this part of the SpoKiGen project we have verified by crosses and that reproductive isolation between populations of N. intermedia is linked to the spore killer haplotype. The results are currently put together into a manuscript, which was included in the PhD-thesis of Jesper Svedberg. And, we see association between spore killers and speciation in Podospora, which is put together in a manuscript that will soon be submitted, and was included in the PhD-thesis of Sandra Lorena Ament-Velasquez. We have explored, but not been able to confirm, a link between spore killers and mating systems transitions.
In the SpoKiGen-project, we have achieved very significant findings on causes of recombination suppression in Neuropora (Svedberg et al., Nat Comm), and the use of genomic and phylogenetic data has revealed multiple origin of spore killers over short evolutionary time, followed by concordant evolution of the accumulation of inversions and deleterious mutations in the spore-killer haplotypes. We anticipate that the SpoKiGen research program will make the Spore killer of Neurospora a primary and pioneering model for the study of selfish genetic elements and their effect on eukaryote genome evolution. Experimental and genomic results from the project will profoundly impact our understanding of the dynamics of segregation distorters as drivers of eukaryote genome evolution, as well as of higher-order macroevolutionary processes. Furthermore, the insights emerging from the project presented are conceptually important for basic evolutionary biology, in the study of natural selection acting a multitude of levels in a biological hierarchy. The concepts that will emerge from this project will be applicable to any project involving biological conflicts as such – for example by increasing our understanding of what drives the progression of cancer tumors at the expense of the individual carrying it.