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In the life cycle of Neopyropia yezoensis, a potential model system for marine macroalgae, both of asexual archeospores and meiosis-related conchospores develop into thalli (gametophyte). To understand this special life phenomenon in macroalgae, we picked out the two kinds of spores (10-30 cells in each sample) and conducted RNA-seq using Smart-seq2. Comparative analysis showed that light capture and carbon fixation associated differentially expressed genes (DEGs) were upregulated in archeospores, thus indicating that archeospores are in a state of rapid vegetative growth. In conchospores, protein synthesis and degradation, especially molecular chaperone, associated DEGs were upregulated, indicating the complex life activities might be occurred in conchospores. There were 68 genes related to DNA replication and repair expressed in conchospores, showing that active DNA replication might occur in conchospores. Moreover, we found that one conchospore specifically expressed DEG (py04595: DNA helicase) was only expressed in diploid stage (conchocelis, sporangial filament) and three archeospore specifically expressed DEGs were only expressed in haploid stage (thalli). These molecular level results indicated that conchospores were closer to diploid, and might be the meiotic mother cells of N. yezoensis. In addition, we found that the knotted-like homeobox gene (PyKNOX), which might relate to the transition of gametophyte from sporophyte, was only expressed in sporophyte generation but not expressed in conchospores, archeospores and thalli, indicating the morphogenesis of gametophyte in N. yezoensis might require the inactivation of PyKNOX.

The red macroalga Pyropia yezoensis is an economically important seaweed widely cultured in Asian countries and is a model organism for molecular biological and commercial research. This species is unique in that it utilizes both phycobilisomes and transmembrane light-harvesting proteins as its antenna system. Here, one of the genes of P. yezoensis (PyLHCI) was selected for introduction into its genome to overexpress PyLHCI. However, the co-suppression phenomenon occurred. This is the first documentation of co-suppression in algae, in which it exhibits a different mechanism from that in higher plants. The transformant (T1) was demonstrated to have higher phycobilisomes and lower LHC binding pigments, resulting in a redder color, higher sensitivity to salt stress, smaller in size, and slower growth rate than the wildtype (WT). The photosynthetic performances of T1 and WT showed similar characteristics; however, P700 reduction was slower in T1. Most importantly, T1 could release a high percentage of carpospores in young blades to switch generation during its life cycle, which was rarely seen in WT. The co-suppression of PyLHCI revealed its key roles in light harvesting, stress resistance, and generation alternation (generation switch from gametophytes to sporophytes, and reproduction from asexual to sexual).

Phytoene and astaxanthin are 2 important carotenoids in the green alga Haematococcus pluvialis. Under environmental stress, the synthesis of phytoene in H. pluvialis increases significantly, and phytoene is converted to astaxanthin through enzymatic catalysis. This paper analyzes the relationship between astaxanthin and phytoene accumulation in carotenoid synthesis pathways under different concentrations of sodium acetate (NaAc) by high-performance liquid chromatography. The highest concentrations of phytoene and astaxanthin were observed at the NaAc concentration of 6 g l-1 on the 12th day of induction. The highest astaxanthin concentration achieved was 2.26 ± 0.28%. Therefore, we concluded that 6 g l-1 NaAc and induction for 12 d provided the optimal inducing conditions for astaxanthin accumulation in H. pluvialis. psy, pds, lcyB, β-carotene ketolase crtw, and crtz, which are genes related to phytoene and astaxanthin synthesis, were cloned and studied at the transcriptional level. crtw and crtz were continuously up-regulated since the first day of induction, while psy, pds, and lcyB were continuously up-regulated starting on the 3rd day of induction. These findings are important for enhancing our understanding of the mechanism of accumulation of phytoene and astaxanthin in H. pluvialis and provide a foundation for identifying the induction conditions necessary for optimizing astaxanthin production and increasing astaxanthin yields.

Haematococcus pluvialis has attracted attention due to its ability to produce astaxanthin, which has many functions such as antioxidation and anticancer. In order to further understand its nitrogen metabolism, the transcription levels and the enzyme levels of glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH) in the process of nitrogen assimilation were studied under different nitrogen concentrations after cloning their cDNA sequences. The cloned cDNA sequence of gs is 1438 bp, including a 178-bp 5′ untranslatable region (UTR), a 114-bp 3′ UTR, and a 1146-bp open reading frame (ORF), which encodes a protein of 381 amino acids. The gogat had a total cDNA of 4931 bp, including a 17-bp 5′ UTR and a 4914-bp ORF, which encodes a protein of 1637 amino acids. The gdh had a total cDNA of 1529 bp, including 131-bp 3′ UTR and a 1398-bp ORF, which encodes a protein of 465 amino acids. During cultivation the transcription levels of the three genes fluctuated slightly during the first 4 days and then declined significantly. At the fourth day, the highest level of the transcription of the three genes was at the nitrogen concentration of 1000 mg L−1. The enzyme level also fluctuated with culture time, which is positively correlated with the transcription level. This study may lay foundation for optimization of nitrogen concentration for cultivation of H. pluvialis.

Neopyropia yezoensis, an important marine crop, reproduces via sporangial filaments. This special sporophyte stage, which directly releases conchospores—the “seed” of gametophytes (thalli)—is poorly understood. Under free-living culture, we found sporangial filaments varied between hollow cells (at high density) and content-enriched bipartite cells (at low density), released as conchospores. Serious intracellular degradation, which might through fusion of a double-membrane coated body with vacuole, was observed in hollow cells but disappeared in newly-formed bipartite cells and reappeared in their subsequent vegetative growth through transmission electron microscope. The bipartite cells can also return to vegetative growth when not released and the conchospores release was obviously inhibited by some growth promoting conditions such as high light (40–100 μmol photons m−2 s−1) and treatment with ampicillin and streptomycin. Based on these results, we summarized that conchopsore release was inhibited by the vegetative growth of bipartite cells and the cell hollowing caused by vacuole-based intracellular degradation in sporangial filaments. These results would increase understanding of sporangial filament development and conchospores release in N. yezoensis.

The previous study revealed that the mutant strain E thalli of Pyropia yezoensis had growth advantage compared with the initial strain NA, and transcriptome analysis revealed the relevant bioprocesses for improved growth. To investigate the growth mechanism at the protein level, this study used isobaric tags for relative and absolute quantification and liquid chromatography-mass spectrometry to analyze proteome of both strains. In total, 277 proteins were identified, among which 41 differentially expressed proteins were screened, including 22 up-regulated proteins and 19 down-regulated proteins. Integrated analysis of proteome and previous transcriptome showed that the proteins related to photosynthesis, protein biosynthesis, glycolysis, and pentose phosphate pathway were enhanced in mutant strain E, which were supposed to facilitate growth of mutant strain E, and the proteins relevant to stress resistance were up-regulated, which might promote the growth of mutant strain E under abiotic stresses, while proteins related to methylation were decreased, which might enhance the expression of growth relevant genes in mutant strain E. This study revealed the growth mechanism in mutant strain E by integrated omics analysis, and also provided theoretical foundation for molecular breeding of Py. yezoensis.

Haematococcus pluvialis is an economic microalga to produce astaxathin. To study the nitrogen metabolic process of H. pluvialis, the transcription level and enzyme content of nitrite reductase at different nitrate and phosphorus concentrations were studied. In this research, nitrite reductase gene (nir) was first cloned from H. pluvialis, which consists of 5592 nucleotides and includes 12 introns. The cDNA ORF is 1776 bp, encoding a 592 amino acid protein with two conserved domains. Phylogenetic analysis showed that the nir gene in H. pluvialis had the highest affinity with other freshwater green algae. Nitrogen and phosphorus play an important role in the growth of H. pluvialis. The single factor experiments of nitrogen on growth conditions showed that the group with 0.2 g/L NaNO3 had a relative high biomass. The single factor experiments of phosphorus on growth conditions showed that the group with 0.06 g/L K2HPO4 had a relative high biomass. The transcription level and enzymatic activity of nitrite reductase were detected at different nitrate and phosphorus concentrations. In the absence of nitrogen and phosphorus in the medium, nitrite reductase activity is the highest. This research provides theoretical guidance for optimization of culture medium for H. pluvialis and also provides an experimental basis for understanding of nitrogen metabolism pathway in H. pluvialis.

Haematococcus pluvialis is a commercial microalga, that produces abundant levels of astaxanthin under stress conditions. Acetate and Fe2+ are reported to be important for astaxanthin accumulation in H. pluvialis. In order to study the synergistic effects of high light stress and these two factors, we obtained transcriptomes for four groups: high light irradiation (HL), addition of 25 mM acetate under high light (HA), addition of 20 μM Fe2+ under high light (HF) and normal green growing cells (HG). Among the total clean reads of the four groups, 156,992 unigenes were found, of which 48.88% were annotated in at least one database (Nr, Nt, Pfam, KOG/COG, SwissProt, KEGG, GO). The statistics for DEGs (differentially expressed genes) showed that there were more than 10 thousand DEGs caused by high light and 1800–1900 DEGs caused by acetate or Fe2+. The results of DEG analysis by GO and KEGG enrichments showed that, under the high light condition, the expression of genes related to many pathways had changed, such as the pathway for carotenoid biosynthesis, fatty acid elongation, photosynthesis-antenna proteins, carbon fixation in photosynthetic organisms and so on. Addition of acetate under high light significantly promoted the expression of key genes related to the pathways for carotenoid biosynthesis and fatty acid elongation. Furthermore, acetate could obviously inhibit the expression of genes related to the pathway for photosynthesis-antenna proteins. For addition of Fe2+, the genes related to photosynthesis-antenna proteins were promoted significantly and there was no obvious change in the gene expressions related to carotenoid and fatty acid synthesis.

Haematococcus pluvialis is a commercial microalga, that produces abundant levels of astaxanthin under stress conditions. Acetate and Fe2+ are reported to be important for astaxanthin accumulation in H. pluvialis. In order to study the synergistic effects of high light stress and these two factors, we obtained transcriptomes for four groups: high light irradiation (HL), addition of 25 mM acetate under high light (HA), addition of 20 μM Fe2+ under high light (HF) and normal green growing cells (HG). Among the total clean reads of the four groups, 156,992 unigenes were found, of which 48.88% were annotated in at least one database (Nr, Nt, Pfam, KOG/COG, SwissProt, KEGG, GO). The statistics for DEGs (differentially expressed genes) showed that there were more than 10 thousand DEGs caused by high light and 1800–1900 DEGs caused by acetate or Fe2+. The results of DEG analysis by GO and KEGG enrichments showed that, under the high light condition, the expression of genes related to many pathways had changed, such as the pathway for carotenoid biosynthesis, fatty acid elongation, photosynthesis-antenna proteins, carbon fixation in photosynthetic organisms and so on. Addition of acetate under high light significantly promoted the expression of key genes related to the pathways for carotenoid biosynthesis and fatty acid elongation. Furthermore, acetate could obviously inhibit the expression of genes related to the pathway for photosynthesis-antenna proteins. For addition of Fe2+, the genes related to photosynthesis-antenna proteins were promoted significantly and there was no obvious change in the gene expressions related to carotenoid and fatty acid synthesis.

To optimize the cultivation media for the growth rate of Haematococcus pluvialis and to study the transcription regulation of the algal nitrate reductase (NR), a key enzyme for nitrogen metabolism.The NR gene from H. pluvialis hd7 consists of 5636 nucleotides, including 14 introns. The cDNA ORF is 2718 bp, encoding a 905 aa protein with three conserved domains. The NR amino acids of H. pluvialis hd7 are hydrophilic and have similarity of 72% compared to that of Dunaliella. NR transcription increased with an increase of nitrate concentration from 0.4 to 1 g/l. A deficiency of nitrogen increased NR transcription significantly. The transcription level of NR increased at phosphorus concentrations from 0.08 to 0.2 g/l, with a maximum at 0.08 g/l. The optimum parameters of medium component for transcription of NR and growth of H. pluvialis were 0.3 g NaNOThis study provides a better understanding of nitrate regulation in H. pluvialis.

Gracilariopsis lemaneiformis (aka Gracilaria lemaneiformis) is a red macroalga rich in phycoerythrin, which can capture light efficiently and transfer it to photosystemⅡ. However, little is known about the synthesis of optically active phycoerythrinin in G. lemaneiformis at the molecular level. With the advent of high-throughput sequencing technology, analysis of genetic information for G. lemaneiformis by transcriptome sequencing is an effective means to get a deeper insight into the molecular mechanism of phycoerythrin synthesis. Illumina technology was employed to sequence the transcriptome of two strains of G. lemaneiformis- the wild type and a green-pigmented mutant. We obtained a total of 86915 assembled unigenes as a reference gene set, and 42884 unigenes were annotated in at least one public database. Taking the above transcriptome sequencing as a reference gene set, 4041 differentially expressed genes were screened to analyze and compare the gene expression profiles of the wild type and green mutant. By GO and KEGG pathway analysis, we concluded that three factors, including a reduction in the expression level of apo-phycoerythrin, an increase of chlorophyll light-harvesting complex synthesis, and reduction of phycoerythrobilin by competitive inhibition, caused the reduction of optically active phycoerythrin in the green-pigmented mutant.