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Red-snow algae are red-pigmented unicellular algae that appear seasonally on the surface of thawing snow worldwide. Here, we analyse the distribution patterns of snow algae sampled from glaciers and snow patches in the Arctic and Antarctica based on nuclear ITS2 sequences, which evolve rapidly. The number of phylotypes is limited in both polar regions, and most are specific to either the Arctic or Antarctica. However, the bipolar phylotypes account for the largest share (37.3%) of all sequences, suggesting that red-algal blooms in polar regions may comprise mainly cosmopolitan phylotypes but also include endemic organisms, which are distributed either in the Arctic or Antarctica. Red-snow algae are red-pigmented unicellular algae that appear seasonally on the surface of thawing snow worldwide. Here, Segawa et al. analyse nuclear ITS2 sequences from snow algae from the Arctic and Antarctica, identifying dominant phylotypes present in both poles as well as endemic organisms.

Microalgal Chlorella has been demonstrated to process wastewater efficiently from piggery industry, yet optimization through genetic engineering of such a bio-treatment is currently challenging, largely due to the limited data and knowledge in genomics. In this study, we first investigated the differential growth rates among three wastewater-processing Chlorella strains: Chlorella sorokiniana BD09, Chlorella sorokiniana BD08 and Chlorella sp . Dachan, and the previously published Chlorella sorokiniana UTEX 1602, showing us that BD09 maintains the best tolerance in synthetic wastewater. We then performed genome sequencing and analysis, resulting in a high-quality assembly for each genome with scaffold N50 > 2 Mb and genomic completeness ≥91%, as well as genome annotation with 9,668, 10,240, 9,821 high-confidence gene models predicted for BD09, BD08, and Dachan, respectively. Comparative genomics study unravels that metabolic pathways, which are involved in nitrogen and phosphorus assimilation, were enriched in the faster-growing strains. We found that gene structural variation and genomic rearrangement might contribute to differential capabilities in wastewater tolerance among the strains, as indicated by gene copy number variation, domain reshuffling of orthologs involved, as well as a ~1 Mb-length chromosomal inversion we observed in BD08 and Dachan. In addition, we speculated that an associated bacterium, Microbacterium chocolatum , which was identified within Dachan, play a possible role in synergizing nutrient removal. Our three newly sequenced Chlorella genomes provide a fundamental foundation to understand the molecular basis of abiotic stress tolerance in wastewater treatment, which is essential for future genetic engineering and strain improvement.

The green alga Chlamydomonas reinhardtii undergoes gametogenesis and mating upon nitrogen starvation. While the steps involved in its sexual reproductive cycle have been extensively characterized, the genome-wide transcriptional and epigenetic changes underlying different life cycle stages have yet to be fully described. Here, we performed transcriptome and methylome sequencing to quantify expression and DNA methylation from vegetative and gametic cells of each mating type and from zygotes. We identified 361 gametic genes with mating type-specific expression patterns and 627 genes that are specifically induced in zygotes; furthermore, these sex-related gene sets were enriched for secretory pathway and alga-specific genes. We also examined the C. reinhardtii nuclear methylation map with base-level resolution at different life cycle stages. Despite having low global levels of nuclear methylation, we detected 23 hypermethylated loci in gene-poor, repeat-rich regions. We observed mating type-specific differences in chloroplast DNA methylation levels in plus versus minus mating type gametes followed by chloroplast DNA hypermethylation in zygotes. Lastly, we examined the expression of candidate DNA methyltransferases and found three, DMT1a, DMT1b, and DMT4, that are differentially expressed during the life cycle and are candidate DNA methylases. The expression and methylation data we present provide insight into cell type-specific transcriptional and epigenetic programs during key stages of the C. reinhardtii life cycle.

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ~120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga. Single-celled parasites cause many severe diseases in humans and animals. The apicomplexans form probably the most successful group of these parasites and include the parasites that cause malaria. Apicomplexans infect a broad range of hosts, including humans, reptiles, birds, and insects, and often have complicated life cycles. For example, the malaria-causing parasites spread by moving from humans to female mosquitoes and then back to humans. Despite significant differences amongst apicomplexans, these single-celled parasites also share a number of features that are not seen in other living species. How and when these features arose remains unclear. It is known from previous work that apicomplexans are closely related to single-celled algae. But unlike apicomplexans, which depend on a host animal to survive, these algae live freely in their environment, often in close association with corals. Woo et al. have now sequenced the genomes of two photosynthetic algae that are thought to be close living relatives of the apicomplexans. These genomes were then compared to each other and to the genomes of other algae and apicomplexans. These comparisons reconfirmed that the two algae that were studied were close relatives of the apicomplexans. Further analyses suggested that thousands of genes were lost as an ancient free-living algae evolved into the apicomplexan ancestor, and further losses occurred as these early parasites evolved into modern species. The lost genes were typically those that are important for free-living organisms, but are either a hindrance to, or not needed in, a parasitic lifestyle. Some of the ancestor's genes, especially those that coded for the building blocks of flagella (structures which free-living algae use to move around), were repurposed in ways that helped the apicomplexans to invade their hosts. Understanding this repurposing process in greater detail will help to identify key molecules in these deadly parasites that could be targeted by drug treatments. It will also offer answers to one of the most fascinating questions in evolutionary biology: how parasites have evolved from free-living organisms.

Despite the long research history on the genus Coelastrella , its species diversity and biotechnological potential have not been fully explored. For the first time, cluster analysis of morphological characteristics was done in the representatives of the said genus. The results obtained have shown that morphological similarity does not necessarily indicate a molecular genetic relationship. It the light of it, the taxonomic status of species can reliably be determined using specific DNA region, such as 18S–ITS1–5.8S–ITS2. The V4 and V9 regions of gene 18S rRNA are relatively conservative fragments which are not suitable for species identification. The ITS2 can be used as a “short barcode”. Among the advanced machine methods for delimitation species, the most effective algorithm for distinguishing Coelastrella species was the Generalized Mixed Yule Coalescent (GMYC) method. This paper represented for the first time our comprehensive review of the works devoted to the analysis of the biotechnological potential of representatives of the genus Coelastrella and shows that fatty acid composition of the three main chemogroups within the studied genus differs. In the future, this may form the basis for predicting the composition of the fatty acid profile of new strains, which is important while searching for organisms with specified biotechnological properties. In conclusion, an integrative approach was employed to describe Coelastrella affinis sp. nov., a new species of the genus Coelastrella with high biotechnological potential. Also, a new description of C. thermophila var. astaxanthina comb. nov. was proposed. Graphical abstract

Background Picoeukaryotes represent an important, yet poorly characterized component of marine phytoplankton. The recent genome availability for two species of Ostreococcus and Micromonas has led to the emergence of picophytoplankton comparative genomics. Sequencing has revealed many unexpected features about genome structure and led to several hypotheses on Ostreococcus biology and physiology. Despite the accumulation of genomic data, little is known about gene expression in eukaryotic picophytoplankton. Results We have conducted a genome-wide analysis of gene expression in Ostreococcus tauri cells exposed to light/dark cycles (L/D). A Bayesian Fourier Clustering method was implemented to cluster rhythmic genes according to their expression waveform. In a single L/D condition nearly all expressed genes displayed rhythmic patterns of expression. Clusters of genes were associated with the main biological processes such as transcription in the nucleus and the organelles, photosynthesis, DNA replication and mitosis. Conclusions Light/Dark time-dependent transcription of the genes involved in the main steps leading to protein synthesis (transcription basic machinery, ribosome biogenesis, translation and aminoacid synthesis) was observed, to an unprecedented extent in eukaryotes, suggesting a major input of transcriptional regulations in Ostreococcus . We propose that the diurnal co-regulation of genes involved in photoprotection, defence against oxidative stress and DNA repair might be an efficient mechanism, which protects cells against photo-damage thereby, contributing to the ability of O. tauri to grow under a wide range of light intensities.

The volvocine algae represent an excellent model lineage in which to study evolution of female and male genders based on comparative analyses of related species. Among these species, Volvox carteri has been extensively studied as a model of an oogamous and complex organism. However, it may have unique derived features that are not present in other species of Volvox. Therefore, information regarding the characteristics of sexual reproduction of other species of Volvox is also important. In 1971, Starr studied four types of sexuality in several global strains identified as Volvox africanus; however, further taxonomic studies of these strains have been lacking, and strains of three of the four sexual types are not available. Here, we studied the morphology, sexual reproduction, and taxonomy of two V. africanus-like species isolated recently from Lake Biwa, Japan. These two species were very similar to two sexual types described by Starr in 1971: one producing dioecious sexual spheroids in heterothallic strains and the other forming both male spheroids and monoecious spheroids in a single strain. The former species produced zygotes with a reticulate cell wall, whereas a smooth zygote wall was observed in the latter species as in V. africanus previously reported from various localities around the world. Our multigene phylogenetic analysis demonstrated that these are sister species to each other. However, the presence of a compensatory base change in the most conserved region of the secondary structure of nuclear ribosomal DNA internal transcribed spacer-2, hybrid inviability demonstrated by intercrossing experiments, and morphological differences in the density of abutment between the gelatinous material of adjacent cells (individual sheaths) in the spheroid supported the recognition of the two species, V. africanus having a smooth zygote wall and V. reticuliferus Nozaki sp. nov. having a reticulate zygote wall.

Recent molecular data has strongly suggested that field-collected cysts of snow algae that are morphologically identifiable as the zygotes of Chloromonas nivalis are composed of multiple species. Motile vegetative cells, however, have not been directly obtained from these cysts because of the difficulties involved in inducing their germination. Recently, our comparative molecular analyses, using both field-collected and cultured materials, demonstrated that one Japanese lineage of \"C. nivalis zygotes\" belongs to C. miwae. Herein, we examined another Japanese lineage of field-collected \"C. nivalis zygotes\" and a new strain originating from Japan. Our molecular data demonstrated that these two different life cycle stages are conspecific, and that they represent a new species that we herein describe as C. muramotoi sp. nov., based on the vegetative and asexual morphological characteristics of the strain. Multigene phylogenetic analyses showed that this new species was sister to C. miwae. Scanning electron microscopy demonstrated that the cysts of C. muramotoi are different from those of C. miwae, based on the arrangement of the flanges developing on the cell wall.

Positive signaling by nitrate in its assimilation pathway has been studied in Chlamydomonas reinhardtii. Among >34,000 lines generated by plasmid insertion, 10 mutants were unable to activate nitrate reductase (NIA1) gene expression and had a Nit⁻ (no growth in nitrate) phenotype. Each of these 10 lines was mutated in the nitrate assimilation-specific regulatory gene NIT2. The complete NIT2 cDNA sequence was obtained, and its deduced amino acid sequence revealed GAF, Gln-rich, Leu zipper, and RWP-RK domains typical of transcription factors and transcriptional coactivators associated with signaling pathways. The predicted Nit2 protein sequence is structurally related to the Nin (for nodule inception) proteins from plants but not to NirA/Nit4/Yna proteins from fungi and yeast. NIT2 expression is negatively regulated by ammonium and is optimal in N-free medium with no need for the presence of nitrate. However, intracellular nitrate is required to allow Nit2 to activate the NIA1 promoter activity. Nit2 protein was expressed in Escherichia coli and shown to bind to specific sequences at the NIA1 gene promoter. Our data indicate that NIT2 is a central regulatory gene required for nitrate signaling on the Chlamydomonas NIA1 gene promoter and that intracellular nitrate is needed for NIT2 function and to modulate NIA1 transcript levels.