Strong population genomic structure of the toxic dinoflagellate Alexandrium minutum inferred from meta-transcriptome samples.

Despite theoretical expectations, marine microeukaryote population are often highly structured and the mechanisms behind such patterns remain to be elucidated. These organisms display huge census population sizes, yet genotyping usually requires clonal strains originating from single cells, hindering proper population sampling. Estimating allelic frequency directly from population wide samples, without any isolation step, offers an interesting alternative. Here, we validate the use of meta-transcriptome environmental samples to determine the population genetic structure of the dinoflagellate Alexandrium minutum. Strain and meta-transcriptome based results both indicated a strong genetic structure for A. minutum in Western Europe, to the level expected between cryptic species. The presence of numerous private alleles, and even fixed polymorphism, would indicate ancient divergence and absence of gene flow between populations. Single nucleotide polymorphisms (SNPs) displaying strong allele frequency differences were distributed throughout the genome, which might indicate pervasive selection from standing genetic variation (soft selective sweeps). However, a few genomic regions displayed extremely low diversity that could result from the fixation of adaptive de novo mutations (hard selective sweeps) within the populations.

Species specific gene expression dynamics during harmful algal blooms.

Harmful algal blooms are caused by specific members of microbial communities. Understanding the dynamics of these events requires comparing the strategies developed by the problematic species to cope with environmental fluctuations to the ones developed by the other members of the community. During three consecutive years, the meta-transcriptome of micro-eukaryote communities was sequenced during blooms of the toxic dinoflagellate Alexandrium minutum. The dataset was analyzed to investigate species specific gene expression dynamics. Major shifts in gene expression were explained by the succession of different species within the community. Although expression patterns were strongly correlated with fluctuation of the abiotic environment, and more specifically with nutrient concentration, transcripts specifically involved in nutrient uptake and metabolism did not display extensive changes in gene expression. Compared to the other members of the community, A. minutum displayed a very specific expression pattern, with lower expression of photosynthesis transcripts and central metabolism genes (TCA cycle, glucose metabolism, glycolysis…) and contrasting expression pattern of ion transporters across environmental conditions. These results suggest the importance of mixotrophy, cell motility and cell-to-cell interactions during A. minutum blooms.

Inter- and Intra-Specific Transcriptional and Phenotypic Responses of Pseudo-nitzschia under Different Nutrient Conditions.

Untangling the functional basis of divergence between closely related species is a step toward understanding species dynamics within communities at both the evolutionary and ecological scales. We investigated cellular (i.e., growth, domoic acid production, and nutrient consumption) and molecular (transcriptomic analyses) responses to varying nutrient concentrations across several strains belonging to three species of the toxic diatom genus Pseudo-nitzschia. Three main results were obtained. First, strains from the same species displayed similar transcriptomic, but not necessarily cellular, responses to the experimental conditions. It showed the importance of considering intraspecific diversity to investigate functional divergence between species. Second, a major exception to the first finding was a strain recently isolated from the natural environment and displaying contrasting gene expression patterns related to cell motility and domoic acid production. This result illustrated the profound modifications that may occur when transferring a cell from the natural to the in vitro environment and asks for future studies to better understand the influence of culture duration and life cycle on expression patterns. Third, transcriptomic responses were more similar between the two species displaying similar ecology in situ, irrespective of the genetic distance. This was especially true for molecular responses related to TCA cycle, photosynthesis, and nitrogen metabolism. However, transcripts related to phosphate uptake were variable between species. It highlighted the importance of considering both overall genetic distance and ecological divergence to explain functional divergence between species.

Evolutionary processes and cellular functions underlying divergence in Alexandrium minutum.

Understanding divergence in the highly dispersive and seemingly homogeneous pelagic environment for organisms living as free drifters in the water column remains a challenge. Here, we analysed the transcriptome-wide mRNA sequences, as well as the morphology of 18 strains of Alexandrium minutum, a dinoflagellate responsible for harmful algal blooms worldwide, to investigate the functional bases of a divergence event. Analysis of the joint site frequency spectrum (JSFS) pointed towards an ancestral divergence in complete isolations followed by a secondary contact resulting in gene flow between the two diverging groups, but heterogeneous across sites. The sites displaying fixed SNPs were associated with a highly restricted gene flow and a strong overrepresentation of nonsynonymous polymorphism, suggesting the importance of selective pressures as drivers of the divergence. The most divergent transcripts were homologs to genes involved in calcium/potassium fluxes across the membrane, calcium transduction signal and saxitoxin production. The implication of these results in terms of ecological divergence and build-up of reproductive isolation is discussed. Dinoflagellates are especially difficult to study in the field at the ecological level due to their small size and the dynamic nature of their natural environment, but also at the genomic level due to their huge and complex genome and the absence of closely related model organism. This study illustrates the possibility to identify the traits of primary importance in ecology and evolution starting from high-throughput sequencing data, even for such organisms.

Comparative paleovirological analysis of crustaceans identifies multiple widespread viral groups.

BACKGROUND: The discovery of many fragments of viral genomes integrated in the genome of their eukaryotic host (endogenous viral elements; EVEs) has recently opened new avenues to further our understanding of viral evolution and of host-virus interactions. Here, we report the results of a comprehensive screen for EVEs in crustaceans. Following up on the recent discovery of EVEs in the terrestrial isopod, Armadillidium vulgare, we scanned the genomes of six crustacean species: a terrestrial isopod (Armadillidium nasatum), two water fleas (Daphnia pulex and D. pulicaria), two copepods (the salmon louse, Lepeophtheirus salmonis and Eurytemora affinis), and a freshwater amphipod (Hyalella azteca). RESULTS: In total, we found 210 EVEs representing 14 different lineages belonging to five different viral groups that are present in two to five species: Bunyaviridae (-ssRNA), Circoviridae (ssDNA), Mononegavirales (-ssRNA), Parvoviridae (ssDNA) and Totiviridae (dsRNA). The identification of shared orthologous insertions between A. nasatum and A. vulgare indicates that EVEs have been maintained over several millions of years, although we did not find any evidence supporting exaptation. Overall, the different degrees of EVE degradation (from none to >10 nonsense mutations) suggest that endogenization has been recurrent during the evolution of the various crustacean taxa. Our study is the first to report EVEs in D. pulicaria, E. affinis and H. azteca, many of which are likely to result from recent endogenization of currently circulating viruses. CONCLUSIONS: In conclusion, we have unearthed a large diversity of EVEs from crustacean genomes, and shown that four of the five viral groups we uncovered (Bunyaviridae, Circoviridae, Mononegavirales, Parvoviridae) were and may still be present in three to four highly divergent crustacean taxa. In addition, the discovery of recent EVEs offers an interesting opportunity to characterize new exogenous viruses currently circulating in economically or ecologically important copepod species.