Biology subjects

Yau, S.

Publications and source records attributed to Yau, S..

11 recordsLinked to original sources

bioRxiv2026

Epidemiological model selection unravels the molecular processes of antiviral resistance from experimental phytoplankton-virus dynamics

Phytoplankton-virus interactions are pivotal in understanding the intertwined dynamics of these key players of the global carbon cycle. Although antiviral resistance is the main hypothesis to solve the apparent paradox of their coexistence, identifying its molecular determinisms and mechanisms, as well as their dynamical consequences, remains challenging. By combining hypotheses about such determinisms and mechanisms, we designed 36 dynamical models and fitted them to experimental infection kinetics in a pioneering selection model approach. Through such a multiple hypotheses testing, we identified that resistance in the model species Ostreococcus tauri is most likely to be predominantly intracellular, to control lysis through budding, and to be acquired by phenotypic plasticity. We further showed that viral kinetics are strongly impacted by both the antiviral resistance's molecular determinants and virions' inactivation through attachment to lysis detritus, as the latter generates a key negative feedback loop during the 'bust' stage of the interaction dynamics.

ecology↗

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 Despite successive improvements to its historical reference genome, previous assemblies retained hundreds of gaps and incomplete genes, hampering high-resolution genomic analyses.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

Single-cell sequencing reveals genome streamlining and functional diversity in ecologically dominant marine protists

A large fraction of marine protists, particularly the smallest ones, belong to uncultured lineages that lack genomic data, limiting insights into their ecological roles and evolutionary strategies. Here, we generated 325 single-cell amplified genomes (SAGs) from 2-5 {micro}m planktonic protists, which resulted in 147 genomes from dominant marine species at varying levels of completeness (40 of them >50%). These genomes matched the in situ community, with Prymnesiophyceae, Mamiellophyceae and Chrysophyceae dominating pigmented cells and MAST, Choanoflagellata and Picozoa prevailing among heterotrophic colourless cells. This resource allowed us to describe the genomic architecture of marine protist species, and revealed a pronounced genome streamlining in ecologically successful lineages. Comparative analyses highlighted unique functions enriched in photosynthetic and heterotrophic taxa (including motility, signal transduction, digestion and secondary metabolism), and revealed a broad distribution of gene families with adaptive traits such as polyketide synthases and rhodopsins. This large-scale single-cell genomics dataset provides a mechanistic foundation for investigating functional diversity, ecological strategies and genome evolution in the ocean.

ecology↗

bioRxiv2026

Metabolomic and Transcriptomic rewiring between virus resistance and susceptibility in Ostreococcus mediterraneus

The genus Ostreococcus, comprising picoeukaryotic unicellular algae, plays a key role in many coastal marine ecosystems. These phytoplankton are infected by lytic double-stranded DNA prasinoviruses against whom they have the capacity to reliably evolve stable antiviral resistance. Regulation of virus resistance and susceptibility is hypothesized to arise through a phenotypic switch, as resistant cell lines can be isolated from susceptible lines after viral exposure and vice versa. To elucidate the molecular mechanisms underlying this resistance, we integrated untargeted metabolomic analyses and transcriptomics in virus-resistant and virus-susceptible lines of O. mediterraneus. Transcriptomic analyses corroborated previous findings in O. tauri, revealing that most gene expression changes were concentrated on a single chromosome. Specifically, a [~]530 kb region was over-transcribed in virus-resistant lines, while a distinct [~]110 kb region was over-expressed in virus-susceptible lines. Comparative metabolomics identified several oxidized galactolipids and oxidized sterols as biomarkers of the susceptible phenotype, while fewer biomarkers were identified for the resistant phenotype. By integrating transcriptomic and metabolomic signatures--focusing on the expression of genes within biosynthetic pathways linked to these metabolite biomarkers--we uncovered candidate molecular mechanisms underlying the cellular physiology of susceptible versus resistant phenotypes. Authors SummaryViruses are the most abundant biological entities in the ocean, shaping the dynamics of phytoplankton communities that underpin marine food webs. Ostreococcus, one of the smallest photosynthetic eukaryotes, is frequently infected by highly abundant prasinoviruses in its natural environment. In this study, we aimed to understand the physiological bases of virus-resistant and susceptible Ostreococcus mediterraneus lines. We compared gene expression and untargeted metabolite profiles between a resistant line and a susceptible line derived from it. The metabolic profiles were much more variable between replicates than the transcriptomic profiles and the most differentially expressed genes did not include those involved in the biosynthetic pathways of the metabolite biomarkers identified. We estimated the congruence between the metabolomes and transcriptomes as the percent of relative expression changes fitting to the relative change in the metabolite. This study provides evidence of the subtle links between gene expression and metabolomic signatures and the importance of integrating multiple levels of cellular processes.

microbiology↗

bioRxiv2025

Chromoanagenesis is a driver of structural variationin the smallest photosynthetic eukaryote

Marine microalgae populations can rapidly evolve resistance to viruses upon infection. In Ostreococcus mediterraneus resistance to the prasinovirus OmV2 emerged within five days in all virus-exposed populations. Whole-genome sequencing of pairs of resistant and susceptible cell lines revealed extensive structural genomic changes, particularly on the Small Outlier Chromosome (SOC). SOC alterations included large deletions, duplications, rearrangements, and whole chromosome duplication, yet no consistent structural variant or single nucleotide polymorphism could be directly associated with resistance. Hybrid de novo assemblies confirmed the unique SOC assembly of each strain, with a highly polymorphic [~]2 kb tandem repeat region exhibiting an "accordion-like" pattern of expansion and contraction. No new viral insertions were found, though endogenous viral elements were conserved across lines. Two interchromosomal translocations between the SOC and chromosomes 2 and 17 provide evidence for chromoplexy, thereby offering novel insights into the mechanisms underlying the distinctive evolutionary path of this chromosome. Together, these findings demonstrate that resistance to OmV2 evolves rapidly and consistently but cannot yet be linked to any specific structural variations; instead, the high rate of localized genomic structural variations points to a distinct mechanism of chromosome evolution. SignificanceThe mechanisms and consequences of structural variation remain poorly understood in many lineages, particularly in ecologically important marine microbes. This study shows that resistance to prasinovirus OmV2 in a cosmopolitan phytoplankton species, Ostreococcus mediterraneus evolves rapidly and consistently, even though no resistance-associated SNPs or shared structural variants were identified on standard chromosomes. Instead, extensive genomic rearrangements--particularly of a single chromosome--occur independently of viral infection. These findings highlight the role of chromoplexy as the driving mechanism underlying the diversification of the enigmatic Small Outlier Chromosome in this lineage.

genomics↗

bioRxiv2025

Genomic analysis of Ostreococcus tauri-infecting viruses reveals a hypervariable region associated with host--virus interactions

While the genus Prasinovirus, known to infect prasinophyte green algae (class Mamiellophyceae), is abundant in the oceans, the genetic mechanisms governing the ecology and (co)evolution of these viruses remain poorly understood. In this study, we sequenced the complete genomes of eighteen viruses infecting the cosmopolitan unicellular green alga Ostreococcus tauri (OtVs) and one specific to Micromonas commoda (McV-20T). Of these viruses, twelve were previously isolated from the coastal Mediterranean Sea and seven were newly isolated from two different geographical locations (i.e., the South Pacific Gyre and the North Sea). Phylogenetic analysis classified these viruses as new members of the Prasinovirus genus and defined three distinct OtV clades: designated OtV-type 1, OtV-type 2a and OtV-type 2b. The OtV-type 1 includes three new viruses isolated from the Pacific Ocean and the previously sequenced genome OtV6. The OtV-type 1 form a large cluster within the Micromonas-infecting virus clade, sharing five unique homologous genes with all Micromonas viruses. In addition, genetic features of OtV-type 1, including a higher number of CDSs ([~]260) and lower GC content ([~]41%), were more closely allied to Micromonas viruses than to those of OtVs, suggesting an alternative host or a recent host switch from Micromonas to O. tauri. By analyzing the OtV genomes, we found a faster-evolving central hypervariable region (HVR), where the OtV-type 2b displayed the largest region, i.e., three times longer than other OtVs. This region encodes genes mainly associated with host cell recognition and attachment and under strong selective pressure (positive and negative). Notably, most viruses associated with OtV-type 2b showed the broadest host range. Infection dynamics between the hosts and the viruses appeared highly specific to host-virus pairs, suggesting complex interactions in the Ostreococcus-prasinovirus system. Finally, by observing viral lysates with electron microscopy, we observed novel morphologies never described for these viruses. Overall, this study provides new insights into the genetic diversity of prasinoviruses and describes for the first time a viral plasticity that might be strongly shaped by antagonistic coevolution with their hosts.

microbiology↗

bioRxiv2019

Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using VirusFISH

One of the major challenges in viral ecology is to assess the impact of viruses in controlling the abundance of specific hosts in the environment. For this, techniques that enable the detection and quantification of virus-host interactions at the single-cell level are essential. With this goal in mind, we implemented VirusFISH (Virus Fluorescence in situ Hybridization) using as a model the marine picoeukaryote Ostreococcus tauri and its virus OtV5. VirusFISH allowed the visualization and quantification of the fraction of infected cells during an infection experiment. We were also able to quantify the abundance of free viruses released during cell lysis and assess the burst size of our non-axenic culture, because we could discriminate OtV5 from phages. Our results showed that although the major lysis of the culture occurred between 24 and 48 h after OtV5 inoculation, some new viruses were produced between 8 and 24 h, propagating the infection. Nevertheless, the production of viral particles increased drastically after 24 h. The burst size for the O. tauri-OtV5 system was 7{+/-}0.4 OtV5 per cell, which was consistent with the estimated amount of viruses inside the cell prior to cell lysis. With this work we demonstrate that VirusFISH is a promising technique to study specific virus-host interactions in non-axenic cultures, and set the ground for its application in complex natural communities.

microbiology↗

bioRxiv2019

Towards an individualised neural assessment of receptive language in children

PurposeWe aimed to develop a non-invasive neural test of language comprehension to use with non-speaking children for whom standard behavioural testing is unreliable (e.g., minimally-verbal autism). Our aims were three-fold. First, we sought to establish the sensitivity of two auditory paradigms to elicit neural responses in individual neurotypical children. Second, we aimed to validate the use of a portable and accessible electroencephalography (EEG) system, by comparing its recordings to those of a research-grade system. Third, in light of substantial inter-individual variability in individuals neural responses, we assessed whether multivariate decoding methods could improve sensitivity. MethodsWe tested the sensitivity of two child-friendly covert N400 paradigms. Thirty-one typically developing children listened to identical spoken words that were either strongly predicted by the preceding context or violated lexical-semantic expectations. Context was given by a cue word (Experiment 1) or sentence frame (Experiment 2) and participants either made an overall judgement on word relatedness or counted lexical-semantic violations. We measured EEG concurrently from a research-grade system, Neuroscans SynAmps2, and an adapted gaming system, Emotivs EPOC+. ResultsWe found substantial inter-individual variability in the timing and topology of N400-like effects. For both paradigms and EEG systems, traditional N400 effects at the expected sensors and time points were statistically significant in around 50% of individuals. Using multivariate analyses, detection rate increased to 88% of individuals for the research-grade system in the sentences paradigm, illustrating the robustness of this method in the face of inter-individual variations in topography. ConclusionsThere was large inter-individual variability in neural responses, suggesting inter-individual variation in either the cognitive response to lexical-semantic violations, and/or the neural substrate of that response. Around half of our neurotypical participants showed the expected N400 effect at the expected location and time point. A low-cost, accessible EEG system provided comparable data for univariate analysis but was not well suited to multivariate decoding. However, multivariate analyses with a research-grade EEG system increased our detection rate to 88% of individuals. This approach provides a strong foundation to establish a neural index of language comprehension in children with limited communication.

animal behavior and cognition↗

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↗

bioRxiv2018

Mantoniella beaufortii and Mantoniella baffinensis sp. now. (Mamiellales, Mamiellophyceae), two new green algal species from the high Arctic

Members of the class Mamiellophyceae comprise species that can dominate picophytoplankton diversity in polar waters. Yet polar species are often morphologically indistinguishable from temperate species, although clearly separated by molecular features. Here we examine four Mamiellophyceae strains from the Canadian Arctic. The 18S rRNA and Internal Transcribed Spacer 2 (ITS2) gene phylogeny place these strains within the family Mamiellaceae (Mamiellales, Mamiellophyceae) in two separate clades of the genus Mantoniella. ITS2 synapomorphies support their placement as two new species, Mantoniella beaufortii and Mantoniella baffinensis. Both species have round green cells with diameter between 3-5 m, one long flagellum and a short reduced flagellum (~1 m) and are covered by spiderweb-like scales, making both species similar to other Mantoniella species. Morphologically, M. beaufortii and M. baffinensis are most similar to the cosmopolitan M. squamata with only minor differences in scale structure distinguishing them. Screening of global marine metabarcoding datasets indicates M. beaufortii has only been recorded in seawater and sea ice samples from the Arctic while no environmental barcode matches M. baffinensis. Like other Mamiellophyceae genera that have distinct polar and temperate species, the polar distribution of these new species suggests they are cold or ice-adapted Mantoniella species.

microbiology↗

bioRxiv2017

Prasinovirus attack of Ostreococcus is furtive by day but savage by night

Prasinoviruses are large DNA viruses that infect diverse genera of green microalgae worldwide in aquatic ecosystems, but molecular knowledge of their life-cycles is lacking. Several complete genomes of both these viruses and their marine algal hosts are now available and have been used to show the pervasive presence of these species in microbial metagenomes. We have analysed the life-cycle of OtV5, a lytic virus, using RNA-Seq from 12 time points of healthy or infected Ostreococcus tauri cells over a day/night cycle in culture. In the day, viral gene transcription remained low while host nitrogen metabolism gene transcription was initially strongly repressed for two successive time points before being induced for 8 hours, but in the night viral transcription increased steeply while host nitrogen metabolism genes were repressed and many host functions that are normally reduced in the night appeared to be compensated either by genes expressed from the virus or by increased expression of a subset of 4.4 % of the hosts genes. Some host cells lysed progressively during the night, but a larger proportion lysed the following morning. Our data suggest that the life-cycles of algal viruses mirror the diurnal rhythms of their hosts.

microbiology↗