Biology subjects

Villalba de la Pena, M.

Publications and source records attributed to Villalba de la Pena, M..

4 recordsLinked to original sources

bioRxiv2026

Centromeres are hotspots of cytosine methylation epimutations in a filamentous fungus

Epimutations are changes in chromatin modifications, such as DNA methylation or histone modifications. Some of these epigenetic changes can be inherited for several generations, and they potentially contribute to evolutionary processes. Estimates of epimutation rates now exists in a few species, but the presence and function of epigenetic marks are not conserved across different species. To understand the properties of epimutations in fungi, we performed a mutation accumulation experiment with the filamentous fungus Neurospora crassa and investigated spontaneous changes in DNA methylation and trimethylation of lysine 9 on histone H3 (H3K9me3) in the mutation accumulation lines. We observed that centromeric regions are hotspots of spontaneous DNA methylation changes in N. crassa. In these hotspot regions, DNA methylation changes were transmitted across mitoses, but changes occurring in euchromatin were not maintained. The rate of DNA methylation changes was around 30 000 fold faster than the genetic mutation rate. We did not observe spontaneous changes in H3K9me3 that were transmitted across mitoses. Our results show that while spontaneous epimutations occur in this species, they occur predominantly in gene poor heterochromatic regions, so their impact for evolutionary adaptation may be limited.

genetics↗

bioRxiv2024

The effect of population size on adaptation to fluctuating temperatures

Climate change exposes populations to more frequent periods of extreme temperatures and faster temperature fluctuations. Theoretical models suggest that different types of adaptations should occur in constant versus fluctuating environments of varying frequency. Furthermore, evolutionary adaptation to one environment may weaken the adaptations to alternative environments due to antagonistically pleiotropic alleles. However, fitness trade-offs are rarely observed in experiments and it has been hypothesized that the number and severity of trade-offs evolving in fluctuating environments might depend on population size. To evaluate whether specific types of adaptations evolve at fluctuating temperatures and how population size affects the evolution of trade-offs, we performed an evolution experiment with fission yeast (Schizosaccharomyces pombe). The small and large populations evolved for 500 generations at constant and fluctuating temperatures, after which the evolved strains competed against ancestral strains in respective selection environments and in alternative environments to detect trade-offs. We observed significant adaptation and maladaptation only to constant heat, but not to fluctuating temperatures. Overall, the population size did not have significant effects on adaptation capacity or trade-offs in alternative environments. Our results suggest that constant extreme temperatures may act as stronger selective pressures than temperature variation and that trade-offs are unlikely to constrain adaptation to fluctuating temperatures.

evolutionary biology↗

bioRxiv2022

Parental effects in a filamentous fungus: phenotype, fitness, and mechanism

Adaptation to changing environments often requires meaningful phenotypic modifications to match the current conditions. However, obtaining information about the surroundings during an organisms own lifetime may only permit accommodating relatively late developmental modifications. Therefore, it may be advantageous to rely on inter-generational or trans-generational cues that provide information about the environment as early as possible to allow development along an optimal trajectory. Transfer of information or resources across generations, known as parental effects, is well documented in animals and plants but not in other eukaryotes, such as fungi. Understanding parental effects and their evolutionary consequences in fungi is of vital importance as they perform crucial ecosystem functions. In this study, we investigated whether parental effects are present in the filamentous fungus Neurospora crassa, how long do they last, are the effects adaptive, and what is their mechanism. We performed a fully factorial match / mismatch experiment for a good and poor quality environment, in which we measured mycelium size of strains that experienced either a matched or mismatched environment in their previous generation. We found a strong silver spoon effect in initial mycelium growth, which lasted for one generation, and increased fitness during competition experiments. By using deletion mutants that lacked key genes in epigenetic processes, we show that epigenetic mechanisms are not involved in this effect. Instead, we show that spore glycogen content, glucose availability and a radical transcription shift in spores are the main mechanisms behind this parental effect.

microbiology↗

bioRxiv2022

Variation in spontaneous mutation rate and spectrum across the genome of Neurospora crassa

While mutation rates have been extensively studied, variation in mutation rates throughout the genome is poorly understood. To understand patterns of genetic variation, it is important to understand how mutation rates vary. Chromatin modifications may be an important factor in determining variation in mutation rates in eukaryotic genomes. To study variation in mutation rates, we performed a mutation accumulation experiment in the filamentous fungus Neurospora crassa, and sequenced the genomes of the 40 MA lines that had been propagated asexually for approximately 1015 [1003, 1026] mitoses. We detected 1322 mutations in total, and observed that the mutation rate was higher in regions of low GC, in domains of H3K9 trimethylation, in centromeric regions, and in domains of H3K27 trimethylation. The rate of single nucleotide mutations in euchromatin was 2.46 [2.19, 2.77] x 10-10. In contrast, the mutation rate in H3K9me3 domains was tenfold higher: 2.43 [2.25, 2.62] x 10-9. We also observed that the spectrum of single nucleotide mutations was different between H3K9me3 and euchromatic domains. Our statistical model of mutation rate variation predicted a moderate amount of extant genetic variation, suggesting that the mutation rate is an important factor in determining levels of natural genetic variation. Furthermore, we characterized mutation rates of structural variants, complex mutations, and the effect of local sequence context on the mutation rate. Our study highlights that chromatin modifications are associated with mutation rates, and accurate evolutionary inferences should take variation in mutation rates across the genome into account.

genetics↗