Bioinformatics. Here, we present its 5,857,781-bp genome, consisting of a circular chromosome and one circular plasmid, in … This species is more likely to bloom under high temperature and high illumination, with optimal conditions at 25 °C and Close Irradiance. Article https://doi.org/10.1093/bioinformatics/btv351. Kwon S-K, Park Y-K, Kim JF. Transcriptomic response of the red tide dinoflagellate, Karenia brevis, to nitrogen and phosphorus depletion and addition. Oxford: Blackwell Scientific Publ. https://doi.org/10.1093/bioinformatics/btn548. GS II gene expression increased in cells taking up NO3. Eur J Phycol. Diatoms take up NO3 and NH4 via membrane transporters and assimilate NO3 using assimilatory nitrate and nitrite reductase (NaR and NiR), and NH4 using glutamine synthetase (GS) and glutamate synthase (GOGAT) (see Chapter 7 by Mulholland and Lomas, this volume, for detailed descriptions). For aquatic vertebrates, standardized tests include acute life-cycle tests and early life-stage tests. We obtained a total of 6.3Gbps from gDNA of S. costatum and used them for de novo assembly. The primary use for silicic acid is in the construction of their frustules . Similarly, natural bacterial communities isolated from an inlet in Kochi (Japan) influenced the growth of the dinoflagellate Gymnodinium nagasakiense and the diatom Skeletonema costatum (Fukami et al., 1991). and Ornithocercus. The strain was also incubated under the same conditions with the experiment-1 at 28 °C for 4 days, then it was put at a lower irradiance of 20 μmol m− 2 s− 1 for 24 h (experiment 2–3). Dari pembelahan sel tersebut akan dihasilkan 2 sel yang ukurannya lebih kecil daripada sel induknya. Sheet-1, The number and length (bp) of each repetitive element in four species, Sheet-2, The number of genes from Harmful algal bloom related genes, selected as shown in the methods, Sheet-3, Highly duplicated genes in Sc, and their annotations. The proportion of conserved genes between Sc and Tp that are closest to Sc were about 65.4%, which were a total of Sc-Tp shared genes (4375-STPV, 3301-STP, 634-STV, and 2352-ST) divided by the total number of Sc genes (11,557 + 4741). As for the temperature (experiment-1), the strain was incubated at 400 mL of the modified f/2 medium under the same conditions with the maintenance cultures, i.e. Privacy Li et al. This work has been supported partly by funding from King Abdullah University of Science and Technology (KAUST) to TG. To examine this observation, sharing pattern of the common genes of the harmful algal bloom and SC-specific genes, and differentially expressed genes in the three different conditions were merged into the same Venn diagram. (1992) in a laboratory study to simulate upwelling measured the response of the gene for the major NO3 assimilation enzyme, nitrate reductase (NaR) in light- and N-limited diatom cells of Skeletonema costatum when given an increase in light and NO3 availability. We estimated the ortholog gene group for S. costatum, T. pseudonana, P. tricornutum, V. brassicaformis using Orthofinder (v1.0.7)  with default parameters. To elucidate the molecular mechanism of the harmful algal bloom, it is necessary to analyze what kind of fluctuation of Sc genes occurs under the harmful algal bloom condition. The completed Pt genome is approximately 27.4 megabases (Mb) in size, which is slightly smaller than Tp (32.4 Mb), and P. tricornutum is predicted to contain fewer genes (10,402 as opposed to 11,776, Table 1). https://doi.org/10.1101/gr.141515.112. GigaScience. In the orthologous gene analysis, we estimated orthologous gene groups using similar length of genes, representing reliable orthologous gene sets. To establish whether GS II and GS III might have these different functions in diatoms, Takabayashi et al (2005) measured expression of the gene responsible for GS II (gln II) in Skeletonema costatum cells grown with either elevated NO3, or NH4 or both forms of DIN. Differentially expressed genes related to Oxidation reduction process and Response to cytokinin on the venn diagram. marine diatom, Skeletonema costatum (Bacillariophyceae) were commercially cultured in laboratory conditions. To obtain genome and gene model of Sc with higher quality, we tried to use four different genome assembly software, WGS, Platanus, Allpaths-LG, SOAPdenovo2, and SPAdes. For example, STPV has 2798 orthologous group as shown in the panel A, and includes 4375 genes in Sc, 3699 genes in Pt. C.S. Data of the whole genomes and the gene models of algae, T. pseudonana, and P. tricornutum were acquired from the Joint Genome Institute project’s home page while those of V. brassicaformis was acquired from Ensembl’s homepage. The culture was incubated for 120hr, althoughnonitrite could bedetected in the medium after 62 hr. 17.4) of physiological response may have a molecular basis. Tréguer P, Nelson DM, van Bennekom JV, DeMaster DJ, Leynaert A, Quéguiner B. Seven genes of silicate and silaffin, Sil1, Sil2, Sil3, SIT1, SIT2, SIT3, and TPSIL2, were extracted from the NCBI DB. Methanol extracts appeared to be effective against all the bacteria tested, while the ethanol extracts showed a weak activity against Proteus mirabilis, S. paratyphi B, S. aureus and V. cholerae and the water extracts did not display any activity (Daniel, 2016). A broader list of bacteria and their targets is presented in Mayali and Azam (2004). Before that, however, it is necessary to establish that the rest of the planktonic biota respond to environmental cues in broadly analogous ways. Geitler L. Der formwechsel der pennaten diatomeen (kieselalgen). Science. Araújo, Ignacio Moreno-Garrido, in Handbook of Marine Microalgae, 2015. Google Scholar. In a simulated upwelling study using Skeletonema costatum in which cells were shifted into high light, there was a rapid increase in GS II gene expression measured as gln II mRNA using quantitative PCR (Barada, 2006). Genome size estimation by k-mer analysis and the common eukaryotic genes conservation rate. d Gene set enrichment analysis of Sc-specific genes. To perform the DAVID analysis, ID from A. thaliana is necessary as they require GO annotations, so we obtained A. thaliana protein sequences and GO annotation file from The Arabidopsis Information Resource (TAIR). Mann DG. Skeletonema costatum | Diatom Order: Biddulphiales Family: Thalassiosiraceae Click on illustration to enlarge . In the analysis, the function related to oxidative stress was significantly enriched in the common genes for the harmful algal bloom and the Sc-specific genes. (1975) Brackish-water and fresh-water species of the diatom genus Skeletonema Grev. For both short- and long-term fish studies (Figure 9.1), Pimephales promelas, Oncorhynchus mykiss, and Danio rerio have been the most frequently used species (more than 10% of studies) (Tarazona et al., 2014). The genes identified as differentially expressed genes (DEGs) with FDR < 0.05 were used for further analysis. Recommended Strains of Algae OECD (2002). Biostatistics. a Differentially expressed genes among Sc culture samples for different temperatures, 10 °C, 18 °C, and 28 °C. Marine phytoplankton would seem appropriate for first consideration. Harmful algal blooms also have adverse effects, such as the suffocation of fish, due to the lowering of the oxygen concentration in the surrounding marine environment or due to the toxins produced by diatoms. Lieselot Balduyck, ... Imogen Foubert, in Handbook of Marine Microalgae, 2015. Preliminary considerations of the types of phytoplankton characterizing the various subdivisions of the sea (Fig. A novel death-specific gene, ScDSP , was obtained from a death stage subtraction cDNA library of the diatom Skeletonema costatum . We searched repeat sequences by RepeatMasker and found that Sc possessed many number of simple repeats comparing with other diatoms, but possessed less SINE and LINE (Additional file 1: Table S1, sheet1-Repetitive element). Cells can also accumulate toxicants in special structures in their cytoplasm (Maeda and Sakaguchi, 1990), and a limited quantity of atoms or molecules of the toxicant in a closed environment removes the results from environmentally relevant data. We classified the information of Gene name, Gene ID, GO categories, and PMID classification. The two thecate dinoflagellates (A. tamarense and H. circularisquama) were relatively unaffected compared with the other species, which suggest that the theca may offer some protection. 2011;12:346. https://doi.org/10.1186/1471-2164-12-346. A. thaliana ID was then converted to RefSeq protein ID using BioMart to perform gene enrichment analysis by DAVID. Since then, a wide variety of aspects of EOC have been intensively studied. It is especially abundant during spring bloom, when densities of million of cells per litre is reported. Consequently, they must restore their cell size by auxospore formation (sexual processes in the strict sense of the word) and vegetative cell enlargement (pseudo-auxospore formation, i.e., an asexual process) . The whole genome of Skeletonema costatum, S c was de- termined by Illumina Hiseq 2000, the next generation Fig. We appreciate the staff of Nagahama Institute of Bio-Science and Technology Genomic diversity laboratory, Ikuyo Takemura for assistance with data analysis. Few gene and protein sequences for nitrate reductase (NaR) have been well characterized from eukaryotic algae. Smith et al. At present, eleven species belong to this genus . Important microalgal carotenoids include lutein, astaxanthin, fucoxanthin, and β-carotene. The ecological importance and the complicated speciation process of the genus Skeletonema motivated us to start the complete genome analysis in these Skeletonema species. 1999;38:437–95. (2010) screened microalgae for polyphenol content and antioxidant activity and found large variations between species. Genome annotations. T1 - Genome sequence of Marinobacter sp. Bioinformatics. Genes involved in these pathways were extracted, and gene expression intensities (FPKM) of these genes were used for heatmap analysis. The genus Thalassiosira contains >100 species, with T. pseudonana being a marine small (4–6 μm), centric, unicellular diatom belonging to the Coscinodiscophyceae and quite indistinctive by light microscopy. Phycologia. In particular QPCR (quantitative polymerase chain reaction) used with reverse transcription, can provide quantitative measurements of gene expression of functional genes involved in nitrogen assimilatory processes by specific microbial cells. Article Basic local alignment search tool. Sc singlet genes represents the number of non-orthologous genes in Sc, and passed to the list of Sc-specific genes. As ascorbic acid is hydrophilic, it is not transferred into the oil when extracted and is therefore of low importance for the stability of processed oils. Spatial differences—among latitudes or between neritic shelf waters and the open oceanic systems— probably also attest to the functional differentiation of the phytoplankton. 2016;32(5):767–9. Cookies policy. Thus, it is of importance to reveal the genetic background of diatoms and the molecular mechanism of the proliferation of diatoms as the molecular mechanism of harmful algal blooms is still unclear. To clarify the common genetic background in the diatom and to specify the genetic novelty of Sc from other diatoms, we estimated orthologous gene groups that share the same common ancestral gene and are supposed to have the same functionality. PubMed Round FE, Crawford RM, Mann DG. This is also consistent with the fact that one of the key genes for the pathway responding to the oxidative stress, ROS, was activated by the light condition. Atsushi Ogura, Yuki Akizuki, Hiroaki Imoda, Katsuhiko Mineta, Takashi Gojobori, Satoshi Nagai, Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom, BMC Genomics, 10.1186/s12864-018-5144-5, 19, 1, (2018). Species of the Skeletonema are harmful and cause a severe economic loss in Japanese aquaculture because they utilize nutrients necessary for the growth of the red algae Porphyra (nori) in winter . These indicates that, in the process of algal bloom, massive photosynthesis occurs and diatoms should response to this stress by duplicating genes related to oxidative stress. In detail, we have conducted genome size estimation using k-mer analysis to assess differences between estimated genome size and assembled genome sizes (Fig. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Early life-stage tests may also be conducted. Restoration of cell size by vegetative cell enlargement in Coscinodiscus wailesii (Bacillariophyceae). Phycologia. 1, Table 2). The fatty acid eicosapentaenoic acid (EPA) synthesized by the diatom Phaeodactylum tricornutum showed significant in vitro activity against S. aureus (Desbois et al., 2009). The authors declare that they have no potential conflict of interest. These 143 genes were then used in the gene set enrichment analysis. Curr Biol. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. California Privacy Statement, From the pioneering Algal Assay Procedure Bottle Test (US EPA, 1971), designed in order to detect aquatic eutrophication, many guidelines for microalgal toxicity tests have been developed (Rand, 1995). Atsushi Ogura, Yuki Akizuki, Hiroaki Imoda, Katsuhiko Mineta, Takashi Gojobori and Satoshi Nagai Areas of frontal activity and of surface upwellings of the deep oceanic circulation currents tend to combine intensive mixing with renewed resources and to select species in the C-R intermedium through much of the year: Gyrodinium spp., Alexandrium tamarense, Thalassiosira leptoporous can be typical assemblage members. Kirsten Heimann, Roger Huerlimann, in Handbook of Marine Microalgae, 2015. Microalgae reduce (lipid) oxidation in living cells using two strategies: antioxidant enzymes and antioxidant molecules. and Cytophaga sp. CAS Skeletonemataceae is a family of diatoms in the order Thalassiosirales.There is currently only one known genera in this family of diatoms known as Skeletonema as reported from diatom.org. A recent study revealed that S. costatum sensu stricto, S. dornii, and S. japonicum distribute widely and abundantly in the western part of Japan ([20, 21], Nagai unpublished). 2005;41:151–76. Differentially and highly expressed genes were extracted, and enrichment analysis was performed to identify functional categories related to the red tide. Robinson MD, Smyth GK. 1984;123:73–80. In the bloom condition, they should adapt to higher oxidative stress condition, so that they can overcome this condition by higher activity of oxidative stress response. We then compared the genome and gene model of Sc with other diatoms and Vb, and it was suggested that Sc had larger genome size than other diatoms, and the number of genes was also larger than that of other diatoms (Additional file 1: Table S1). 2011;6:26–34. Crude extracts of Amphora cf capitellata and Nitzschia communis at a concentration of 100 μg/mL inhibited the growth of S. aureus by 83% and 100%, respectively (Montalvão et al., 2016). Detailed light and scanning electron microscopy, complemented with molecular work by Sarno and Kooistra (2005) and Zingone et al. Morphological and genetic variation within the diatom Skeletonema costatum (Bacillariophyta): evidence for a new species, Skeletonema pseudocostatum. As a result, the oxidation-reduction process and response to cadmium ion were shown from the common genes for the harmful algal bloom, the Sc-specific genes, and the Sc-duplicated genes (Fig. Pathways was modified from the figures in “The new insights into cadmium” (Jagna Chmielowska-Bąk et al.,2014), and “Antagonistic roles of abscisic acid and cytokinin” (Yandu Lu et al.,2014), respectively. Based on the estimation of silicate and silaffin genes in the four species (Additional file 1: Table S1, sheet4-#silicate & silaffin), Tp possessed higher number of genes comparing with other species, whereas Sc has also high number of silicate-related genes. For the whole genome analysis, the strain was incubated in 3 × 400 mL of the modified f/2 medium under the same conditions for the maintenance culture for one week, and the vegetative cells were harvested by filtrating through 1-μm-pore-size polycarbonate filters (Nuclepore membrane, GE Healthcare, Tokyo, Japan).