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Sea cucumbers play an important role in sediment bioturbation in coral reef and rocky intertidal ecosystems, and bacteria were a commonly-reported component of holothuroid diets. Bacterial community composition in the foregut and hindgut of two common tropical sea cucumbers (Holothuria atra and H. leucospilota) and the ambient surface sediment were investigated using high throughput sequencing based on 16S rRNA gene analysis. A total of 5 584 operational taxonomic units (OTUs) were obtained from 25 samples based on a 97% threshold, and more than half of the OTUs (n=3 694, 66.2%) were shared by the gut contents of two species of sea cucumbers and surrounding sediments. Bacterial richness and diversity in sediment samples were significantly higher than those in the gut content samples (P

Giant clams Tridacna crocea harbor symbiotic zooxanthellae in tubular systems and display high growth rate when exposed to light. Light/dark alternation plays an important role in growth performance and physiological change of giant clam–zooxanthellae symbiosis in natural ecosystems. In this study, photosynthetic performance, antioxidant enzymes, transcriptome, and expression of eight illumination-related genes were investigated in the mantle of giant clam at different treatment times of 12-h light/12-h dark (15,000 lx). (1) The effective photochemical quantum yield of PSII (Y(II)) was high in the early morning, but significantly decreased to a low level at 6 h of light treatment (P

Biomorphic 2D Co3O4 nanosheets/mesoporous carbon microtube composites are solvothermally prepared and subsequently calcined using ramie as a biotemplate. The as-prepared composites are fabricated using two sides of Co3O4 nanosheets (NSs) supported on porous carbon microtubes and exhibit a unique tubular morphology and porous features. The present biomorphic materials show a specific capacitance of 1280.6 F g−1 at 1 A g−1, and outstanding charge–discharge cycle stability with a capacitance retention of 96.89% after 15 000 cycles. The remarkable pseudocapacitive performance and cyclability are attributed to the unique microstructure, the high specific surface area and the optimized hierarchical microstructure inherited from the biotemplate.

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.

Background Pyropia yezoensis (Rhodophyta) is widely cultivated in East Asia and plays important economic, ecological and research roles. Although inorganic carbon utilization of P. yezoensis has been investigated from a physiological aspect, the carbon concentration mechanism (CCM) of P. yezoensis remains unclear. To explore the CCM of P. yezoensis, especially during its different life stages, we tracked changes in the transcriptome, photosynthetic efficiency and in key enzyme activities under different inorganic carbon concentrations. Results Photosynthetic efficiency demonstrated that sporophytes were more sensitive to low carbon (LC) than gametophytes, with increased photosynthesis rate during both life stages under high carbon (HC) compared to normal carbon (NC) conditions. The amount of starch and number of plastoglobuli in cells corresponded with the growth reaction to different inorganic carbon (Ci) concentrations. We constructed 18 cDNA libraries from 18 samples (three biological replicates per Ci treatment at two life cycles stages) and sequenced these using the Illumina platform. De novo assembly generated 182,564 unigenes, including approximately 275 unigenes related to CCM. Most genes encoding internal carbonic anhydrase (CA) and bicarbonate transporters involved in the biophysical CCM pathway were induced under LC in comparison with NC, with transcript abundance of some PyCAs in gametophytes typically higher than that in sporophytes. We identified all key genes participating in the C4 pathway and showed that their RNA abundances changed with varying Ci conditions. High decarboxylating activity of PEPCKase and low PEPCase activity were observed in P. yezoensis. Activities of other key enzymes involved in the C4-like pathway were higher under HC than under the other two conditions. Pyruvate carboxylase (PYC) showed higher carboxylation activity than PEPC under these Ci conditions. Isocitrate lyase (ICL) showed high activity, but the activity of malate synthase (MS) was very low. Conclusion We elucidated the CCM of P. yezoensis from transcriptome and enzyme activity levels. All results indicated at least two types of CCM in P. yezoensis, one involving CA and an anion exchanger (transporter), and a second, C4-like pathway belonging to the PEPCK subtype. PYC may play the main carboxylation role in this C4-like pathway, which functions in both the sporophyte and gametophyte life cycles.

Additional file 1: Table S1. Statistics of quality control on RNA-seq data of gametophytes and sporophytes samples of P. yezoensis under different Ci conditions.

Additional file 2: Figure S1. Sequence length distribution of transcriptome.

Additional file 4: Table S3. The identity value and subtype of some unigenes of P. yezoensis involved in biochemical and biophysical CCM.

Additional file 6: Table S5. Primers used for qRT-PCR.

Additional file 5: Table S4. Predicted subcellular localization of some unigenes which encoding the key enzymes involved in biochemical and biophysical CCM in P.yezoensis. The analysis is based on predictions from various computational programs. Abbreviations: Y: Yes; -, not detected; C, chloroplast; M, mitochondrion; O, other; SP, signal peptide.

Additional file 3: Table S2. Summary of P. yezoensis transcriptome.

Pyropia haitanensis has prominent stress-resistance characteristics and is endemic to China. Studies into the stress responses in these algae could provide valuable information on the stress-response mechanisms in the intertidal Rhodophyta. Here, the effects of salinity and light intensity on the quantum yield of photosystem II in Py. haitanensis were investigated using pulse-amplitude-modulation fluorometry. Total RNA and genomic DNA of the samples under different stress conditions were isolated. By normalizing to the genomic DNA quantity, the RNA content in each sample was evaluated. The cDNA was synthesized and the expression levels of seven potential internal control genes were evaluated using qRT-PCR method. Then, we used geNorm, a common statistical algorithm, to analyze the qRT-PCR data of seven reference genes. Potential genes that may constantly be expressed under different conditions were selected, and these genes showed stable expression levels in samples under a salinity treatment, while tubulin, glyceraldehyde-3-phosphate dehydrogenase and actin showed stability in samples stressed by strong light. Based on the results of the pulse amplitude-modulation fluorometry, an absolute quantification was performed to obtain gene copy numbers in certain stress-treated samples. The stably expressed genes as determined by the absolute quantification in certain samples conformed to the results of the geNorm screening. Based on the results of the software analysis and absolute quantification, we proposed that elongation factor 3 and 18S ribosomal RNA could be used as internal control genes when the Py. haitanensis blades were subjected to salinity stress, and that α-tubulin and 18S ribosomal RNA could be used as the internal control genes when the stress was from strong light. In general, our findings provide a convenient reference for the selection of internal control genes when designing experiments related to stress responses in Py. haitanensis.

Photoprotection mechanisms protect photosynthetic organisms, especially under stress conditions, against photodamage that may inhibit photosynthesis. We investigated the effects of short-term immersion in hypo- and hypersalinity sea water on the photosynthesis and xanthophyll cycle in Sargassum fusiforme (Harvey) Setchell. The results indicated that under moderate light [110 mu mol(photon) m(-2) s(-1)], the effective quantum yield of PSII was not reduced in S. fusiforme fronds after 1 h in hyposalinity conditions, even in fresh water, but it was significantly affected by extreme hypersalinity treatment (90aEuro degrees sea water). Under high light [HL, 800 mu mol(photon) m(-2) s(-1)], photoprotective mechanisms operated efficiently in fronds immersed in fresh water as indicated by high reversible nonphotochemical quenching of chlorophyll fluorescence (NPQ) and de-epoxidation state; the quantum yield of PSII recovered during the subsequent relaxation period. In contrast, fronds immersed in 90aEuro degrees sea water did not withstand HL, barely developed reversible NPQ, and accumulated little antheraxanthin and zeaxanthin during HL, while recovery of the quantum yield of PSII was severely inhibited during the subsequent relaxation period. The data provided concrete evidence supporting the short-term tolerance of S. fusiforme to immersion in fresh water compared to hypersalinity conditions. The potential practical implications of these results were also discussed.

This study investigated the large-scale use of the red macroalga Gracilaria tenuistipitata to extract partially purified R-phycoerythrin in combination with the sequential extraction of agar. The main objective was to investigate the purification of R-PE, the extraction of agar and treatment of wastewater from the whole extraction process using the green macroalga Ulva prolifera. Results showed that the processing of 1 kg fresh biomass of G. tenuistipitata yielded a 30.34 μg/g R-phycoerythrin (purification ratio > 4) with 13.83% extraction efficiency. Initial phycobiliprotein extraction had no effect on the agar yield. The physicochemical properties of the agar had industrial applications. This method of extraction reduced the water volume and alkali requirement compared with that from direct extraction from algae. In addition, the removal rates (mean ± standard deviation) from wastewater of BOD, COD, total nitrogen, inorganic nitrogen, ammonia nitrogen, nitrate, nitrite, total phosphorus and inorganic phosphorus were 28.34 ± 0.10%, 23.50 ± 3.47%, 45.59 ± 6.31%, 63.82 ± 2.94%, 40.77 ± 0.95%, 74.06 ± 5.63%, 70.37 ± 2.59%, 65.26 ± 5.77%, and 72.40 ± 5.43% after the treatment with 2 days respectively. This extraction and subsequently eco-friendly wastewater treatment method could have practical application in the agar industry.

Light drives photosynthesis but may also cause photodamage. Oxygenic photosynthetic organisms have evolved various photoprotective responses to adapt to excessive light. Zeaxanthin and its precursor, β-carotene, play key photoprotective roles in higher plants and in most algae; however, it remains unclear if they are also involved in photoprotective responses in red algae. Here, we report that the concentrations of β-carotene and zeaxanthin increased significantly in response to high light conditions in Pyropia yezoensis (Bangiales, Rhodophyta) sporophytes. However, the response was relatively minor, and the accumulated zeaxanthin did not reduce when the stress was eliminated. The accumulation of β-carotene and zeaxanthin in P. yezoensis was accompanied with variations in non-photochemical quenching kinetics when the sporophytes were subjected to high light stress. We cloned the cDNAs encoding lycopene ϵ-cyclase and β-carotene hydroxylase in P. yezoensis, and quantified their expression levels. Our results suggested that the accumulation of β-carotene and zeaxanthin was attributed to the reduced expression levels of lycopene ϵ-cyclase and increased expression levels of β-carotene hydroxylase. Therefore, we propose that although red algae have evolved a common response to high light stress by accumulating β-carotene and zeaxanthin, the mechanism is not as flexible as in higher plants and other algae using the xanthophyll cycle. Rather than binding to PSII as in higher plants and other algae, the accumulated zeaxanthin may bind to PSI-light harvesting complex I in P. yezoensis, and in turn protect PSI against high light-induced photodamage.

Cell penetrating peptides (CPPs) are effective molecular tools that can deliver various exogenous cargoes into different types of cells. However, no study to date has evaluated the use of CPPs to import nucleic acid substances into microalgae, which would be advantageous for numerous research and commercial applications. In this study, we tested the ability of nona-(L)-arginine (R9) to conduct CPP-mediated double-stranded RNA (dsRNA) translocations into four microalgal species (Chlamydomonas reinhardtii, Chlorella vulgaris, Phaeodactylum tricornutum, and Dunaliella salina). R9 successfully transported dsRNA into D. salina, whereas dsRNA internalizations were not detected in the other three algal species. Calcofluor white staining showed that the cell wall structure of D. salina differs from that of the other three species. These results indicate that the efficiency of CPP-mediated dsRNA transductions is closely related to algal cell wall structures, which vary in their ability to block entry of the CPP/ dsRNA complex. (C) 2015 Elsevier B.V. All rights reserved.

China is rich in seaweed resources and is currently the largest seaweed producer in the world. The current study identified and investigated the geographical distribution of economically important red seaweed species around the Chinese coast, all of which are potential candidates for development in the seaweed farming industry. The study also highlighted progress made in research related to red seaweed farming in China. Farming of Pyropia and Gracilaria species continues to show steady growth, although with the occasional emergence of biological or ecological stresses. However, farming of eucheumatoid species is facing challenges because of devastating diseases and, therefore, we propose that the ‘seedling problem’ is a major obstacle in the cultivation of agarophytes and carrageenanophytes. Integrated multitrophic aquaculture systems and modern marine ranching represent the future direction of the aquaculture industry, represented by high outputs and ecologically friendly processes; seaweed farming is also likely to be able to supply feedstock for the future production of bioactive compounds and bioethanol. Overall, the utilization of red seaweeds in China is converting from traditional scattered domestic uses to modern large-scale commercial uses; thus, such high-efficiency and high-value utilization represent the future for red seaweeds in China.

To screen the stable expression genes related to the stress (strong light, dehydration and temperature shock) we applied Absolute real-time PCR technology to determine the transcription numbers of the selected test genes in Porphyra yezoensis, which has been regarded as a potential model species responding the stress conditions in the intertidal. Absolute real-time PCR technology was applied to determine the transcription numbers of the selected test genes in Porphyra yezoensis, which has been regarded as a potential model species in stress responding. According to the results of photosynthesis parameters, we observed that Y(II) and F-v/F-m were significantly affected when stress was imposed on the thalli of Porphyra yezoensis, but underwent almost completely recovered under normal conditions, which were collected for the following experiments. Then three samples, which were treated with different grade stresses combined with salinity, irradiation and temperature, were collected. The transcription numbers of seven constitutive expression genes in above samples were determined after RNA extraction and cDNA synthesis. Finally, a general insight into the selection of internal control genes during stress response was obtained. We found that there were no obvious effects in terms of salinity stress (at salinity 90) on transcription of most genes used in the study. The 18S ribosomal RNA gene had the highest expression level, varying remarkably among different tested groups. RPS8 expression showed a high irregular variance between samples. GAPDH presented comparatively stable expression and could thus be selected as the internal control. EF-1 alpha showed stable expression during the series of multiple-stress tests. Our research provided available references for the selection of internal control genes for transcripts determination of P. yezoensis.

Gloiopeltis furcata (Postels & Ruprecht) J. Agardh, a macroalga, which grows in an upper, intertidal zone, can withstand drastic environmental changes caused by the periodic tides. In this study, the photosynthetic and morphological characteristics of G. furcata were investigated. The photosynthetic performance and electron flows of the thalli showed significant variations in response to desiccation and salinity compared with the control group. Both PSII and PSI activities declined gradually when the thalli were under stress. However, the electron transport rate of PSI showed still a low value during severe conditions, while the rate of PSII approached zero. Furthermore, PSI activity of the treated thalli recovered faster than PSII after being submerged in seawater. Even though the linear electron flow was inhibited by DCMU [3-(3, 4-dichlorophenyl)-1,1-dimethylurea], the cyclic electron flow could still be restored. The rate of cyclic electron flow recovery declined with the increasing time of dark treatment, which suggested that stromal reductants from starch degradation played an important role in the donation of electrons to PSI. This study demonstrated that PSII was more sensitive than PSI to desiccation and salinity in G. furcata and that the cyclic electron flow around PSI played a significant physiological role. In addition, G. furcata had branches, which were hollow inside and contained considerable quantities of funoran. These might be the most important factors in allowing G. furcata to adapt to adverse intertidal environments.

The life cycle of Pyropia yezoensis contains two obviously different stages: the conchocelis and the blade, which have different ploidy and morphology. The conchocelis grows in a calcareous matrix within subtidal zone and cannot live without seawater. However, the blades live on intertidal rocks and experience severe stress conditions at low tide. When exposed to air, external salt concentration increases around the algal tissues. It has been reported that the blade has high tolerance to various stresses, including high salinity stress. However, it is unknown whether carbon fixation still occurs when the blade is exposed to high salinity stress. Furthermore, there has been very little research on the conchocelis response to salt stress. Therefore, it is important to comprehensively compare the responses of the conchocelis and the blades to salinity. In this study, photosynthesis performance, carbon metabolism, and metabolite production were measured. The Y(II) for the conchocelis was almost zero (0.006) after 1 h at 120 practical salinity units (psu), whereas Y(I) was high (0.175). The Y(II) of the blade was only 0.008 whereas its Y(I) was 0.304 after 72 h at 120 psu, which suggests that PSII is more sensitive to salinity than PSI in both the conchocelis and the blade. Higher relative abundance was detected in the blade over the whole experimental period, which showed that the blade had higher carbon fixation efficiency than the conchocelis. The proline and trehalose contents were also higher in the blade, which might explain why the blade can tolerate higher salinities than the conchocelis.

Pyropia yezoensis, an intertidal seaweed, experiences regular dehydration and rehydration with the tides. In this study, the responses of P. yezoensis to dehydration and rehydration under high and low CO2 concentrations ((600-700)x10(-6) and (40-80)x10(-6), named Group I and Group II respectively) were investigated. The thalli of Group I had a significantly higher effective photosystem II quantum yield than the thalli of Group II at 71% absolute water content (AWC). There was little difference between thalli morphology, total Rubisco activity and total protein content at 100% and 71% AWC, which might be the basis for the normal performance of photosynthesis during moderate dehydration. A higher effective photosystem I quantum yield was observed in the thalli subjected to a low CO2 concentration during moderate dehydration, which might be caused by the enhancement of cyclic electron flow. These results suggested that P. yezoensis can directly utilize CO2 in ambient air during moderate dehydration.

Diatoms and dinoflagellates not only have extensive distribution and a huge biomass in marine ecosystems, but also have high lipid accumulation in nature or after physiological and genetic modification, which indicates that these organisms may be optimal candidate algal strains for biodiesel production. In this study, we determined the content of intracellular neutral lipids (triacylglycerol [TAG]) in the dinoflagellate Prorocentrum micans and in the diatom Phaeodactylum tricornutum using NR and BODIPY 505/515 staining. The freshwater green alga Scenedesmus obliquus was used as a control. Optimum concentrations of 1.000 and 1.500 μg mL−1 were determined for neutral lipid Nile red (NR) staining in P. micans and P. tricornutum. Unlike NR staining, the optimal concentrations of BODIPY 505/515 staining in P. micans and P. tricornutum were lower, at 0.100 and 0.075 μg mL−1, respectively. High correlation coefficients of R2 = 0.990 and R2 = 0.989 were obtained for P. micans and P. tricornutum intracellular neutral lipid content and the relative fluorescence intensity with NR staining, while the reference alga, S. obliquus, had a relatively low correlation coefficient of R2 = 0.908 when stained with NR. The neutral lipid content determined by thin-layer chromatography-flame ionization detector matched the analytical data from fluorescence measurements. These results indicated that NR and BODIPY 505/515 staining can be used as an excellent high-throughput approach to screen marine diatoms and dinoflagellates.

Phosphoenolpyruvate carboxykinase (PEPCK) catalyzes carboxylation of phosphoenolpyruvate or decarboxylation of oxaloacetate, which plays an important role in some C-4 plants and algae. The full-length cDNA of the PEPCK gene cloned from Porphyra haitanensisT. J. Chang et B. F. Zheng (Bangiales, Rhodophyta), was denoted Phpepck. It had a nucleotide sequence of 2300 bp, including a 5-untranslated region (UTR) of 147 bp, a 3-UTR of 329 bp and an open reading frame of 1824 bp. The expression of PEPCK in P.haitanensis sporophytes and gametophytes was examined at the levels of transcription, translation and enzyme activity. Both PEPCK abundance and activity were higher in sporophytes than those in gametophytes, suggesting that a C-4-like carbon-fixation mechanism might be functional in P.haitanensis sporophytes.

Pyropia yezoensis (Ueda) M. S. Hwang et H. G. Choi (previously called Porphyra yezoensis) is an economically important alga. The blades generated from conchospores are genetic chimeras, which are not suitable for genetic similarity analysis. In this study, two types of blades from a single filament of P. yezoensis sporophyte filament were obtained. One type, ConB, consisted of 40 blades that had germinated from conchospores. The other type, ArcB, consisted of 88 blades that had germinated from archeospores released from ConB. Both of them were analyzed by amplified fragment length polymorphism. The low genetic similarity levels for both conchospore-germinated and archeospore-germinated blades demonstrated that the conchcelis we used was cross-fertilized. Furthermore, a higher polymorphic loci ratio (98.6%) was detected in ArcB than in ConB (80.7%), and the average genetic similarity of ArcB (average 0.61) was lower than that of ConB (average 0.71). These differences indicated that genetic analysis using ArcB gives more accurate results.

Porphyra yezoensis has a macroscopic foliage gametophyte phase with only a single cell layer, and is ideally suited for the study of the sexual differentiation process, from the vegetative cell to the spermatia. Firstly, we compared variations in the responses of the vegetative and male sectors to desiccation. Later, cell tracking experiments were carried out during the formation of spermatia from vegetative cells. The two sectors showed similar tolerance to desiccation, and the formation of spermatia from vegetative cells was independent of the degree of desiccation. Both light and scanning electron microscopy (SEM) observations of the differentiation process showed that the formation of spermatia could be divided into six phases: the one-cell, two-cell, four-cell, eight-cell, pre-release and spermatia phases. Photomicrographs of Fluorescent Brightener staining showed that the released spermatia had no cell walls. Photosynthetic data showed that there was a significant rise in Y(II) in the four-cell phase, indicating an increase in photosynthetic efficiency of PSII during this phase. We propose that this photosynthetic rise may be substantial and provide the increased energy needed for the formation and release of spermatia in P. yezoensis.

The development of microalgae on an industrial scale largely depends on the economic feasibility of mass production. High light induces productive suspensions during cultivation in a tubular photobioreactor. Herein, we report that high light, which inhibited the growth of Chlorella sorokiniana under autotrophic conditions, enhanced the growth of this alga in the presence of acetate. We compared pigments, proteomics and the metabolic flux ratio in C. sorokiniana cultivated under high light (HL) and under low light (LL) in the presence of acetate. Our results showed that high light induced the synthesis of xanthophyll and suppressed the synthesis of chlorophylls. Acetate in the medium was exhausted much more rapidly in HL than in LL. The data obtained from LC-MS/MS indicated that high light enhanced photorespiration, the Calvin cycle and the glyoxylate cycle of mixotrophic C. sorokiniana. The results of metabolic flux ratio analysis showed that the majority of the assimilated carbon derived from supplemented acetate, and photorespiratory glyoxylate could enter the glyoxylate cycle. Based on these data, we conclude that photorespiration provides glyoxylate to speed up the glyoxylate cycle, and releases acetate-derived CO2 for the Calvin cycle. Thus, photorespiration connects the glyoxylate cycle and the Calvin cycle, and participates in the assimilation of supplemented acetate in C. sorokiniana under high light.

Under high light (HL) stress, astaxanthin-accumulating Haematococcus pluvialis and β-carotene-accumulating Dunaliella salina showed different responsive patterns. To elucidate cellular-regulating strategies photosynthetically and metabolically, thylakoid membrane proteins in H. pluvialis and D. salina were extracted and relatively quantified after 0 h, 24 h and 48 h of HL stress. Proteomic analysis showed that three subunits of the cytochrome b6/f complex were greatly reduced under HL stress in H. pluvialis, while they were increased in D. salina. Additionally, the major subunits of both photosystem (PS) II and PSI reaction center proteins were first reduced and subsequently recovered in H. pluvialis, while they were gradually reduced in D. salina. D. salina also showed a greater ability to function using the xanthophyll-cycle and the cyclic photosynthetic electron transfer pathway compared to H. pluvialis. We propose a reoriented and effective HL-responsive strategy in H. pluvialis, enabling it to acclimate under HL. The promising metabolic pathway described here contains a reorganized pentose phosphate pathway, Calvin cycle and glycolysis pathway participating in carbon sink formation under HL in H. pluvialis. Additionally, the efficient carbon reorientation strategy in H. pluvialis was verified by elevated extracellular carbon assimilation and rapid conversion into astaxanthin.

Phaeodactylum tricornutum Bohlin is an ideal model diatom; its complete genome is known, and it is an important economic microalgae. Although silicon is not required in laboratory and factory culture of this species, previous studies have shown that silicon starvation can lead to differential expression of miRNAs. The role that silicon plays in P. tricornutum growth in nature is poorly understood. In this study, we compared the growth rate of silicon starved P. tricornutum with that of normal cultured cells under different culture conditions. Pigment analysis, photosynthesis measurement, lipid analysis, and proteomic analysis showed that silicon plays an important role in P. tricornutum growth and that its presence allows the organism to grow well under green light and low temperature.

Porphyra yezoensisUeda is an intertidal marine red algae that has received increasing attention as a model organism owing to its important role in biological research and the agronomic industry. The two generations ofPorphyra yezoensis, the sporophyte and the gametophyte, have the same genome but show great differences in many aspects, including structural features, habitat, and gene expression. To identify miRNAs and their probable roles inP. yezoensisdevelopment, we constructed and sequenced libraries of small RNA fromP. yezoensissporophytes and gametophytes. The sequencing data were analyzed, and 14 miRNAs were identified, with only one common to these two samples. Our results show thatP. yezoensishas a complex small RNA processing system containing novel miRNAs that have no identifiable homolog in other organisms. These miRNAs might have important regulatory roles in development of the different generations ofP. yezoensis.

Gracilaria lemaneiformis (Bory de Saint-Vincent) Greville, an important marine alga, has great economic and nutritional value. However, during the nonreproductive period, it is difficult to distinguish the sporophyte, male gametophyte, and female gametophyte from each other by appearance. Amplified fragment length polymorphism (AFLP) is a multilocus marker technique, which was used in this study to identify markers associated with G. lemaneiformis sex type. By applying 80 primer combinations in the screening process, three fragments were found that were specific to male or female forms of the alga. A 173 bp band and an 89 bp band were found in the sporophyte and the male gametophyte by using primer E-AGG/M-CGT. E-ACC/M-CGG was used to amplify a 118 bp specific fragment in the sporophyte and the female gametophyte. Sequence characterized amplified region (SCAR) primers were designed and showed the expected bands at the corresponding stages. This suggested that the SCAR markers that had been developed were successful. The joint use of the three primer pairs allowed us to characterize sex and the G. lemaneiformis developmental phase in the nondescript stages. Rapid gender testing is expected to improve cross-breeding experiments and other genetic research in this economically important seaweed.

The genome sequences of Phaeodactylum tricornutum , Thalassiosira pseudonana , and Cyanidioschyzon merolae have provided significant evidence for the secondary endosymbiosis of diatoms in regard to the genome. Yet little about their relationships in regard to gene regulation pattern, such as microRNA (miRNA), has been reported. Using a homology search based on genomic sequences, 13, 3, and 7 predicted miRNA genes were found in genomes from P. tricornutum, T. pseudonana, and C. merolae, respectively. Of the 23 miRNA genes, 18 had homology with animal miRNAs, implying that they are ancestral miRNAs. A phylogenetic tree based on common miRNA families shared by these three unicellular algae, higher plants, and animals showed that P. tricornutum shared most miRNAs with animals. The phylogenetic tree also showed that C. merolae shared more miRNAs with plants than did the two diatoms, and the majority of its miRNAs were shared with the two diatoms. Our results were consistent with diatoms originating from a secondary endosymbiosis.

Background Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, revealing some characteristics of the diatoms' mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify microRNAs (miRNAs) from P. tricornutum and to study their probable roles in nitrogen and silicon metabolism, we constructed and sequenced small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions. Results A total of 13 miRNAs were identified. They were probable P. tricornutum-specific novel miRNAs. These miRNAs were sequenced from P. tricornutum under normal, nitrogen-limited and/or silicon-limited conditions, and their potential targets were involved in various processes, such as signal transduction, protein amino acid phosphorylation, fatty acid biosynthetic process, regulation of transcription and so on. Conclusions Our results indicated that P. tricornutum contained novel miRNAs that have no identifiable homologs in other organisms and that they might play important regulator roles in P. tricornutum metabolism.

The seaweed Ulva prolifera exists in 2 different states; attached to rocks or free-floating. However, there is little difference between the structures of the 2 states. U. prolifera thalli show significant differences in growth rate, with the attached thalli growing at a normal rate and free-floating thalli growing at a much faster rate. This raised the possibility that the growth of the two states may be regulated differently. miRNAs are important post-transcriptional regulators. In higher plants and animals, miRNAs have been extensively studied but they have been rarely studied in algae. To identify U. prolifera miRNAs and to investigate their possible roles in proliferation, we constructed and sequenced small RNA (sRNA) libraries from U. prolifera. Our results show that U. prolifera has a complex small RNA system that might play important roles in various processes.