Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype

Channels of Evolution: Unveiling Evolutionary Patterns in Diatom Ca2+ Signalling

Diatoms are important primary producers in marine and freshwater environments, but little is known about the signalling mechanisms they use to detect changes in their environment. All eukaryotic organisms use Ca2+ signalling to perceive and respond to environmental stimuli, employing a range of Ca2+-permeable ion channels to facilitate the movement of Ca2+ across cellular membranes. We investigated the distribution of different families of Ca2+ channels in diatom genomes, with comparison to other members of the stramenopile lineage. The four-domain voltage-gated Ca2+ channels (Cav) are present in some centric diatoms but almost completely absent in pennate diatoms, whereas single-domain voltage-gated EukCatA channels were found in all diatoms. Glutamate receptors (GLRs) and pentameric ligand-gated ion channels (pLGICs) also appear to have been lost in several pennate species. Transient receptor potential (TRP) channels are present in all diatoms, but have not undergone the significant expansion seen in brown algae. All diatom species analysed lacked the mitochondrial uniporter (MCU), a highly conserved channel type found in many eukaryotes, including several stramenopile lineages. These results highlight the unique Ca2+-signalling toolkit of diatoms and indicate that evolutionary gains or losses of different Ca2+ channels may contribute to differences in cellular-signalling mechanisms between species.

MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes

Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.

Expansion of photoreception-related gene families may drive ecological adaptation of the dominant diatom species Skeletonema marinoi

Diatom species of the genus Skeletonema are dominant in global coastal waters with important roles in marine primary production and global biogeochemical cycling. Many Skeletonema species have been extensively studied also because they can cause harmful algae blooms (HABs) with negative impacts on marine ecosystems and aquaculture. In this study, the first chromosome-level assembly of the genome of Skeletonema marinoi was constructed. The genome size was 64.99 Mb with a contig N50 of 1.95 Mb. Up to 97.12 % of contigs were successfully anchored on 24 chromosomes. Analysis of the annotated genes revealed 28 large syntenic blocks with 2397 collinear gene pairs in the genome of S. marinoi, suggesting large-scale segmental duplication events in evolution. Substantial expansion of light-harvesting genes encoding fucoxanthin-chlorophyll a/c binding proteins, as well as expansion of photoreceptor gene families encoding aureochromes and cyptochromes (CRY) in S. marinoi were found, which may have shaped ecological adaptation of S. marinoi. In conclusion, the construction of the first high-quality Skeletonema genome assembly offers valuable clues on the ecological and evolutionary characteristics of this dominant coastal diatom species.

The dynamic duo: how DNA methylation and gene transcription help diatoms thrive in modern oceans

This article comments on:

Wan J, Zhou Y, Beardall J, Raven JA, Lin J, Huang J, Lu Y, Liang S, Ye M, Xiao M, Zhao J, Dai X, Xia J, Jin P. 2023. DNA methylation and gene transcription act cooperatively in driving the adaptation of a marine diatom to global change. Journal of Experimental Botany74, 4259–4276.

Scaling the invisible wall: Molecular acclimation of a salinity-tolerant diatom to freshwater

In aquatic ecosystems, marine and freshwater environments are separated by steep salinity gradients. The osmotic stress induced by this 'invisible wall' forms an insurmountable barrier for many aquatic lifeforms, including bacteria, algae and animals. Because the osmotic differences when transiting a salinity divide are so hard to overcome, most species have adapted exclusively to a marine or a freshwater lifestyle. A major consequence of this physiological specialization into marine and freshwater organisms is that transitions are relatively rare, impeding regular contact and colonization. While some animals use specialized organs or behaviour to cope with unfavourable salinity levels, unicellular algae such as diatoms are completely dependent on cellular mechanisms to mitigate salinity stress. In this issue of Molecular Ecology, Downey and colleagues investigate the transcriptomic response of a salinity-tolerant diatom to a shock treatment with freshwater (Molecular Ecology, 2023). Through frequent sampling and integration of existing RNA sequencing data, a fine-grained model of the acclimation to hypo-osmotic stress emerges. Deciphering the pathways that drive the acute and long-term acclimation to freshwater has major implications for diatom ecology, diversification and resilience to global change.

DNA methylation and gene transcription act cooperatively in driving the adaptation of a marine diatom to global change

Genetic changes together with epigenetic modifications such as DNA methylation have been demonstrated to regulate many biological processes and thereby govern the response of organisms to environmental changes. However, how DNA methylation might act cooperatively with gene transcription and thereby mediate the long-term adaptive responses of marine microalgae to global change is virtually unknown. Here we performed a transcriptomic analysis, and a whole-genome bisulfite sequencing, along with phenotypic analysis of a model marine diatom Phaeodactylum tricornutum adapted for two years to high CO2 and/or warming conditions. Our results show that the methylated islands (peaks of methylation) mCHH were positively correlated with expression of genes in the sub-region of the gene body when the populations were grown under high CO2 or its combination with warming for ~2 years. We further identified the differentially expressed genes (DEGs) and hence the metabolic pathways in which they function, at the transcriptomics level in differentially methylated regions (DMRs). Although DEGs in DMRs contributed only 18-24% of the total DEGs, we found that those DEGs acted cooperatively with DNA methylation and then regulated key processes such as central carbon metabolism, amino acid metabolism, ribosome biogenesis, terpenoid backbone biosynthesis, and degradation of misfolded proteins. Taken together, by integrating transcriptomic, epigenetic and phenotypic analysis, our study provides evidence for DNA methylation acting cooperatively with gene transcription to contribute to the adaptation of microalgae to global changes.

An attempt to simultaneously quantify the polysaccharide, total lipid, protein and pigment in single Cyclotella cryptica cell by Raman spectroscopy

BACKGROUND

At present, the conventional methods for determining photosynthetic products of microalgae are usually based on a large number of cell mass to reach the measurement baseline, and the result can only reveal the average state at the population level, which is not feasible for large-scale and rapid screening of specific phenotypes from a large number of potential microalgae mutants. In recent years, single-cell Raman spectra (SCRS) has been proved to be able to rapidly and simultaneously quantify the biochemical components of microalgae. However, this method has not been reported to analyze the biochemical components of Cyclotella cryptica (C. cryptica). Thus, SCRS was first attempt to determine these four biochemical components in this diatom.

RESULTS

The method based on SCRS was established to simultaneously quantify the contents of polysaccharide, total lipids, protein and Chl-a in C. cryptica, with thirteen Raman bands were found to be the main marker bands for the diatom components. Moreover, Partial Least Square Regression (PLSR) models based on full spectrum can reliably predict these four cellular components, with Pearson correlation coefficient for these components reached 0.949, 0.904, 0.801 and 0.917, respectively. Finally, based on SCRS data of one isogenic sample, the pairwise correlation and dynamic transformation process of these components can be analyzed by Intra-ramanome Correlation Analysis (IRCA), and the results showed silicon starvation could promote the carbon in C. cryptica cells to flow from protein and pigment metabolism to polysaccharide and lipid metabolism.

CONCLUSIONS

First, method for the simultaneous quantification of the polysaccharide, total lipid, protein and pigment in single C. cryptica cell are established. Second, the instant interconversion of intracellular components was constructed through IRCA, which is based on data set of one isogenic population and more precision and timeliness. Finally, total results indicated that silicon deficiency could promote the carbon in C. cryptica cells to flow from protein and pigment metabolism to polysaccharide and lipid metabolism.

The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases

Cytosine methylation is an important epigenetic mark involved in the transcriptional control of transposable elements in mammals, plants and fungi. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes, including the phytoplankton groups diatoms and dinoflagellates. However, little is known about their DNA methyltransferase diversity. Here, we performed an in-silico analysis of DNA methyltransferases found in marine microeukaryotes and showed that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes. Furthermore, we found three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrated that the loss of the DNMT5a gene correlates with a global depletion of DNA methylation and overexpression of young transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a view of the structure and function of a DNMT family in the SAR supergroup using an attractive model species.

Characterization of a Marine Diatom Chitin Synthase Using a Combination of Meta-Omics, Genomics, and Heterologous Expression Approaches

β-Chitin has important ecological and physiological roles and potential for widespread applications, but the characterization of chitin-related enzymes from β-chitin producers was rarely reported. Querying against the Tara Oceans Gene Atlas, 4,939 chitin-related unique sequences from 12 Pfam accessions were found in Bacillariophyta metatranscriptomes. Putative chitin synthase (CHS) sequences are decreasingly present in Crustacea (39%), Stramenopiles (16%) and Insecta (14%) from the Marine Atlas of Tara Oceans Unigenes version 1 Metatranscriptomes (MATOUv1+T) database. A CHS gene from the model diatom Thalassiosira pseudonana (Thaps3_J4413, designated TpCHS1) was identified. Homology analysis of TpCHS1 in Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP), PhycoCosm, and the PLAZA diatom omics data set showed that Mediophyceae and Thalassionemales species were potential new β-chitin producers besides Thalassiosirales. TpCHS1 was overexpressed in Saccharomyces cerevisiae and Phaeodactylum tricornutum. In transgenic P. tricornutum lines, TpCHS1-eGFP localizes to the Golgi apparatus and plasma membrane and predominantly accumulates in the cleavage furrow during cell division. Enhanced TpCHS1 expression could induce abnormal cell morphology and reduce growth rates in P. tricornutum, which might be ascribed to the inhibition of the G2/M phase. S. cerevisiae was proved to be a better system for expressing large amounts of active TpCHS1, which effectively incorporates UDP-N-acetylglucosamine in radiometric in vitro assays. Our study expands the knowledge on chitin synthase taxonomic distribution in marine eukaryotic microbes, and is the first to collectively characterize an active marine diatom CHS which may play an important role during cell division. IMPORTANCE As the most abundant biopolymer in the oceans, the significance of chitin and its biosynthesis is rarely demonstrated in diatoms, which are the main contributors to the primary productivity of the oceans, ascribed to their huge biomass and efficient photosynthesis. We retrieved genes involved in chitin-based metabolism against the Tara Oceans Gene Atlas to expand our knowledge about their diversity and distribution in the marine environment. Potential new producers of chitin were found from the analysis of various algal transcriptome and genome databases. Heterologous expression confirms that Thalassiosira pseudonana contains an active chitin synthase (CHS) which may play an important role in the cell division process of diatoms. This study provides new insight into CHS geographic and taxonomic distribution in marine eukaryotic microbes, as well as into a new CHS functioning in the biosynthesis of β-chitin in diatoms.

DNA Methylation in Algae and Its Impact on Abiotic Stress Responses

Epigenetics, referring to heritable gene regulatory information that is independent of changes in DNA sequences, is an important mechanism involved both in organism development and in the response to environmental events. About the epigenetic marks, DNA methylation is one of the most conserved mechanisms, playing a pivotal role in organism response to several biotic and abiotic stressors. Indeed, stress can induce changes in gene expression through hypo- or hyper-methylation of DNA at specific loci and/or in DNA methylation at the genome-wide level, which has an adaptive significance and can direct genome evolution. Exploring DNA methylation in responses to abiotic stress could have important implications for improving stress tolerance in algae. This article summarises the DNA methylation pattern in algae and its impact on abiotic stress, such as heavy metals, nutrients and temperature. Our discussion provides information for further research in algae for a better comprehension of the epigenetic response under abiotic stress, which could favour important implications to sustain algae growth under abiotic stress conditions, often related to high biosynthesis of interesting metabolites.

Light-driven processes: key players of the functional biodiversity in microalgae

Microalgae are prominent aquatic organisms, responsible for about half of the photosynthetic activity on Earth. Over the past two decades, breakthroughs in genomics and ecosystem biology, as well as the development of genetic resources in model species, have redrawn the boundaries of our knowledge on the relevance of these microbes in global ecosystems. However, considering their vast biodiversity and complex evolutionary history, our comprehension of algal biology remains limited. As algae rely on light, both as their main source of energy and for information about their environment, we focus here on photosynthesis, photoperception, and chloroplast biogenesis in the green alga Chlamydomonas reinhardtii and marine diatoms. We describe how the studies of light-driven processes are key to assessing functional biodiversity in evolutionary distant microalgae. We also emphasize that integration of laboratory and environmental studies, and dialogues between different scientific communities are both timely and essential to understand the life of phototrophs in complex ecosystems and to properly assess the consequences of environmental changes on aquatic environments globally.

Microalgae-Based PUFAs for Food and Feed: Current Applications, Future Possibilities, and Constraints

Microalgae are currently considered an attractive source of highly valuable compounds for human and animal consumption, including polyunsaturated fatty acids (PUFAs). Several microalgae-derived compounds, such as ω-3 fatty acids, pigments, and whole dried biomasses are available on the market and are mainly produced by culturing microalgae in open ponds, which can be achieved with low setup and maintenance costs with respect to enclosed systems. However, open tanks are more susceptible to bacterial and other environmental contamination, do not guarantee a high reproducibility of algal biochemical profiles and productivities, and constrain massive cultivation to a limited number of species. Genetic engineering techniques have substantially improved over the last decade, and several model microalgae have been successfully modified to promote the accumulation of specific value-added compounds. However, transgenic strains should be cultured in closed photobioreactors (PBRs) to minimize risks of contamination of aquatic environments with allochthonous species; in addition, faster growth rates and higher yields of compounds of interest can be achieved in PBRs compared to open ponds. In this review, we present information collected about the major microalgae-derived commodities (with a special focus on PUFAs) produced at industrial scale, as well genetically-engineered microalgae to increase PUFA production. We also critically analyzed the main bottlenecks that make large-scale production of algal commodities difficult, as well as possible solutions to overcome the main problems and render the processes economically and environmentally safe.

Recent Progress on Systems and Synthetic Biology of Diatoms for Improving Algal Productivity

Microalgae have drawn much attention for their potential applications as a sustainable source for developing bioactive compounds, functional foods, feeds, and biofuels. Diatoms, as one major group of microalgae with high yields and strong adaptability to the environment, have shown advantages in developing photosynthetic cell factories to produce value-added compounds, including heterologous bioactive products. However, the commercialization of diatoms has encountered several obstacles that limit the potential mass production, such as the limitation of algal productivity and low photosynthetic efficiency. In recent years, systems and synthetic biology have dramatically improved the efficiency of diatom cell factories. In this review, we discussed first the genome sequencing and genome-scale metabolic models (GEMs) of diatoms. Then, approaches to optimizing photosynthetic efficiency are introduced with a focus on the enhancement of biomass productivity in diatoms. We also reviewed genome engineering technologies, including CRISPR (clustered regularly interspaced short palindromic repeats) gene-editing to produce bioactive compounds in diatoms. Finally, we summarized the recent progress on the diatom cell factory for producing heterologous compounds through genome engineering to introduce foreign genes into host diatoms. This review also pinpointed the bottlenecks in algal engineering development and provided critical insights into the future direction of algal production.

The possible fates of Fragilariopsis cylindrus (polar diatom) cells exposed to prolonged darkness

At high latitudes, the polar night poses a great challenge to photosynthetic organisms that must survive up to six months without light. Numerous studies have already shed light on the physiological changes involved in the acclimation of microalgae to prolonged darkness and subsequent re-illumination. However, these studies have never considered inter-individual variability because they have mainly been conducted with bulk measurements. On the other hand, such long periods are likely to impact within-population selection processes. In this study, we hypothesized that distinct subpopulations with specific traits may emerge during acclimation of a population of diatoms to darkness. We addressed this hypothesis using flow cytometry (FCM), which allow to individually characterize large numbers of cells. The ecologically dominant polar pennate diatom Fragilariopsis cylindrus was subjected to three dark acclimation (DA) experiments of one, three, and five months duration, during which all cultures showed signs of recovery once light became available again. Our results suggest that darkness survival of F. cylindrus relies on reduction of metabolic activity and consumption of carbon reserves. In addition, FCM allowed us to record three different causes of death, each shared by significant numbers of individuals. The first rendered cells were unable to survive the stress caused by the return to light, probably due to a lack of sufficient photoprotective defenses. The other two were observed in two subpopulations of cells whose physiological state deviated from the original population. The data suggest that starvation and failure to maintain dormancy were the cause of cell mortality in these two subpopulations.

What Was Old Is New Again: The Pennate Diatom Haslea ostrearia (Gaillon) Simonsen in the Multi-Omic Age

The marine pennate diatom Haslea ostrearia has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue Haslea species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities—e.g., antibacterial, antioxidant and antiproliferative—with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing H. ostrearia as a new model organism by presenting its pros and cons—i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest).

Diatoms as a biotechnological resource for the sustainable biofuel production: a state-of-the-art review

The greenhouse gas emission from fossil fuel and higher economic cost in its transportation are stimulating scientists to explore biomass energy production at the local level. In the present review, the authors have explored the prospects of commercial-scale biofuels production from the microalgal group, diatoms. Insights on suitability of mass cultivation systems for large-scale production of diatoms have been deliberated based on published literature. Diatoms can proliferate extracting nutrients from the wastewater and the same biomass can be harvested for biofuel production. Residues can be further utilized for the formation of other bioproducts and biofertilizers. The residual applications of diatoms from mass culture are estimated to compensate for the additional costs incurred in the removal of impurities. Well-planned research is required to optimize the commercial-scale production of biofuels from diatoms. The aim of this review is therefore, to demonstrate the economically feasible, hygienically safe cultivation of diatoms on nutrients from wastewater, limitations in using diatoms for biofuel production, and how these limitations can be shorted out for optimum utilization of diatom for biofuel production.

Latest Expansions in Lipid Enhancement of Microalgae for Biodiesel Production: An Update

Research progress on sustainable and renewable biofuel has gained motion over the years, not just due to the rapid reduction of dwindling fossil fuel supplies but also due to environmental and potential energy security issues as well. Intense interest in microalgae (photosynthetic microbes) as a promising feedstock for third-generation biofuels has grown over recent years. Fuels derived from algae are now considered sustainable biofuels that are promising, renewable, and clean. Therefore, selecting the robust species of microalgae with substantial features for quality biodiesel production is the first step in the way of biofuel production. A contemporary investigation is more focused on several strategies and techniques to achieve higher biomass and triglycerides in microalgae. The improvement in lipid enhancement in microalgae species by genetic manipulation approaches, such as metabolic or genetic alteration, and the use of nanotechnology are the most recent ways of improving the production of biomass and lipids. Hence, the current review collects up-to-date approaches for microalgae lipid increase and biodiesel generation. The strategies for high biomass and high lipid yield are discussed. Additionally, various pretreatment procedures that may aid in lipid harvesting efficiency and improve lipid recovery rate are described.

Molecular phylogeny of fucoxanthin-chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity

Diatoms adapt to various aquatic light environments and play major roles in the global carbon cycle using their unique light-harvesting system, i.e. fucoxanthin chlorophyll a/c binding proteins (FCPs). Structural analyses of photosystem II (PSII)-FCPII and photosystem I (PSI)-FCPI complexes from the diatom Chaetoceros gracilis have revealed the localization and interactions of many FCPs; however, the entire set of FCPs has not been characterized. Here, we identify 46 FCPs in the newly assembled genome and transcriptome of C. gracilis. Phylogenetic analyses suggest that these FCPs can be classified into five subfamilies: Lhcr, Lhcf, Lhcx, Lhcz, and the novel Lhcq, in addition to a distinct type of Lhcr, CgLhcr9. The FCPs in Lhcr, including CgLhcr9 and some Lhcqs, have orthologous proteins in other diatoms, particularly those found in the PSI-FCPI structure. By contrast, the Lhcf subfamily, some of which were found in the PSII-FCPII complex, seems to be diversified in each diatom species, and the number of Lhcqs differs among species, indicating that their diversification may contribute to species-specific adaptations to light. Further phylogenetic analyses of FCPs/light-harvesting complex (LHC) proteins using genome data and assembled transcriptomes of other diatoms and microalgae in public databases suggest that our proposed classification of FCPs is common among various red-lineage algae derived from secondary endosymbiosis of red algae, including Haptophyta. These results provide insights into the loss and gain of FCP/LHC subfamilies during the evolutionary history of the red algal lineage.

The Draft Genome of the Centric Diatom Conticribra weissflogii (Coscinodiscophyceae, Ochrophyta)

Here, we present a 231 Mb draft genome of the centric diatom Conticribra weissflogii CCMP1336. Comparative genomics of C. weissflogii and other Ochrophyta support the existence of unique carbon-concentrating mechanisms and chitin metabolic processes in diatoms. The whole-genome project is available at CNSA (https://db.cngb.org/search/project/CNP0001903/).

The epigenetic origin of life history transitions in plants and algae

Plants and algae have a complex life history that transitions between distinct life forms called the sporophyte and the gametophyte. This phenomenon-called the alternation of generations-has fascinated botanists and phycologists for over 170 years. Despite the mesmerizing array of life histories described in plants and algae, we are only now beginning to learn about the molecular mechanisms controlling them and how they evolved. Epigenetic silencing plays an essential role in regulating gene expression during multicellular development in eukaryotes, raising questions about its impact on the life history strategy of plants and algae. Here, we trace the origin and function of epigenetic mechanisms across the plant kingdom, from unicellular green algae through to angiosperms, and attempt to reconstruct the evolutionary steps that influenced life history transitions during plant evolution. Central to this evolutionary scenario is the adaption of epigenetic silencing from a mechanism of genome defense to the repression and control of alternating generations. We extend our discussion beyond the green lineage and highlight the peculiar case of the brown algae. Unlike their unicellular diatom relatives, brown algae lack epigenetic silencing pathways common to animals and plants yet display complex life histories, hinting at the emergence of novel life history controls during stramenopile evolution.

The genome of a nonphotosynthetic diatom provides insights into the metabolic shift to heterotrophy and constraints on the loss of photosynthesis

Although most of the tens of thousands of diatom species are photoautotrophs, a small number of heterotrophic species no longer photosynthesize. We sequenced the genome of a nonphotosynthetic diatom, Nitzschia Nitz4, to determine how carbon metabolism was altered in the wake of this trophic shift. Nitzschia Nitz4 has retained its plastid and plastid genome, but changes associated with the transition to heterotrophy were cellular-wide and included losses of photosynthesis-related genes from the nuclear and plastid genomes, elimination of isoprenoid biosynthesis in the plastid, and remodeling of mitochondrial glycolysis to maximize adenosine triphosphte (ATP) yield. The genome contains a β-ketoadipate pathway that may allow Nitzschia Nitz4 to metabolize lignin-derived compounds. Diatom plastids lack an oxidative pentose phosphate pathway (oPPP), leaving photosynthesis as the primary source of NADPH to support essential biosynthetic pathways in the plastid and, by extension, limiting available sources of NADPH in nonphotosynthetic plastids. The genome revealed similarities between nonphotosynthetic diatoms and apicomplexan parasites for provisioning NADPH in their plastids and highlighted the ancestral absence of a plastid oPPP as a potentially important constraint on loss of photosynthesis, a hypothesis supported by the higher frequency of transitions to parasitism or heterotrophy in lineages that have a plastid oPPP.

Mixotrophy in diatoms: Molecular mechanism and industrial potential

Diatoms are microalgae well known for their high variability and high primary productivity, being responsible for about 20% of the annual global carbon fixation. Moreover, they are interesting as potential feedstocks for the production of biofuels and high-value lipids and carotenoids. Diatoms exhibit trophic flexibility and, under certain conditions, they can grow mixotrophically by combing photosynthesis and respiration. So far, only a few species of diatoms have been tested for their mixotrophic metabolism; in some cases, they produced more biomass and with higher lipid content when grown under this condition. Phaeodactylum tricornutum is the most studied diatom species for its mixotrophic metabolism due to available genome sequence and molecular tools. However, studies in additional species are needed to better understand the conservation of this process in diatoms and its potential in industrial applications. Here, we describe the photosynthetic and respiratory pathways involved in mixotrophy and provide an overview of the trophic variability in diatoms. This review also highlights promising areas of industrial applications for diatoms when cultivated under mixotrophy.

Microalgal Co-Cultivation Prospecting to Modulate Vitamin and Bioactive Compounds Production

Microalgal biotechnology is gaining importance. However, key issues in the pipeline from species selection towards large biomass production still require improvements to maximize the yield and lower the microalgal production costs. This study explores a co-cultivation strategy to improve the bioactive compounds richness of the harvested microalgal biomass. Based on their biotechnological potential, two diatoms (Skeletonema marinoi, Cyclotella cryptica) and one eustigmatophyte (Nannochloropsis oceanica) were grown alone or in combination. Concentrations of ten vitamins (A, B₁, B₂, B₆, B₁₂, C, D₂, D₃, E and H), carotenoids and polyphenols, together with total flavonoids, sterols, lipids, proteins and carbohydrates, were compared. Moreover, antioxidant capacity and chemopreventive potential in terms inhibiting four human tumor-derived and normal cell lines proliferation were evaluated. Co-cultivation can engender biomass with emergent properties regarding bioactivity or bioactive chemical profile, depending on the combined species. The high vitamin content of C. cryptica or N. oceanica further enhanced (until 10% more) when co-cultivated, explaining the two-fold increase of the antioxidant capacity of the combined C. cryptica and N. oceanica biomass. Differently, the chemopreventive activity was valuably enhanced when coupling the two diatoms C. cryptica and S. marinoi. The results obtained in this pilot study promote microalgal co-cultivation as a valuable strategy aiming to boost their application in eco-sustainable biotechnology.

Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom

A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production.

Full-Length Transcriptome of Thalassiosira weissflogii as a Reference Resource and Mining of Chitin-Related Genes

β-Chitin produced by diatoms is expected to have significant economic and ecological value due to its structure, which consists of parallel chains of chitin, its properties and the high abundance of diatoms. Nevertheless, few studies have functionally characterised chitin-related genes in diatoms owing to the lack of omics-based information. In this study, we first compared the chitin content of three representative Thalassiosira species. Cell wall glycosidic linkage analysis and chitin/chitosan staining assays showed that Thalassiosira weissflogii was an appropriate candidate chitin producer. A full-length (FL) transcriptome of T. weissflogii was obtained via PacBio sequencing. In total, the FL transcriptome comprised 23,362 annotated unigenes, 710 long non-coding RNAs (lncRNAs), 363 transcription factors (TFs), 3113 alternative splicing (AS) events and 3295 simple sequence repeats (SSRs). More specifically, 234 genes related to chitin metabolism were identified and the complete biosynthetic pathways of chitin and chitosan were explored. The information presented here will facilitate T. weissflogii molecular research and the exploitation of β-chitin-derived high-value enzymes and products.

Re-examination of two diatom reference genomes using long-read sequencing

Background

The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group. Their reference genomes, published in 2004 and 2008, respectively, were the product of traditional Sanger sequencing. In the case of T. pseudonana, optical restriction site mapping was employed to further clarify and contextualize chromosome-level scaffolds. While both genomes are considered highly accurate and reasonably contiguous, they still contain many unresolved regions and unordered/unlinked scaffolds.

Results

We have used Oxford Nanopore Technologies long-read sequencing to update and validate the quality and contiguity of the T. pseudonana and P. tricornutum genomes. Fine-scale assessment of our long-read derived genome assemblies allowed us to resolve previously uncertain genomic regions, further characterize complex structural variation, and re-evaluate the repetitive DNA content of both genomes. We also identified 1862 previously undescribed genes in T. pseudonana. In P. tricornutum, we used transposable element detection software to identify 33 novel copia-type LTR-RT insertions, indicating ongoing activity and rapid expansion of this superfamily as the organism continues to be maintained in culture. Finally, Bionano optical mapping of P. tricornutum chromosomes was combined with long-read sequence data to explore the potential of long-read sequencing and optical mapping for resolving haplotypes.

Conclusion

Despite its potential to yield highly contiguous scaffolds, long-read sequencing is not a panacea. Even for relatively small nuclear genomes such as those investigated herein, repetitive DNA sequences cause problems for current genome assembly algorithms. Determining whether a long-read derived genomic assembly is ‘better’ than one produced using traditional sequence data is not straightforward. Our revised reference genomes for P. tricornutum and T. pseudonana nevertheless provide additional insight into the structure and evolution of both genomes, thereby providing a more robust foundation for future diatom research.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07666-3.

Comprehensive and Functional Analysis of Horizontal Gene Transfer Events in Diatoms

Diatoms are a diverse group of mainly photosynthetic algae, responsible for 20% of worldwide oxygen production, which can rapidly respond to favorable conditions and often outcompete other phytoplankton. We investigated the contribution of horizontal gene transfer (HGT) to its ecological success. A large-scale phylogeny-based prokaryotic HGT detection procedure across nine sequenced diatoms showed that 3-5% of their proteome has a horizontal origin and a large influx occurred at the ancestor of diatoms. More than 90% of HGT genes are expressed, and species-specific HGT genes in Phaeodactylum tricornutum undergo strong purifying selection. Genes derived from HGT are implicated in several processes including environmental sensing and expand the metabolic toolbox. Cobalamin (vitamin B12) is an essential cofactor for roughly half of the diatoms and is only produced by bacteria. Five consecutive genes involved in the final synthesis of the cobalamin biosynthetic pathway, which could function as scavenging and repair genes, were detected as HGT. The full suite of these genes was detected in the cold-adapted diatom Fragilariopsis cylindrus. This might give diatoms originating from the Southern Ocean, a region typically depleted in cobalamin, a competitive advantage. Overall, we show that HGT is a prevalent mechanism that is actively used in diatoms to expand its adaptive capabilities.

Integrative omics identification, evolutionary and structural analysis of low affinity nitrate transporters in diatoms, diNPFs

Diatoms are one of the major and most diverse groups of phytoplankton, with chimeric genomes harbouring a combination of genes of bacterial, animal and plant origin. They have developed sophisticated mechanisms to face environmental variations. In marine environments, nutrients concentration shows significant temporal and spatial variability, influencing phytoplankton growth. Among nutrients, nitrogen, present at micromolar levels, is often a limiting resource. Here, we report a comprehensive characterization of the Nitrate Transporter 1/Peptide Transporter Family (NPF) in diatoms, diNPFs. NPFs are well characterized in many organisms where they recognize a broad range of substrates, ranging from short-chained di- and tri-peptides in bacteria, fungi and mammals to a wide variety of molecules including nitrate in higher plants. Scarce information is available for diNPFs. We integrated-omics, phylogenetic, structural and expression analyses, to infer information on their role in diatoms. diNPF genes diverged to produce two distinct clades with strong sequence and structural homology with either bacterial or plant NPFs, with different predicted sub-cellular localization, suggesting that the divergence resulted in functional diversification. Moreover, transcription analysis of diNPF genes under different laboratory and environmental growth conditions suggests that diNPF diversification led to genetic adaptations that might contribute to diatoms ability to flourish in diverse environmental conditions.

New paradigm in diatom omics and genetic manipulation

Diatoms are one of the most heterogeneous eukaryotic plankton known for regulating earth's biogeochemical cycles and maintaining the marine ecosystems ever since the late Eocene epoch. The advent of multidisciplinary omics approach has both epitomized and revolutionized the nature of their chimeric genetic toolkit, ecophysiology, and metabolic adaptability as well as their interaction with other communities. In addition, advanced functional annotation of transcriptomic and proteomic data using cutting edge bioinformatics tools together with high-resolution genome-scale mathematical modeling has effectively proven as the catapult in solving genetic bottlenecks in microbial as well as diatom exploration. In this review, a corroborative summation of the robust work done in manipulating, engineering, and sequencing of the diatom genomes besides underpinning the holistic application of omics in transcription and translation has been discussed in order to shrewd their multifarious novel potential in the field of biotechnology and provide an insight into their dynamic evolutionary relevance.

Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses

BACKGROUND

The nitrogen-containing polysaccharide chitin is the second most abundant biopolymer on earth and is found in the cell walls of diatoms, where it serves as a scaffold for biosilica deposition. Diatom chitin is an important source of carbon and nitrogen in the marine environment, but surprisingly little is known about basic chitinase metabolism in diatoms.

RESULTS

Here, we identify and fully characterize 24 chitinase genes from the model centric diatom Thalassiosira pseudonana. We demonstrate that their expression is broadly upregulated under abiotic stresses, despite the fact that chitinase activity itself remains unchanged, and we discuss several explanations for this result. We also examine the potential transcriptional complexity of the intron-rich T. pseudonana chitinase genes and provide evidence for two separate tandem duplication events during their evolution.

CONCLUSIONS

Given the many applications of chitin and chitin derivatives in suture production, wound healing, drug delivery, and other processes, new insight into diatom chitin metabolism has both theoretical and practical value.

Transcriptional Response of Osmolyte Synthetic Pathways and Membrane Transporters in a Euryhaline Diatom During Long-term Acclimation to a Salinity Gradient

How diatoms respond to fluctuations in osmotic pressure is important from both ecological and applied perspectives. It is well known that osmotic stress affects photosynthesis and can result in the accumulation of compounds desirable in pharmaceutical and alternative fuel industries. Gene expression responses to osmotic stress have been studied in short-term trials, but it is unclear whether the same mechanisms are recruited during long-term acclimation. We used RNA-seq to study the genome-wide transcription patterns in the euryhaline diatom, Cyclotella cryptica, following long-term acclimation to salinity that spanned the natural range of fresh to oceanic water. Long-term acclimated C. cryptica exhibited induced synthesis or repressed degradation of the osmolytes glycine betaine, taurine and dimethylsulfoniopropionate (DMSP). Although changes in proline concentration is one of the main responses in short-term osmotic stress, we did not detect a transcriptional change in proline biosynthetic pathways in our long-term experiment. Expression of membrane transporters showed a general tendency for increased import of potassium and export of sodium, consistent with the electrochemical gradients and dependence on co-transported molecules. Our results show substantial between-genotype differences in growth and gene expression reaction norms and suggest that the regulation of proline synthesis important in short-term osmotic stress might not be maintained in long-term acclimation. Further examination using time-course gene expression experiments, metabolomics and genetic validation of gene functions would reinforce patterns inferred from RNA-seq data.

Role of DNA methylation in the chromium tolerance of Scenedesmus acutus (Chlorophyceae) and its impact on the sulfate pathway regulation

DNA methylation is a very important epigenetic modification that participates in many biological functions. Although many researches on DNA methylation have been reported in various plant species, few studies have assessed the global DNA methylation pattern in algae. Even more the complex mechanisms by which DNA methylation modulates stress in algae are yet largely unresolved, mainly with respect to heavy metal stress, for which in plants, metal- and species- specific responses were instead evidenced. In this work, we performed a comparative Whole-Genome Bisulfite Sequencing (WGBS) on two strains of the green alga Scenedesmus acutus with different Cr(VI) sensitivity. The pattern of distribution of 5-mC showed significant differences between the two strains concerning both differentially methylated local contexts (CG, CHG and CHH) and Differentially Methylated Regions (DMRs) as well. We also demonstrated that DNA methylation plays an important role in modulating some genes for sulfate uptake/assimilation confirming the involvement of the sulfate pathway in the Cr-tolerance. Our results suggest that DNA methylation may be of particular importance in defining signal specificity associated with Cr-tolerance and in establishing new epigenetic marks which contribute to the adaptation to metal stress and also to transmit the epigenomic traits to the progeny.

Genome Sequences of Bacteria Associated with the Diatom Cyclotella cryptica Strain CCMP332

We report draft genomes of two bacterial strains in the genera Hyphobacterium and Reichenbachiella, which are associated with the diatom Cyclotella cryptica strain CCMP332. Genomes from these strains were 2,691,501 bp and 3,325,829 bp in size, respectively, and will be useful for understanding interactions between diatoms and bacteria.

We report draft genomes of two bacterial strains in the genera Hyphobacterium and Reichenbachiella, which are associated with the diatom Cyclotella cryptica strain CCMP332. Genomes from these strains were 2,691,501 bp and 3,325,829 bp, respectively, and will be useful for understanding interactions between diatoms and bacteria.

Improved Reference Genome for Cyclotella cryptica CCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta)

The diatom, Cyclotella cryptica, is a well-established model species for physiological studies and biotechnology applications of diatoms. To further facilitate its use as a model diatom, we report an improved reference genome assembly and annotation for C. cryptica strain CCMP332. We used a combination of long- and short-read sequencing to assemble a high-quality and contaminant-free genome. The genome is 171 Mb in size and consists of 662 scaffolds with a scaffold N50 of 494 kb. This represents a 176-fold decrease in scaffold number and 41-fold increase in scaffold N50 compared to the previous assembly. The genome contains 21,250 predicted genes, 75% of which were assigned putative functions. Repetitive DNA comprises 59% of the genome, and an improved classification of repetitive elements indicated that a historically steady accumulation of transposable elements has contributed to the relatively large size of the C. cryptica genome. The high-quality C. cryptica genome will serve as a valuable reference for ecological, genetic, and biotechnology studies of diatoms.

An intimate view into the silica deposition vesicles of diatoms

Diatoms are single-celled microalgae that produce silica-based cell walls with intricate nano- and micropatterns. Biogenesis of diatom biosilica is a bottom-up process that occurs in large intracellular compartments termed silica deposition vesicles (SDVs). Investigating the mechanisms of silica morphogenesis has so far been severely limited by the lack of methods for imaging the entire volume of an SDV with high spatial resolution during all stages of development. Here we have developed a method that allows for rapid identification and electron microscopy imaging of many different, full sized SDVs that are in the process of producing biosilica valves. This enabled visualizing the development of characteristic morphological biosilica features with unprecedented spatio-temporal resolution. During early to mid-term development, valve SDVs contained ~ 20 nm sized particles that were primarily associated with the radially expanding rib-like biosilica structures. The results from electron dispersive X-ray analysis suggests that the immature biosilica patterns are silica-organic composites. This supports the hypothesis that silica morphogenesis is dependent on organic biomolecules inside the SDV lumen.

Screening of High Temperature-Tolerant Oleaginous Diatoms

Screening suitable strains with high temperature adaptability is of great importance for reducing the cost of temperature control in microalgae cultivation, especially in summer. To obtain high temperature-tolerant diatoms, water samples were collected in summer from 7 different regions of China across the Northeast, North and East. A total of 731 water samples was collected and from them 131 diatom strains were isolated and identified based on the 18S rRNA sequences. Forty-nine strains out of the 131 diatoms could survive at 30°C, and 6 strains with relatively high biomass and lipid content at high temperature were selected and were found to be able to grow at 35°C. Cyclotella sp. HB162 had the highest dry biomass of 0.46 g/l and relatively high triacylglycerol (TAG) content of 237.4 mg/g dry biomass. The highest TAG content of 246.4 mg/g dry biomass was obtained in Fistulifera sp. HB236, while Nitzschia palea HB170 had high dry biomass (0.33 g/l) but relatively low TAG content (105.9 mg/g dry biomass). N. palea HB170 and Fistulifera sp. HB236 presented relatively stable growth rates and lipid yields under fluctuating temperatures ranging from 28 to 35°C, while Cyclotella HB162 maintained high lipid yield at temperatures below 25°C. The percentage of saturated fatty acids and monounsaturated fatty acids in all the 6 strains was 84-91% in total lipids and 90-94% in TAGs, which makes them the ideal feedstock for biodiesel.

Regulation of Carbon Metabolism by Environmental Conditions: A Perspective From Diatoms and Other Chromalveolates

Diatoms belong to a major, diverse and species-rich eukaryotic clade, the Heterokonta, within the polyphyletic chromalveolates. They evolved as a result of secondary endosymbiosis with one or more Plantae ancestors, but their precise evolutionary history is enigmatic. Nevertheless, this has conferred them with unique structural and biochemical properties that have allowed them to flourish in a wide range of different environments and cope with highly variable conditions. We review the effect of pH, light and dark, and CO2 concentration on the regulation of carbon uptake and assimilation. We discuss the regulation of the Calvin-Benson-Bassham cycle, glycolysis, lipid synthesis, and carbohydrate synthesis at the level of gene transcripts (transcriptomics), proteins (proteomics) and enzyme activity. In contrast to Viridiplantae where redox regulation of metabolic enzymes is important, it appears to be less common in diatoms, based on the current evidence, but regulation at the transcriptional level seems to be widespread. The role of post-translational modifications such as phosphorylation, glutathionylation, etc., and of protein-protein interactions, has been overlooked and should be investigated further. Diatoms and other chromalveolates are understudied compared to the Viridiplantae, especially given their ecological importance, but we believe that the ever-growing number of sequenced genomes combined with proteomics, metabolomics, enzyme measurements, and the application of novel techniques will provide a better understanding of how this important group of algae maintain their productivity under changing conditions.

Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity

Diatoms are the world's most diverse group of algae, comprising at least 100,000 species. Contributing ∼20% of annual global carbon fixation, they underpin major aquatic food webs and drive global biogeochemical cycles. Over the past two decades, Thalassiosira pseudonana and Phaeodactylum tricornutum have become the most important model systems for diatom molecular research, ranging from cell biology to ecophysiology, due to their rapid growth rates, small genomes, and the cumulative wealth of associated genetic resources. To explore the evolutionary divergence of diatoms, additional model species are emerging, such as Fragilariopsis cylindrus and Pseudo-nitzschia multistriata Here, we describe how functional genomics and reverse genetics have contributed to our understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations. Our review will also highlight promising areas of investigation into the diversity of these photosynthetic organisms, including the discovery of new molecular pathways governing the life of secondary plastid-bearing organisms in aquatic environments.

Transgenic microalgae as bioreactors

Microalgae are unicellular organisms that act as the crucial primary producers all over the world, typically found in marine and freshwater environments. Most of them can live photo-autotrophically, reproduce rapidly, and accumulate biomass in a short period efficiently. To adapt to the uninterrupted change of the environment, they evolve and differentiate continuously. As a result, some of them evolve special abilities such as toleration of extreme environment, generation of sophisticated structure to adapt to the environment, and avoid predators. Microalgae are believed to be promising bioreactors because of their high lipid and pigment contents. Genetic engineering technologies have given revolutions in the microalgal industry, which decoded the secrets of microalgal genes, express recombinant genes in microalgal genomes, and largely soar the accumulation of interested components in transgenic microalgae. However, owing to several obstructions, the industry of transgenic microalgae is still immature. Here, we provide an overview to emphasize the advantage and imperfection of the existing transgenic microalgal bioreactors.

Overexpression of acetyl-CoA carboxylase increases fatty acid production in the green alga Chlamydomonas reinhardtii

Chlamydomonas reinhardtii is a photosynthetic unicellular model algae with multiple biotechnological advantages, and its fatty acids can be used to produce biofuels. Numerous studies suggest that acetyl-coA carboxylase (ACCa) catalyzes the first committed and rate-limiting step of fatty acid biosynthesis, thereby playing a central role in oil accumulation. Here, we cloned and overexpressed ACCa in C. reinhardtii to directly evaluate its effect on fatty acid synthesis. GC-MS analysis found that the unsaturated FAs contents of the CW15-24 and CW15-85 strains were 55.45% and 56.15%, which were significantly enriched compared to the wild type CW15 (48.39%). Under the optimized conditions, the content of lipid by overexpressed the ACCa gene in the mutant CW15-85 (0.46 g/l) was 1.16-fold greater than control through optimization of N and P sources. Altogether, our data clearly demonstrate that ACCa overexpression in C. reinhardtii can directly increase the synthesis of fatty acids.

Marine Natural Products from Microalgae: An -Omics Overview

Over the last decade, genome sequences and other -omics datasets have been produced for a wide range of microalgae, and several others are on the way. Marine microalgae possess distinct and unique metabolic pathways, and can potentially produce specific secondary metabolites with biological activity (e.g., antipredator, allelopathic, antiproliferative, cytotoxic, anticancer, photoprotective, as well as anti-infective and antifouling activities). Because microalgae are very diverse, and adapted to a broad variety of environmental conditions, the chances to find novel and unexplored bioactive metabolites with properties of interest for biotechnological and biomedical applications are high. This review presents a comprehensive overview of the current efforts and of the available solutions to produce, explore and exploit -omics datasets, with the aim of identifying species and strains with the highest potential for the identification of novel marine natural products. In addition, funding efforts for the implementation of marine microalgal -omics resources and future perspectives are presented as well.

Comparative and Functional Algal Genomics

Over 100 whole-genome sequences from algae are published or soon to be published. The rapidly increasing availability of these fundamental resources is changing how we understand one of the most diverse, complex, and understudied groups of photosynthetic eukaryotes. Genome sequences provide a window into the functional potential of individual algae, with phylogenomics and functional genomics as tools for contextualizing and transferring knowledge from reference organisms into less well-characterized systems. Remarkably, over half of the proteins encoded by algal genomes are of unknown function, highlighting the volume of functional capabilities yet to be discovered. In this review, we provide an overview of publicly available algal genomes, their associated protein inventories, and their quality, with a summary of the statuses of protein function understanding and predictions.

Fucoxanthin-Chlorophyll Protein Complexes of the Centric Diatom Cyclotella Meneghiniana Differ in Lhcx1 and Lhcx6_1 Content

The ecological success of diatoms, key contributors to photosynthesis, is partly based on their ability to perfectly balance efficient light harvesting and photoprotection. Diatoms contain higher numbers of antenna proteins than vascular plants for light harvesting and for photoprotection. These proteins are arranged in fucoxanthin-chlorophyll protein (FCP) complexes. The number of FCP complexes, their subunit composition, and their interactions in the thylakoid membranes remain elusive in different diatoms. We used the recently available genome sequence of the centric diatom Cyclotella cryptica to analyze gene sequences for putative light-harvesting proteins in C. meneghiniana, and to elucidate the FCP complex composition. We analyzed two pools of FCP complexes that were trimeric (FCPa) and nonameric (FCPb). FCPa was composed of four different trimeric subtypes. Two different nonameric FCPb complexes were present. All were distinguished by their polypeptide composition and partly by pigmentation. With use of a milder purification method, two fractions composed of different FCP complexes were isolated. One was enriched in FCPs incorporating the photoprotective subunit Lhcx1, such as the newly identified nonameric FCPb2 and the major trimeric FCPa4 complex, which are predetermined to be involved in energy-dependent nonphotochemical quenching. The other fraction contained mainly FCPs that were devoid of Lhcx1, FCPa3, and FCPb1. Both fractions also included small amounts of trimeric FCPa complexes with the centric diatom-specific Lhcx protein, Lhcx6_1, as subunit. Thus, the antenna organization of centric diatoms, as well as the distribution of different photoprotective Lhcx proteins, differs from that of other diatoms, as well as from plants.

Comparative characterization of putative chitin deacetylases from Phaeodactylum tricornutum and Thalassiosira pseudonana highlights the potential for distinct chitin-based metabolic processes in diatoms

Chitin is generally considered to be present in centric diatoms but not in pennate species. Many aspects of chitin biosynthetic pathways have not been explored in diatoms. We retrieved chitin metabolic genes from pennate (Phaeodactylum tricornutum) and centric (Thalassiosira pseudonana) diatom genomes. Chitin deacetylase (CDA) genes from each genome (PtCDA and TpCDA) were overexpressed in P. tricornutum. We performed comparative analysis of their sequence structure, phylogeny, transcriptional profiles, localization and enzymatic activities. The chitin relevant proteins show complex subcellular compartmentation. PtCDA was likely acquired by horizontal gene transfer from prokaryotes, whereas TpCDA has closer relationships with sequences in Opisthokonta. Using transgenic P. tricornutum lines expressing CDA-green fluorescent protein (GFP) fusion proteins, PtCDA predominantly localizes to Golgi apparatus whereas TpCDA localizes to endoplasmic reticulum/chloroplast endoplasmic reticulum membrane. CDA-GFP overexpression upregulated the transcription of chitin synthases and potentially enhanced the ability of chitin synthesis. Although both CDAs are active on GlcNAc₅ , TpCDA is more active on the highly acetylated chitin polymer DA60. We have addressed the ambiguous characters of CDAs from P. tricornutum and T. pseudonana. Differences in localization, evolution, expression and activities provide explanations underlying the greater potential of centric diatoms for chitin biosynthesis. This study paves the way for in vitro applications of novel CDAs.