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.
