Redefining Pyropia (Bangiales, Rhodophyta): Four New Genera, Resurrection of Porphyrella and Description of Calidia pseudolobata sp. nov. From China

Dynamics of green macroalgal micro-propagules and the influencing factors in the southern Yellow Sea, China

Micro-propagules (banks of microscopic forms) play important roles in the expansion of green tides, which are spreading on eutrophic coasts worldwide. In particular, large-scale green tides (Yellow Sea Green Tide, YSGTs) have persisted in the Yellow Sea for over 15 years, but the dynamics and functions of micro-propagules in their development remain unclear. In the present study, year-round field surveys were conducted to identify the reservoirs and investigate the persistence mechanisms and associated biotic and abiotic factors driving the temporal and spatial variations of micro-propagules. Micro-propagules in the southern Yellow Sea (SYS) showed evident spatial heterogeneity in terms of seasonal patterns and major influencing factors. Offshore of the SYS, the micro-propagule population underwent ephemeral expansion along with a large-scale bloom of floating Ulva algae in late spring and early summer. The Subei Shoal, particularly the sediments in the central raft region, had the highest micro-propagule abundance (MA) and was a major reservoir. The pronounced seasonal variation of MA in the Subei Shoal was primarily associated with the attached Ulva algae on Neopyropia aquaculture rafts. Vast aquaculture rafts provided essential substrates for micro-propagules to complete their life cycle and replenish the seed bank, thereby sustaining persistent YSGTs. It implied that habitat modification has pronounced ecological impacts on this intertidal muddy flat. The unique environmental conditions (enriched nutrients, esp. nitrate, favourable seawater temperatures in spring, and strong tidal mixing) facilitated the abundance, seasonal variation and recruitment of micro-propagules in the Subei Shoal. Given the current mitigation measures implemented in the raft region, further research is required to monitor and investigate the physiological and ecological responses of micro-propagule populations to the complex hydrobiological, geochemical, and physical matrices.

Syncopation and synchrony: Phenological dynamics of Pyropia nereocystis (Bangiophyceae) in central California

Pyropia nereocystis is an annual northeastern Pacific-bladed bangialean species whose macroscopic stage epiphytized the annual canopy forming bull kelp Nereocystis luetkeana. I examined three in situ facets of these epiphyte-host dynamics in the central California region: (1) spatial and temporal variation in the presence of P. nereocystis epiphytes as a function of host density, (2) the relationship between individual host morphology and epiphytic P. nereocystis biomass, and (3) the ecophysiological growth ramifications for subtidal transplants of both life stages of P. nereocystis. Swath canopy surveys and whole host collections were conducted at five sites between November 2017 and February 2019. Additionally, transplants of P. nereocystis gametophytes and sporophytes were conducted across multiple subtidal depths. I observed temporal changes in the proportions of hosts epiphytized by P. nereocystis, with differences in seasonal persistence of P. nereocystis among sites and between years. Biomass of P. nereocystis was positively correlated with individual host stipe length, stipe surface area, and the primary principal component (PC) of stipe morphometrics denoted by principal component analysis (PCA). Gametogenesis in P. nereocystis epiphytes was spatially heterogeneous and limited for the 2018-2019 cohort due to comprehensive removal of hosts by the February 2019 sampling period. Transplants of P. nereocystis gametophytes yielded similar growth responses among depths, and sporophyte (conchocelis) transplant areal growth was positively correlated with transplant depth. These findings detail spatiotemporal complexity and multi-scale (individual, site, and whole region) phenological nuances for central Californian P. nereocystis epiphytes.

Functional Characterization of the First Bona Fide Phytoene Synthase in Red Algae from Pyropia yezoensis

The formation of phytoene by condensing two geranylgeranyl diphosphate molecules catalyzed by phytoene synthase (PSY) is the first committed and rate-limiting step in carotenoid biosynthesis, which has been extensively investigated in bacteria, land plants and microalgae. However, this step in macroalgae remains unknown. In the present study, a gene encoding putative phytoene synthase was cloned from the economic red alga Pyropia yezoensis-a species that has long been used in food and pharmaceuticals. The conservative motifs/domains and the tertiary structure predicted using bioinformatic tools suggested that the cloned PyPSY should encode a phytoene synthase; this was empirically confirmed by pigment complementation in E. coli. This phytoene synthase was encoded by a single copy gene, whose expression was presumably regulated by many factors. The phylogenetic relationship of PSYs from different organisms suggested that red algae are probably the progeny of primary endosymbiosis and plastid donors of secondary endosymbiosis.

How many species of algae are there? A reprise. Four kingdoms, 14 phyla, 63 classes and still growing

To date (1 November 2023), the online database AlgaeBase has documented 50,589 species of living algae and 10,556 fossil species here referred to four kingdoms (Eubacteria, Chromista, Plantae, and Protozoa), 14 phyla, and 63 classes. The algae are the third most speciose grouping of plant-like organisms after the flowering plants (≈382,000 species) and fungi (≈170,000 species, including lichens) but are the least well defined of all the botanical groupings. Priority is given to phyla and class names that are familiar to phycologists and that are nomenclaturally valid. The most species-rich phylum is the Heterokontophyta to which 18 classes are referred with 21,052 living species and which is dominated by the diatoms in three classes with 18,673 species (16,427 living; 2239 fossil). The next most species-rich phyla are the red algae (7276 living), the green algae (6851 living), the blue-green algae (Cyanobacteria, 5723 living), the charophytes (4950 living, including the Charophyceae, 511 species living, and the Zygnematophyceae, 4335 living species), Dinoflagellata (2956 living, including the Dinophyceae, 2828 extant), and haptophytes (Haptophyta 1722 species, 517 living).

Characterization and comparative analysis of the complete organelle genomes of three red macroalgae species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis) and development of molecular makers for their identification

BACKGROUND

Many species of red algae belonging to the phylum Rhodophyta are consumed by humans as raw materials for nutrition and medicine. As the seaweed market grows, the importance of the laver species has increased. The classification of red algal species has changed significantly, and the accuracy of this classification has improved significantly in recent years. Here, we report the complete circular genomes of the chloroplasts (cp) and mitochondria (mt) of three laver species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis).

OBJECTIVE

This study aims to assemble, annotate, and characterize the organization of the organelle genomes of three laver species, conduct comparative genomic studies, and develop molecular markers based on SNPs.

METHODS

We analyzed organelle genome structures, repeat sequences, sequence divergence, gene rearrangements, and phylogenetic relationships of three laver species.

RESULTS

The chloroplast genomes of the three species contained an average of 212 protein-coding genes (PCGs), while the mitochondrial genomes contained an average of 25 PCGs. We reconstructed the phylogenetic trees based on both chloroplast and mitochondrial genomes using 201 and 23 PCGs (in cp and mt genomes, respectively) shared in the class Bangiophyceae (and five species of Florideophyceae class used as an outgroup). In addition, 12 species-specific molecular markers were developed for qRT-PCR analysis.

CONCLUSIONS

This is the first report of Neoporphyra seriata complete organellar genomes. With the results, this study provides useful genetic information regarding taxonomic discrepancies, the reconstruction of phylogenetic trees, and the evolution of red algae. Moreover, the species-specific markers can be used as fast and easy methods to identify a target species.

Identification of genes regulated by lipids from seaweed Susabinori (Pyropia yezoensis) involved in the improvement of hepatic steatosis: Insights from RNA-Seq analysis in obese db/db mice

Hepatic steatosis is an early stage in the progression of non-alcoholic fatty liver disease (NAFLD) and can lead to the development of non-alcoholic steatohepatitis (NASH), a major cause of liver-related morbidity and mortality. Identification of dietary components that can alleviate hepatic steatosis is crucial for developing effective therapeutic strategies for NAFLD. Recently, we demonstrated the impact of lipids extracted from the marine red alga Susabinori (Pyropia yezoensis) in a murine model of type 2-diabete (db/db). We found that Susabinori lipids (SNL), abundant in eicosapentaenoic acid (EPA)-containing polar lipids, protected against obesity-induced hepatic steatosis in db/db mice. To understand the specific genes or biological pathways underlying the effects of SNL, we conducted RNA-Seq analysis of the hepatic transcriptome. By performing comparative analysis of differentially expressed genes between normal mice and db/db mice consuming a control diet, as well as SNL-fed db/db mice, we identified the 15 SNL-dependent up-regulated genes that were down-regulated in db/db mice but up-regulated by SNL feeding. Gene ontology and pathway analysis on these 15 genes demonstrated a significant association with the metabolisms of arachidonic acid (AA) and linoleic acid (LA). Furthermore, we observed alterations in the expression levels of monoacylglycerol lipase (Magl) and fatty acid-binding protein 4 (Fabp4) in the SNL-fed db/db mice, both of which are implicated in AA and LA metabolism. Additionally, the livers of SNL-fed db/db mice exhibited reduced levels of AA and LA, but a high accumulation of EPA. In conclusion, the SNL diet might affect the metabolisms of AA and LA, which contribute to the improvement of hepatic steatosis. Our findings provide insights into the molecular mechanisms underlying the beneficial effects of SNL.

Characterization and organelle genome sequencing of Pyropia species from Myanmar

Pyropia is a genus comprising red algae of the Bangiaceae family that is commonly found in intertidal zones worldwide. However, understanding of Pyropia species that are prone to tropical regions remains limited despite recent breakthroughs in genomic research. Within the realm of Pyropia species thriving in tropical regions, P. vietnamensis stands out as a widely recognized species. In this study, we aimed to investigate Pyropia species in the southwest coast of Myanmar using physiological and molecular approaches, culture-based analyses, chloroplast rbcL and nuclear SSU gene sequencing, and whole chloroplast and mitochondrial genome sequencing. Physiological analysis showed that the Myanmar samples were more heat-tolerant than their Japanese counterparts, including those of subtropical origin. Additionally, molecular characterization revealed that the Myanmar samples were closely related to P. vietnamensis from India. This study is the first to sequence the chloroplast and mitochondrial genomes of Pyropia species from tropical regions. A unique deletion event was observed within a ribosomal RNA gene cluster in the chloroplast genome of the studied Pyropia species, which is a deviation from the usual characteristics of most Pyropia species. This study improves current understanding of the physiological and molecular characteristics of this comparatively understudied Pyropia species that grows in tropical regions.

Characterization of histone acetyltransferases and deacetylases and their roles in response to dehydration stress in Pyropia yezoensis (Rhodophyta)

Histone acetylation is one of the most pivotal epigenetic mechanisms in eukaryotes and has been tightly linked to the regulation of various genes controlling growth, development and response to environmental stresses in both animals and plants. Till date, the association of histone acetylation to dehydration stress in red algae and genes encoding the enzymes responsible for histone acetylation: histone acetyltransferases (HATs) or histone deacetylases (HDACs), remains largely unknown. In this study, in silico analysis of the red seaweed Pyropia yezoensis identified 6 HAT genes and 10 HDAC genes. These genes displayed good synteny in genome loci with their Pyropia haitanensis orthologs except for a putative gene duplication event in HDAC and a loss of one HAT gene in P. yezoensis. According to the conserved domains and phylogenetic analysis, they encoded three GCNA5-, one TAFII250- and one MYST-HAT, as well as five HDA1-and five SIRT-HDACs. The sirtuin-domain of Py06502 harbored a ~100 aa insert and interestingly, this insertion was specifically observed in Bangiales species. Two nuclear-localized HATs were transcriptionally up-regulated at the early stage of dehydration and so were two nuclear HDA1s when moderate dehydration started, suggesting their potential roles in modulating downstream gene expression to facilitate dehydration adaptation by changing histone acetylation patterns on relevant regulatory elements. This was experimentally confirmed by the increased decline in photosynthesis efficiency during dehydration when HAT and HDAC activities were inhibited by SAHA and MB-3, respectively. Transcriptional patterns of multiple dehydration-responsive genes after water loss were strongly affected by MB-3 or SAHA treatment. This study provides the first insight into the regulation and function of HAT/HDAC during stress adaptation in red algae.

ChIP-Based Nuclear DNA Isolation for Genome Sequencing in Pyropia to Remove Cytosol and Bacterial DNA Contamination

Contamination from cytosolic DNA (plastid and mitochondrion) and epiphytic bacteria is challenging the efficiency and accuracy of genome-wide analysis of nori-producing marine seaweed Pyropia yezoensis. Unlike bacteria and organellar DNA, Pyropia nuclear DNA is closely associated with histone proteins. In this study, we applied Chromatin Immunoprecipitation (ChIP) of histone H3 to isolate nuclear DNA, followed by high-throughput sequencing. More than 99.41% of ChIP-sequencing data were successfully aligned to the reference nuclear genome; this was remarkably higher than those from direct extraction and direct extraction data, in which 40.96% to 42.95% are from plastids. The proportion of data that were mapped to the bacterial database when using ChIP extraction was very low. Additionally, ChIP data can cover up to 89.00% of the nuclear genome, higher than direct extraction data at equal data size and comparable to the latter at equal sequencing depth. The uncovered regions from the three methods are mostly overlapping, suggesting that incomplete sequencing accounts for the missing data, rather than failed chromatin-antibody binding in the ChIP extraction method. This ChIP extraction method can successfully separate nuclear DNA from cytosolic DNA and bacterial DNA, thus overwhelmingly reducing the sequencing cost in a genome resequencing project and providing strictly purified reference data for genome assembly. The method's applicability to other macroalgae makes it a valuable contribution to the algal research community.

The drifting and spreading mechanism of floating Ulva mass in the waterways of Subei shoal, the Yellow Sea of China - Application for abating the world's largest green tides

The large-scale green tides have been prevailing in the Yellow Sea over a decade. Prevention and control techniques in the source region (Subei Shoal) are urgently needed to minimize its adverse ecological and social impacts. Drifting and spreading mechanism of Ulva mass was investigated in the Subei Shoal in order to develop the early containment measures. The multidisciplinary surveys suggested twelve major waterways transporting the initial Ulva mass which was closely related to the basin topology and water circulation in the shoal. The epiphytic algal mass from the northern and eastern raft regions contributed 82.7 % of the initial floating biomass, and moved out in 4-6 days with an average drifting velocity of 0.28 m s^-1. Accordingly, two series of algae-blocking lines were proposed to remove floating mass from the shoal. And the primary field trial in 2018 confirmed the feasibility of this strategy to abate the green tides.

Overexpression of putative glutathione peroxidase from Neopyropia-associated microorganisms in Chlamydomonas to respond to abiotic stress

Lipid accumulation in microalgae can be substantially enhanced by exposing the microalgae to abiotic stress, thus increasing biofuel production. However, this also generates reactive oxygen species (ROS), which disrupts cell metabolism and reduces their productivity. Previous mRNA sequencing analyses in Neopyropia yezoensis and its associated microorganisms elucidated a putative glutathione peroxidase (PuGPx) gene. Here, this putative glutathione peroxidase was overexpressed in the microalga Chlamydomonas reinhardtii, which increased cell growth and survival rates compared to the control group under abiotic stress. Additionally, increased lipid accumulation was observed under salinity stress, high-temperature stress, and hydrogen peroxide (H₂O₂)-induced oxidative stress. These results suggest that PuGPx plays a protective role against abiotic stress in C. reinhardtii and stimulates lipid accumulation, which could be considered advantageous in terms of biofuel production.

Influences of environmental factors on the dissipation of green tides in the Yellow Sea, China

Green tides attack the Yellow Sea every year since 2007 and have caused substantial financial loss. Based on Haiyang-1C/Coastal zone imager (HY-1C/CZI) and Terra/MODIS satellite images, the temporal and spatial distribution of green tides floating in the Yellow Sea during 2019 was extracted. The relationships between the growth rate of the green tides and the environmental factors including sea surface temperature (SST), photosynthetically active radiation (PAR), sea surface salinity (SSS), nitrate and phosphate during the green tides' dissipation phase has been detected. Based on the maximum likelihood estimation, a regression model that includes SST, PAR and phosphate was recommended to predict the growth rate of the green tides in the dissipation phase (R² = 0.63), and this model was also examined using Bayesian information criterion and Akaike information criterion. When the average SST in the study area was above 23.6 °C, the coverage of green tides began to decrease with the increase in temperature under the influence of PAR. The growth rate of the green tides was related to SST (R = -0.38), PAR (R = -0.67) and phosphate (R = 0.40) in the dissipation phase. Compared with HY-1C/CZI, the green tide area extracted using Terra/MODIS tended to be underestimated when the green tide patches were smaller than 11.2 km². Otherwise, the lower spatial resolution of MODIS resulted in larger mixed pixels of water and algae, which would overestimate the total area of the green tides.

Life cycle and reproduction dynamics of Bangiales in response to environmental stresses

Red algae of the order Bangiales are notable for exhibiting flexible promotion of sexual and asexual reproductive processes by environmental stresses. This flexibility indicates that a trade-off between vegetative growth and reproduction occurs in response to environmental stresses that influence the timing of phase transition within the life cycle. Despite their high phylogenetic divergence, both filamentous and foliose red alga in the order Bangiales exhibit a haploid-diploid life cycle, with a haploid leafy or filamentous gametophyte (thallus) and a diploid filamentous sporophyte (conchocelis). Unlike haploid-diploid life cycles in other orders, the gametophyte in Bangiales is generated independently of meiosis; the regulation of this generation transition is not fully understood. Based on transcriptome and gene expression analyses, the originally proposed biphasic model for alternation of generations in Bangiales was recently updated to include a third stage. Along with the haploid gametophyte and diploid sporophyte, the triphasic framework recognizes a diploid conchosporophyte-a conchosporangium generated on the conchocelis-phase and previously considered to be part of the sporophyte. In addition to this sexual life cycle, some Bangiales species have an asexual life cycle in which vegetative cells of the thallus develop into haploid asexual spores, which are then released from the thallus to produce clonal thalli. Here, we summarize the current knowledge of the triphasic life cycle and life cycle trade-off in Neopyropia yezoensis and 'Bangia' sp. as model organisms for the Bangiales.

Histone acetylation functions in the wound-induced spore formation in nori

The red macroalgae Pyropia yezoensis is one of the most economically important marine crops. In the asexual reproduction process, released archeospores could provide secondary seedling resources in nori farming and be used to establish asexual seeding strategies. We previously found that wounds could induce the somatic cells in sectioned Pyropia thalli to develop into large number of asexual wound-induced spores (WIS) in a short time. Many genes involved in signaling pathways, cell division, cell wall remodeling, etc. exhibited transcriptional variation in this cell fate transition process. However, the regulatory mechanisms controlling gene transcription remain elusive. In this study, we found that suberoylanilide hydroxamic acid (SAHA), the inhibitor of histone deacetylase, strongly repressed WIS formation after wounding. The lack of a sharp increase in HDAC activity after wounding, as well as the hyperacetylated status of histone H3 and H4, were observed in SAHA-treated thalli fragments, thus confirming a histone deacetylation-related epigenetic mechanism of wound-induced cell fate reprogramming. Moreover, histone deacetylation is required in the whole process of WIS formation and release. We further compared the genome-wide transcriptional variations after SAHA treatment. SAHA-responsive genes were identified, including some transcriptional factors, chromatin remodeling complex proteins, protein kinases, etc. Transcription of RBOH genes was also altered by SAHA, and moreover, ROS signals in cut fragments were attenuated, both indicating that the ROS systematic signaling pathway is closely associated with histone deacetylation. Our findings provide insights into the biological significance of dynamic histone acetylation states in WIS formation in P. yezoensis.

The Identification of Filamentous Cyanobacteria Isolated from Neopyropia Germplasm Bank Illustrates the Pattern of Contamination

The germplasm bank of economic algae provides biological insurance against environmental changes and pressures for the cultivation industry. However, the red algal free-living conchocelis germplasm of Neopyropia was easily contaminated with filamentous cyanobacteria, which severely affected the growth of Neopyropia germplasm. To date, what and how the filamentous cyanobacteria contaminated Neopyropia germplasm remained unknown. Here, we combined cytological observations with light and electron microscopes and molecular analysis of the 16S rRNA gene to elucidate the pattern of cyanobacteria contamination. Nine filamentous cyanobacteria samples isolated from the Neopyropia germplasm bank were selected. Integrating microscopy observations and phylogenetic analyses of 16S rRNA gene sequences, nine cyanobacteria samples were divided into three groups, including two Leptolyngbya with red pigments (YCR1 and YCR2) and one Nodosilinea with green pigments (YCG3). They had the same asexual reproduction mode, releasing hormogonia to grow new filaments. Due to the high reproductive ability, Leptolyngbya and Nodosilinea were easy to spread in the Neopyropia germplasm. Based on 16S rRNA gene high-throughput sequencing analyses, we found the thallus of Neopyropia (NP1, NP2, and NP3) and surrounding seawater (SW1, SW2, and SW3) were enriched with cyanobacteria, especially with Leptolyngbya and Nodosilinea, indicating the filamentous cyanobacteria contaminated Neopyropia germplasm came from the thallus of Neopyropia or seawater. The results provided a better understanding of the prevention and control of cyanobacteria contamination in the Neopyropia germplasm bank.

Comparative Gene Expression and Physiological Analyses Reveal Molecular Mechanisms in Wound-Induced Spore Formation in the Edible Seaweed Nori

Genetic reprogramming of differentiated cells is studied broadly in multicellular Viridiplantae as an adaptation to herbivory or damage; however, mechanisms underlying cell development and redifferentiation are largely unknown in red algae, their nearest multicellular relatives. Here we investgate cell reprogramming in the widely cultivated, edible seaweed Neopyropia yezoesis ("nori"), where vegetative cells in wounded blades differentiate and release as large numbers of asexual spores. Based upon physiological changes and transcriptomic dynamics after wound stress in N. yezoensis and its congener Neoporphyra haitanensis, another cultivar that does not differentiate spores after wounding, we propose a three-phase model of wound-induced spore development in N. yezoensis. In Phase I, propagation of ROS by RBOH and SOD elicites systematic transduction of the wound signal, while Ca²⁺ dependent signaling induces cell reprogramming. In Phase II, a TOR signaling pathway and regulation of cyclin and CDK genes result in cell divisions that spread inward from the wound edge. Once sporangia form, Phase III involves expression of proteins required for spore maturation and cell wall softening. Our analyses not only provide the first model for core molecular processes controlling cellular reprogramming in rhodophytes, but also have practical implications for achieving greater control over seeding in commercial nori farming.

Development of Quantitative Real-Time PCR for Detecting Environmental DNA Derived from Marine Macrophytes and Its Application to a Field Survey in Hiroshima Bay, Japan

The sequestration and storage of carbon dioxide by marine macrophytes is called blue carbon; this ecosystem function of coastal marine ecosystems constitutes an important countermeasure to global climate change. The contribution of marine macrophytes to blue carbon requires a detailed examination of the organic carbon stock released by these macrophytes. Here, we introduce a quantitative real-time polymerase chain reaction (qPCR)-based environmental DNA (eDNA) system for the species-specific detection of marine macrophytes. and report its application in a field survey in Hiroshima Bay, Japan. A method of qPCR-based quantification was developed for mangrove, seagrass, Phaeophyceae, Rhodophyta and Chlorophyta species, or species-complex, collected from the Japanese coast to investigate their dynamics after they wither and die in the marine environment. A trial of the designed qPCR system was conducted using sediment samples from Hiroshima Bay. Ulva spp. were abundant in coastal areas of the bay, yet their eDNA in the sediments was scarce. In contrast, Zostera marina and the Sargassum subgenus Bactrophycus spp. were found at various sites in the bay, and high amounts of their eDNA were detected in the sediments. These results suggest that the fate of macrophyte-derived organic carbon after death varies among species.

Establishment of a Live-Imaging Analysis for Polarized Growth of Conchocelis in the Multicellular Red Alga Neopyropia yezoensis

A wide range of tip-growing cells in plants display polarized cell growth, which is an essential cellular process for the form and function of individual cells. Understanding of the regulatory mechanisms underlying tip growth in terrestrial plants has improved. Cellular processes involved in tip growth have also been investigated in some algae species that form filamentous cells, but their regulatory mechanisms remain unclear. In the macro red alga Neopyropia yezoensis, for which genome information has recently been released, the conchocelis apical cell exhibits tip growth and forms a filamentous structure. Here, we report a live-imaging technique using high-resolution microscopy to analyze the tip growth and cell division of N. yezoensis conchocelis. This imaging analysis addressed tip growth dynamics and cell division in conchocelis apical cells. The directionality and tip growth expansion were disrupted by the application of cytoskeletal drugs, suggesting the involvement of microtubules (MTs) and actin filaments (AFs) in these processes. A growing apical cell mostly contained a single chloroplast that moved toward the expanding part of the apical cell. Drug application also inhibited chloroplast movement, implying that the movement may be dependent on the cytoskeleton. The study determined that live-imaging analysis is a versatile approach for exploring the dynamics of tip growth and cell division in N. yezoensis conchocelis, which provides insights into the regulatory mechanisms underlying cellular growth in multicellular red algae.

Insights into the Ancient Adaptation to Intertidal Environments by Red Algae Based on a Genomic and Multiomics Investigation of Neoporphyra haitanensis

Colonization of land from marine environments was a major transition for biological life on Earth, and intertidal adaptation was a key evolutionary event in the transition from marine- to land-based lifestyles. Multicellular intertidal red algae exhibit the earliest, systematic, and successful adaptation to intertidal environments, with Porphyra sensu lato (Bangiales, Rhodophyta) being a typical example. Here, a chromosome-level 49.67 Mb genome for Neoporphyra haitanensis comprising 9,496 gene loci is described based on metagenome-Hi-C-assisted whole-genome assembly, which allowed the isolation of epiphytic bacterial genome sequences from a seaweed genome for the first time. The compact, function-rich N. haitanensis genome revealed that ancestral lineages of red algae share common horizontal gene transfer events and close relationships with epiphytic bacterial populations. Specifically, the ancestor of N. haitanensis obtained unique lipoxygenase family genes from bacteria for complex chemical defense, carbonic anhydrases for survival in shell-borne conchocelis lifestyle stages, and numerous genes involved in stress tolerance. Combined proteomic, transcriptomic, and metabolomic analyses revealed complex regulation of rapid responses to intertidal dehydration/rehydration cycling within N. haitanensis. These adaptations include rapid regulation of its photosynthetic system, a readily available capacity to utilize ribosomal stores, increased methylation activity to rapidly synthesize proteins, and a strong anti-oxidation system to dissipate excess redox energy upon exposure to air. These novel insights into the unique adaptations of red algae to intertidal lifestyles inform our understanding of adaptations to intertidal ecosystems and the unique evolutionary steps required for intertidal colonization by biological life.

Detection and Characterization of RNA Viruses in Red Macroalgae (Bangiaceae) and Their Food Product (Nori Sheets)

Persistent RNA viruses, which have been suggested to form symbiotic relationships with their hosts, have been reported to occur in eukaryotes, such as plants, fungi, and algae. Based on empirical findings, these viruses may also be present in commercially cultivated macroalgae. Accordingly, the present study aimed to screen red macroalgae (family Bangiaceae conchocelis and Neopyropia yezoensis thallus) and processed nori sheets (N. yezoensis) for persistent RNA viruses using fragmented and primer-ligated dsRNA sequencing (FLDS) and targeted reverse transcription PCR (RT-PCR). A Totiviridae-related virus was detected in the conchocelis of Neoporphyra haitanensis, which is widely cultivated in China, while two Mitoviridae-related viruses were found in several conchocelis samples and all N. yezoensis-derived samples (thallus and nori sheets). Mitoviridae-related viruses in N. yezoensis are widespread among cultivated species and not expected to inhibit host growth. Mitoviridae-related viruses were also detected in several phylogenetically distant species in the family Bangiaceae, which suggests that these viruses persisted and coexist in the family Bangiaceae over a long period of time. The present study is the first to report persistent RNA viruses in nori sheets and their raw materials.

Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution

Accurate species identification often relies on public repositories to compare the barcode sequences of the investigated individual(s) with taxonomically assigned sequences. However, the accuracy of identifications in public repositories is often questionable, and the names originally given are rarely updated. For instance, species of the Sea Lettuce (Ulva spp.; Ulvophyceae, Ulvales, Ulvaceae) are frequently misidentified in public repositories, including herbaria and gene banks, making species identification based on traditional barcoding unreliable. We DNA barcoded 295 individual distromatic foliose strains of Ulva from the North-East Atlantic for three loci (rbcL, tufA, ITS1). Seven distinct species were found, and we compared our results with all worldwide Ulva spp. sequences present in the NCBI database for the three barcodes rbcL, tufA and the ITS1. Our results demonstrate a large degree of species misidentification, where we estimate that 24%-32% of the entries pertaining to foliose species are misannotated and provide an exhaustive list of NCBI sequences reannotations. An analysis of the global distribution of registered samples from foliose species also indicates possible geographical isolation for some species, and the absence of U. lactuca from Northern Europe. We extended our analytical framework to three other genera, Fucus, Porphyra and Pyropia and also identified erroneously labelled accessions and possibly new synonymies, albeit less than for Ulva spp. Altogether, exhaustive taxonomic clarification by aggregation of a library of barcode sequences highlights misannotations and delivers an improved representation of species diversity and distribution.

Cytoskeletal diversification across 1 billion years: What red algae can teach us about the cytoskeleton, and vice versa

The cytoskeleton has a central role in eukaryotic biology, enabling cells to organize internally, polarize, and translocate. Studying cytoskeletal machinery across the tree of life can identify common elements, illuminate fundamental mechanisms, and provide insight into processes specific to less-characterized organisms. Red algae represent an ancient lineage that is diverse, ecologically significant, and biomedically relevant. Recent genomic analysis shows that red algae have a surprising paucity of cytoskeletal elements, particularly molecular motors. Here, we review the genomic and cell biological evidence and propose testable models of how red algal cells might perform processes including cell motility, cytokinesis, intracellular transport, and secretion, given their reduced cytoskeletons. In addition to enhancing understanding of red algae and lineages that evolved from red algal endosymbioses (e.g., apicomplexan parasites), these ideas may also provide insight into cytoskeletal processes in animal cells.

Characterization of ACE Inhibitory Peptides Prepared from Pyropia pseudolinearis Protein

More than 7000 red algae species have been classified. Although most of them are underused, they are a protein-rich marine resource. The hydrolysates of red algal proteins are good candidates for the inhibition of the angiotensin-I-converting enzyme (ACE). The ACE is one of the key factors for cardiovascular disease, and the inhibition of ACE activity is related to the prevention of high blood pressure. To better understand the relationship between the hydrolysates of red algal proteins and the inhibition of ACE activity, we attempted to identify novel ACE inhibitory peptides from Pyropia pseudolinearis. We prepared water soluble proteins (WSP) containing phycoerythrin, phycocyanin, allophycocyanin, and ribulose 1,5-bisphosphate carboxylase/oxygenase. In vitro analysis showed that the thermolysin hydrolysate of the WSP had high ACE inhibitory activity compared to that of WSP. We then identified 42 peptides in the hydrolysate by high-performance liquid chromatography and mass spectrometry. Among 42 peptides, 23 peptides were found in chloroplast proteins. We then synthesized the uncharacterized peptides ARY, YLR, and LRM and measured the ACE inhibitory activity. LRM showed a low IC₅₀ value (0.15 μmol) compared to ARY and YLR (1.3 and 5.8 μmol). In silico analysis revealed that the LRM sequence was conserved in cpcA from Bangiales and Florideophyceae, indicating that the novel ACE inhibitory peptide LRM was highly conserved in red algae.

Comparative Quantitative Proteomics Reveals the Desiccation Stress Responses of the Intertidal Seaweed NEOPORPHYRA haitanensis

Neoporphyra haitanensis is an economically important red seaweed that inhabits upper intertidal zones. The thallus tolerates extreme fluctuating environmental stresses (e.g., surviving more than 80% water loss during low tides). To elucidate the global molecular responses relevant to this outstanding desiccation tolerance, a quantitative proteomics analysis of N. haitanensis under different desiccation treatments as well as rehydration was performed. According to the clustering of expression patterns and the functional interpretation of the 483 significantly differentially expressed proteins, a three-stage cellular response to desiccation stress and subsequent rehydration was proposed. Stage I: at the beginning of water loss, multiple signal transduction pathways were triggered including lipid signaling, protein phosphorylation cascades, and histone acetylation controlling acetate biosynthesis to further modulate downstream hormone signaling. Protein protection by peptidyl-prolyl isomerase and ROS scavenging systems were also immediately switched on. Stage II: with the aggravation of stress, increases in antioxidant systems, the accumulation of LEA proteins, and the temporary biosynthesis of branched starch were observed. Multiple enzymes involved in redox homeostasis, including peroxiredoxin, thioredoxin, ascorbate peroxidase, superoxide dismutase, glutathione peroxidase, and glutathione reductase, were hypothesized to function in specific cellular compartments. Stage III: when the desiccated thalli had rehydrated for 30 mins, photosynthesis and carbon fixation were recovered, and antioxidant activities and protein structure protection were maintained at a high level. This work increases the understanding of the molecular responses to environmental stresses via a proteomic approach in red seaweeds and paves the way for further functional studies and genetic engineering.