Biology subjects

Krasovec, M.

Publications and source records attributed to Krasovec, M..

9 recordsLinked to original sources

bioRxiv2026

Plasticity of the mutation rate and spectrum in eukaryotic marine phytoplankton

The ability to adapt shapes the future of any species or population. Adaptive potential is primarily determined by the spontaneous mutation rate {micro} and the mutation spectrum, which define the new genetic variation available to selection. Increasing evidence points to the plasticity of the mutation rate and spectrum, which vary according to environment. However, data is lacking for marine phytoplankton, an essential group for marine ecosystems as well as a major player in biogeochemical cycles. Here, we measure the plasticity of mutation rates and spectra in the chlorophyte Ostreococcus tauri by mutation accumulation experiments in 4 different conditions: low salinity, high salinity, low temperature, and high temperature. {micro}SNM is lowest under low salinity, doubles under high salinity and low temperature and quadruples under high temperature. SNM spectra become increasingly biased towards C:G[->]T:A transitions with increasing {micro}SNM. While {micro}ID does not change with the environment, the structural mutation rate {micro}SM is higher at low temperature, likely due to transposon activity. Given the rapid environmental changes associated with global climate change, mutation rates and spectra plasticity may critically influence the adaptive potential of marine primary producers.

evolutionary biology↗

bioRxiv2026

A gapless telomere-to-telomere reference genome of Ostreococcus tauri RCC4221 with expanded annotation of medium-sized ncRNAs

Marine photosynthetic microbes contribute substantially to global primary production, yet many algal lineages still lack reference genomes with the continuity and annotation quality required for fine-scale structural, regulatory and comparative analyses. Ostreococcus tauri, one of the smallest known free-living photosynthetic eukaryotes, has been a model marine picoeukaryote for over two decades. Despite successive improvements to its historical reference genome, previous assemblies retained hundreds of gaps and incomplete genes, hampering high-resolution genomic analyses. Here, we present O. tauri RCC4221 genome version 2026, a telomere-to-telomere assembly of all 20 chromosomes spanning 13.34 Mb with no gaps. This assembly combines PacBio long-read sequencing, Illumina short-read polishing, correction of unresolved regions guided by independent Nanopore-based assemblies. The updated reference supports a curated annotation comprising 7,683 protein-coding genes, 48 tRNA genes, 3 rRNA operons, 116 medium-sized noncoding RNAs, one signal recognition particle RNA and 138 small nucleolar RNAs. It also improves gene-model integrity and recovers candidate coding loci absent from the 2014 reference. Structural analyses resolved the organization of the two atypical low-GC chromosome 2 and 19 that contain duplicated regions that were collapsed or misrepresented in previous assemblies. Finally, bisulfite sequencing and PacBio SMRT sequencing revealed a dual DNA methylation landscape, with CG-context cytosine methylation concentrated in gene bodies and N6-methyladenosine (m6A) enriched at the start codon. The updated O. tauri 2026 assembly provides a complete and curated reference resource for chromosome biology, comparative genomics, epigenomics and RNA biology in a model marine picoeukaryote.

genomics↗

bioRxiv2026

Ancient eukaryotic immunity through genome editing of viral sequences

Mutations provide the raw material for evolution, but mutation rates are not uniform across genomes. Using a mutation accumulation experiment in the marine phytoplankton Bigelowiella natans, we discovered extreme local variation in mutation rate: over 1000-fold differences across its nuclear genome. While the baseline single-nucleotide mutation rate is approximately 3.5x10-10 per site per generation, a common value for unicellular species, two genomic regions derived from integrated viruses exhibit strikingly elevated rates of about 6x10-7. These two regions show a distinctive mutational signature with almost exclusively T/A[->]C/G transitions, a pattern also found in other non-eukaryote derived sequences in B. natans, contrary to the usual GC to AT mutation bias. Notably, hypermutation occurs only on TpA dinucleotides, and only in a subset of experimental lines, suggesting a regulated process rather than random genomic instability. We propose that B. natans targets invading DNA through localized hypermutation, reminiscent of deamination-based antiviral defense systems in animals, prompting the idea of genome editing as a conserved immune system in eukaryotes. Significance StatementDe novo mutations provide the raw material for adaptation, but at high frequencies they can compromise genome integrity. Here, we describe a hypermutable process targeting two integrated viral genomes in a chlorarachniophyte alga, resulting in a mutation rate 1000 times higher than in other regions and a very particular mutation spectrum. These observations are reminiscent of hypermutation-based antiviral defenses described in humans against HIV and influenza; whereby host-mediated deamination of the viral genome increases its mutation rate such that the virus loses its infectivity.

genomics↗

bioRxiv2025

Environmental complexity constrains evolutionary adaptation across taxa

Complex environments combining multiple stressors are the new norm worldwide. Adaptive evolution will be critical to population persistence under these combined challenges, but how environmental complexity affects the pace of evolution remains poorly understood. Using a meta-experimental evolution approach, we exposed 14 species, from bacteria to unicellular eukaryotes and plants, to single stressors and their pairwise combinations for multiple generations, while keeping the overall stress level comparable. Populations evolving under combined stressors tended to have lower fitness increase in the selective environments, higher fitness reductions in the control environment, and shallower relation between initial maladaptation and fitness gain, than under single stressors. However, these responses varied with species and stressor type. Accounting for such constraints on evolutionary dynamics should prove crucial for the management of biodiversity. Significance StatementA pressing challenges for modern science and society in the face of ongoing global change is understanding what limits the capacity of living organisms to adapt to complex environments combining multiple stressors. To answer to this question, we conducted a large-scale meta-experimental evolution design across a diversity of organisms, exposing them for multiple generations to either single or combined-stress treatments. Combined stressors led to less adaptive fitness gain than single stressors, and imposed additional costs through reduced fitness in non-stressful conditions. This unique combination of meta-experimental approach with a careful distinction between environmental complexity and overall stress allowed us to gain robust quantitative evidence on how environmental complexity can impact the pace of evolution.

evolutionary biology↗

bioRxiv2025

Effect of cellular nutrient economy on the evolution of genome size in phytoplankton

The origin of genome size variation remains a central question in evolutionary biology. Previous analyses suggest that the energetic costs of small insertions and deletions (indels) influence genome size by altering the cellular energy budget. Here, we present a theoretical framework for genome evolution in phytoplankton--the main producers of the sunlit ocean--whose growth depends on nutrient availability. We derive an expression for the selection coefficient on indels as a function of the minimum amount of nutrient inside the cell. Parameter estimates indicate that 1-bp indels can be counterselected in phytoplankton with minimal nutrient requirements. We then test three predictions of nutrient-driven selection on genome evolution. Altogether, this model provides a quantitative and mathematical basis for the genome streamlining hypothesis.

ecology↗

bioRxiv2022

Low spontaneous mutation rate in a complex multicellular eukaryote with a haploid-diploid life cycle

The spontaneous mutation rate {micro} is a crucial parameter driving evolution and biodiversity. Mutation rates are highly variable across species, suggesting that {micro} is susceptible to selection and drift and that species life cycle and life history may impact its evolution. In particular, asexual reproduction and haploid selection are expected to affect mutation rate, but very little empirical data is available to test this expectation. Here, we sequence 30 genomes of a parent-offspring pedigree in the brown algae Ectocarpus to test the impact of its life cycle on mutation rate. Ectocarpus alternates between a haploid and a diploid stage, both multicellular and free living, and utilizes both sexual and asexual reproduction. Ectocarpus is therefore a unique model to empirically test expectations of the effect of asexual reproduction and haploid selection on mutation rate evolution. We estimate that Ectocarpus has a nucleotide mutation rate of {micro}bs=4.07x10-10 per site per generation, a surprisingly low number for a multicellular complex eukaryote. Effective population size (Ne) and genome size could not explain this low mutation rate. We propose that the haploid-diploid life cycle, combined with extensive asexual reproduction may be key drivers of mutation rate.

evolutionary biology↗

bioRxiv2022

Very small spontaneous structural mutation rate in green algae

Structural mutations led to major innovations, but our knowledge of the spontaneous structural mutation rate is very limited. We cannot have a complete view of the adaptive potential of species and new variants in a population without addressing this question. Here, we used Illumina genomic data from mutation accumulation experiments of five green algae species and measured very low structural mutation rate, between 5x10-12 to 2x10-11 mutations per site, at least ten times lower than the nucleotide mutation rate in these species. Such low rates of structural mutations may be a consequence of selection. Assuming that structural mutations have higher fitness effect than point mutations because they impact a larger portion of the genome, selection toward a small structural mutation rate may be stronger than for point mutations. A second explanation could be the rate of true positive detection of de novo structural mutations, that is globally poor and variable between methods. This highlights the necessity of long read sequencing in future mutation accumulation studies. SIGNIFICANCE STATEMENTMutations are the first source of all biodiversity. Biologists tried since a century to measure the spontaneous mutation rate, but our knowledge on the structural spontaneous mutation rate, st, is still poor. Here we measured st in five species of phytoplankton, and found a very small rate compared to nucleotide and short insertion-deletion mutations.

evolutionary biology↗

bioRxiv2022

High rates of spontaneous chromosomal duplications are compensated by translational regulation in a photosynthetic unicellular eukaryote

While duplications have long been recognized as a fundamental process driving major evolutionary innovations, direct estimations of spontaneous chromosome duplication rates, leading to aneuploid karyotypes, are scarce. Here, we provide the first estimations of spontaneous chromosome duplication rates in six unicellular eukaryotic species from mutation accumulation (MA) experiments. The spontaneous chromosome duplication rates reach 1x10-4 to 1x10-3 per genome per generation, which is ~4 to ~50 times less frequent than spontaneous point mutations per genome, whereas chromosome duplication events can affect 1 to 7% of the total genome size. Comparative transcriptomics between MA lines with different chromosome duplications reveals a strong positive correlation between RNA expression rate and DNA copy number. However, comparative analyses of the translation rate of mRNAs estimated by polysome profiling unravel a chromosome specific dosage compensation mechanism. In particular, one chromosome with a gene average of 2.1 excess of mRNAs is compensated by an average of ~0.7 decrease in translation rates. Altogether, our results are consistent with previous observations of a chromosome dependent effect of dosage compensation and provide evidence that it may occur during translation. These results support the existence of a yet unknown post-transcriptional mechanism orchestrating the modification of translation of hundreds of transcripts from genes located on duplicated regions in eukaryotes.

evolutionary biology↗

bioRxiv2019

Virus-host coexistence in phytoplankton through the genomic lens

Phytoplankton-virus interactions are major determinants of geochemical cycles in the oceans. Viruses are responsible for the redirection of carbon and nutrients away from larger organisms back towards microorganisms via the lysis of microalgae in a process coined the viral shunt. Virus-host interactions are generally expected to follow boom and bust dynamics, whereby a numerically dominant strain is lysed and replaced by a virus resistant strain. Here, we isolated a microalga and its infective nucleo-cytoplasmic large DNA virus (NCLDV) concomitantly from the environment in the surface NW Mediterranean Sea, Ostreococcus mediterraneus, and show continuous growth in culture of both the microalga and the virus. Evolution experiments through single cell bottlenecks demonstrate that, in the absence of the virus, susceptible cells evolve from one ancestral resistant single cell, and vice-versa; that is that resistant cells evolve from one ancestral susceptible cell. This provides evidence that the observed sustained viral production is the consequence of a minority of virus-susceptible cells. The emergence of these cells is explained by low-level phase switching between virus-resistant and virus-susceptible phenotypes, akin to a bet hedging strategy. Whole genome sequencing and analysis of the ~14 Mb microalga and the ~200 kb virus points towards ancient speciation of the microalga within the Ostreococcus species complex and frequent gene exchanges between prasinoviruses infecting Ostreococcus species. Re-sequencing of one susceptible strain demonstrated that the phase switch involved a large 60 Kb deletion of one chromosome. This chromosome is an outlier chromosome compared to the streamlined, gene dense, GC-rich standard chromosomes, as it contains many repeats and few orthologous genes. While this chromosome has been described in three different genera, its size increments have been previously associated to antiviral immunity and resistance in another species from the same genus. Mathematical modelling of this mechanism predicts microalga-virus population dynamics consistent with the observation of continuous growth of both virus and microalga. Altogether, our results suggest a previously overlooked strategy in phytoplankton-virus interactions.

evolutionary biology↗