Few gene and protein sequences for nitrate reductase (NaR) have been well characterized from eukaryotic algae. Therefore, the biogeochemical cycle of silicon is dominated by the activity of the diatoms in marine systems [10], and it has been estimated that globally, the diatoms uptake and process 240 Tmol Si per year. 5b). 2016;32(5):767–9. BMC Genomics 19, 765 (2018). Bioinformatics. As results, we found that both evolutionary genomic and comparative transcriptomic studies revealed genes for oxidative stress response and response to cytokinin is a key for the proliferation of the diatom. By continuing you agree to the use of cookies. BMC Genomics Thus, in spite of their limitations, microalgal bioassays in batch cultures can provide useful and comparable information about the toxicity of substances and effluents. For aquatic systems, plants, invertebrates and vertebrates are tested. To generate a more accurate Sc. The genome size of Sc was 46.9 Mb, and the number of genes was 16,449, both of which were larger than other diatoms. 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). However, it is not a legal authority for statutory or regulatory purposes. Genes related to cell proliferation such as cell division and mitotic nuclear division seem also important to fit rapid proliferation during algal blooms. For invertebrates in freshwater, the water fleas, Daphnia magna and Ceriodaphnia spp., are used for acute assay and chronic studies that include one life cycle. C.S. Kooistra WHCF, Sarno D, Balzano S, Balzano S, Gu H, Andersen RA, Zingone A. As mentioned in Chapter 6, analyses of ecotoxicity data submitted within the framework of Registration, Evaluation, and Authorization of Chemicals in Europe regulation have been mainly based on single-species bioassays. Brigitte Berthet, in Aquatic Ecotoxicology, 2015. Braker 1 utilized unsupervised training of GeneMark-ET using RNA-seq dataSince Braker utilizes Genome file and Bam file to perform gene prediction, we created a Bam file by applying RNA-seq data to mapping software Tophat. A good example of these tests can be found in ISO (1995) for seawater (involving Phaeodactylum tricornutum or Skeletonema costatum) and in OECD (1998) for freshwater environments (involving Raphidocelis subcapitata, formerly known as Selenastrum capricornutum and Pseudokirchneriella subcapitata, Scenedesmus subspicatus, or Chlorella vulgaris). 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). https://doi.org/10.1126/science.281.5374.237, https://doi.org/10.1093/bioinformatics/btn548, https://doi.org/10.1093/bioinformatics/btv661, https://doi.org/10.1093/bioinformatics/btv351, https://doi.org/10.1093/bioinformatics/btu638, https://doi.org/10.1093/biostatistics/kxm030, https://doi.org/10.1186/s13059-015-0721-2, http://creativecommons.org/licenses/by/4.0/, http://creativecommons.org/publicdomain/zero/1.0/, https://doi.org/10.1186/s12864-018-5144-5. b Differentially expressed genes among Sc culture samples for different light conditions. 2014;24(8):1384–95. T1 - Genome sequence of Marinobacter sp. From the transcriptome analysis, genes related to oxidative stress were significantly enriched under temperature, light, and nutrient conditions in which the red tide is likely to occur as the same as genome analysis. Sc singlet genes represents the number of non-orthologous genes in Sc, and passed to the list of Sc-specific genes. From this analysis, WGS (238 complete genes) and Platanus (223 complete genes) showed higher quality than others. Blooms of Phaeocystis may follow, before giving place to ceratians. Nature. Other chapters (e.g., Chapter 30 by Zehr and Jenkins, this volume; Chapter 7 by Mulholland and Lomas, this volume) describe our knowledge to date for prokaryotic members of the microbial community. In detail, we have conducted genome size estimation using k-mer analysis to assess differences between estimated genome size and assembled genome sizes (Fig. The n-hexane extracts exhibited a growth inhibition of S. aureus, B. subtilis and E. coli with a MIC of 250 μg/mL. Google Scholar. Copyright © 2020 Elsevier B.V. or its licensors or contributors. Global diversity and biogeography of Skeletonema species (Bacillariophyta). 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). Marine phytoplankton would seem appropriate for first consideration. 233 genes were extracted as highly expressed genes at abundant nitrogen condition. PubMed Google Scholar. Genome annotations. Mann DG. When comparing the results from the genome and transcriptome analysis, the same category of genes, response to the oxidative stress and response to cytokinin seemed to be enriched in both results. Pelagic Ecosystems.. Phytoplankton species illustrating the taxonomic diversity as well as the shape and size of these organisms, which are an important component of the pelagic food web. Cookies policy. The authors declare that they have no potential conflict of interest. The sexual reproduction of oogamous is where reproduction occurs by the union of mobile male and immobile female gametes. Armbrust EV, et al. 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. 150:243–372. Google Scholar. Molecular approaches can now be used to examine what components of the phytoplankton population have the capacity to synthesize and make the correct enzymes to assimilate different forms of N in response to environmental factors. The whole genome analysis of Thalassiosira pseudonana yielded a genome that encodes multiple NO3 and NH4 transporters (Armbrust et al., 2004). CAS  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. Although we know about the characteristics of this diatom, we do not know the whole genome. 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. I. Skeletonema subsalsum (A.Cleve) Bethge Phycologia 14 :283-297 Eur J Phycol. This confirms that GS II is using NH4 derived from NO3. 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). 3b, c). nov. J Phycol. 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). Am Nat. Before this, our understanding of nitrogen dynamics in upwelling areas was restricted to measuring bulk changes in water constituents by the entire phytoplankton community (i.e., the particulate fraction that is caught on a filter). The authors declare that they have no potential conflict of interest. Antibacterial activity was tested against S. aureus, MRSA, E. coli, P. aeruginosa and Enterococcus faecalis. 1). Fogg et al. The reason for using A. thaliana and C. reinhardtii is that they are the model organism for primitive photosynthetic organisms (Additional file 1: Table S1, sheet6-HAB genes in At, Additional file 1: Table S1, sheet7-HAB genes in Cr). Mar Ecol Prog Ser. 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). Genome Res. We compared the assembly results with others from the viewpoint of genome size, the number of contigs, the largest contig, total length, GC content, N50, BUSCO assessment for the common eukaryotic genes conservation rate (ECR). However, these genetic diversities of silicate-related genes might reflect the complexity of diatom structures. It can be regarded as a toxic species since it produces a toxin that causes diarrohetic shellfish poisoning. The whole genome of Skeletonema costatum, Sc was determined by Illumina Hiseq 2000, the next generation sequencer. One isolate, Micrococcus sp LG-1, displayed high lethality and selectivity for C. polykrikoides. 1984;123:73–80. The genes that related to proliferation were significantly enriched in the orthologous gene group found in the red tide causing diatoms. Data was trimmed by default with the Solexa QA (v3.1.7.1) [27], which is quality control software that eliminates unreliable parts of sequences extracted by the Illumina Hiseq 2000. The nuclear genome was extracted by removing the sequence (mitochondria: 41, chloroplast: 232) and was obtained as a result of a coincidence rate of 99% or more from SC12 _ gapClosed_platanus.fa. Science. They showed increases in levels of NaR-specific messenger RNA (i.e., showing increased transcription of the gene for NaR) that coincided with the acceleration (shift-up) in NO3 assimilation measured with 15N. Keith R. Solomon, in Hayes' Handbook of Pesticide Toxicology (Third Edition), 2010. These genes were associated with the proliferation of cells and related to the harmful algal bloom. We therefore conducted orthologous gene groups estimation analysis using OrthoFinder and classified orthologous gene groups by conservation patterns that were shown in the Venn diagram (Fig. Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom. 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. Poulsen and Kroger (2005) also showed that NaR expression was inducible in transgenic Cylindrotheca fusiformis when cells were given NO3. The source of NH4 may be externally supplied or internally as a product of NO3 reduction or photorespiration. It has been suggested that one isoform is found in the cytoplasm of the cell and functions to assimilate external source of NH4 whereas the other is located in the chloroplast (where nitrate reductase is found) and is responsible for assimilating NH4 that has resulted from NO3 reduction (reviewed in Anderson, 1999). The chemical basis for diatom morphogenesis. (1994) showed that D. pulex was more sensitive to pollutants than other daphnids. Int.J.Curr.Microbiol.App.Sci (2014) 3(11) 129-136 130 The intercalary valves of the chains Skeletonema are all alike and different from the separation valves (Crawford, 1979). ; and the threespine stickleback, Gasterosteus aculeatus. Genomic DNA was extracted from the harvested cells on the filter with a modified SDS-Proteinase K method (TE buffer: 10% SDS: 20 mg mL-1 Proteinase K (Qiagen) = 16:15:1). Science. Zingone A, Percopo I, Sims PA, Sarno D. Diversity in the genus Skeletonema (Bacillariophyceae) I. 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. Traditional methods, such as tracer techniques (Chapter 31 by Lipschultz, this volume) or measuring enzyme assimilation rates (e.g., Berges, 1997; Berges and Harrison, 1995; Berges et al., 1995; Slawyk et al., 1997; Chapter 32 by Berges and Mulholland, this volume) provide nitrogen uptake/assimilation (productivity) rates, but do not identify the major players involved in mass transformation, or the physiology of the phytoplankton involved. Allen et al. Other tests for responses such as endocrine disruption are under development (Ankley et al., 2001; U.S. EPA, 2007a). No permission was required to collect diatom samples. Araújo, Ignacio Moreno-Garrido, in Handbook of Marine Microalgae, 2015. Here we sequenced the genome of Skeletonema costatum, which is the dominant diatom in Japan causing a harmful algal bloom, and also performed RNA-sequencing analysis for conditions where harmful algal blooms often occur. 3b). Skeletonema costatum gained duplicated genes of growth related genes such as cytokinin for rapid growth for algal bloom, by which the diatom can proliferate when the environmental condition matched to their preferences. II. Yool A, Tyrrell T. Role of diatoms in regulating the ocean’s silicon cycle. strain MCTG268 isolated from the cosmopolitan marine diatom Skeletonema costatum AU - Gutierrez, Tony AU - Whitman, William B. Miller JR, Delcher AL, Koren S, et al. (1997) isolated 28 strains of bacteria from various genera that could kill Gymnodinium (now Karenia) mikimotoi after a bloom that occurred in Tanabe Bay (Japan). © 2020 BioMed Central Ltd unless otherwise stated. 2015;31(2):166–9. Early life-stage tests may also be conducted. (C) Dinophyceae, Dinophysis norvegica, a solitary dinoflagellate, normally found in cold waters, between 48 and 67 μm and width between 39 and 53 μm. The shell of this diatom is a cylinder, about 22 μm in diameter, and is common in the bay and coastal waters. GigaScience. In Korea, the distribution and lethality of algaecidal bacteria against Cochlodinium polykrikoides were studied in a local bay. Enrichment analysis performed on the identified genes indicated that the category, “oxidation-reduction process,” (related to oxidative stress) was significantly highlighted. 2014;30(1):31–7. The digit indicates the number of orthologous gene groups. Genes and proteins extracted from the paper studying the harmful algal bloom were used as the candidates for the harmful algal bloom causing factors in the diatom ([40, 41], Additional file 1: Table S1, sheet5-HAB genes publication). The valves of vegetative cells are elliptical (4.5–20 μm in diameter) in valve view with four long setae (one on each corner of the epi- and hypovalves, respectively), while auxospores are spherical (6 μm in diameter) and more heavily silicified, but nonetheless unornamented by light and scanning electron microscopy (Reinke, 1984). 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). an irradiance of 100 μmol m− 2 s− 1 with a 12:12 h L:D cycle, at three different temperatures of 10, 18 and 28 °C during their exponential growth phases (4–7 days). Skeletonema costatum is eurythermal (Liao et al., 1983). As a model for physiological studies, T. pseudonana was the first marine phytoplankton for which the genome was completely sequenced (Armbrust et al., 2004). J Phycol. (Chlorophyta) and Gelidinium sp (Rhodophyta). Distribution of species reported by Tarazona et al. Article  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. GS II-specific messenger RNA (i.e., transcript abundance of gln II, the gene that encodes for the enzyme isoform GS II) and total GS enzyme activity were increased 2–3.5 times above background in cells taking up NO3 but not cells taking up NH4. For this purpose, we performed a transcriptome analysis that could comprehensively analyze the expression status of genes in various conditions imitated for the harmful algal bloom causing situations. However, in the context of industrial use, it is relevant to note that S. costatum cultures CCAP 1077/3 (Genbank accession number X85395), CCMP 780, UBC18/C (Genbank accession number M54988.1), and CCAP1077/6 (CS76 see reference in (Sarno and Kooistra, 2005)) have been misidentified, with CCAP1077/6 from Australian waters being S.  pseudocostatum, while the others are S. grethae. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. In the US, Doucette et al. Yoshinaga et al. Robinson MD, Smyth GK. 1997;65:1–11. In the case of metals, for instance, adsorption to the cellular surface seems to be a very quick process (Garnham et al., 1992) and real metal concentration in culture media can dramatically decrease in a few hours or even minutes. The former can be detected as 27 Sc-specific orthologous groups that consist of 151 genes, and the latter can be detected as genes without any homology to other species, 4741 Sc-singlet genes, which genes might be important for functional novelty in Sc. For instance, as days lengthen over the open seas of the temperate latitudes, an initial typical spring bloom of such chain-forming diatoms as Thalassiosira nordenskioldi, Skeletonema costatum, and Chaetoceros (all manifestly having R-type, attuning characters) gives place in summer to relatively large, motile, S-like peridinians (e.g., Scrippsiella trochoidea) and ceratians (e.g., Ceratium tripos), which are often followed, in autumn, by chain-forming (Chaetocerosspp.) Aggressive assembly of pyrosequencing reads with mates. f/2 medium was modified by addition of 10 μM of selenious acid (H2SeO3) and without copper sulfate hydrate in the stock solution of the metal mixture (Nagai et al. 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. Nishikawa T, Hori Y, Nagai S, Miyahara K, Nakamura Y, Harada K, Tada K, Imai I. The whole genome of Skeletonema costatum, S c was de- termined by Illumina Hiseq 2000, the next generation Fig. The red tide is named after the color of the water, which changes to reddish brown, depending on the pigment of plankton. 3a). 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) [1]. We conducted transcriptome analysis with two biological replicates. Genome-wide screening and identification of factors affecting the biosynthesis of Prodigiosin by Hahella chejuensis, using Escherichia coli as a surrogate host. A key feature of this class is the production of a siliceous frustule covering the cell, and many are used as aquaculture feed (see below). 2010;33:417–27. Restoration of cell size by vegetative cell enlargement in Coscinodiscus wailesii (Bacillariophyceae). On the other hand, genes that are only found in Sc but have not in other species could be regarded as Sc-specific genes, which might be related to the functional novelty in Sc. Skeletonema costatum is a major bloom-forming species widely distributed around the world. 2011;45:113–24. A biological function for cadmium in marine diatoms. As one orthologous gene groups could contain more than one genes, the number of genes and the number of the orthologous gene groups was different, which were shown in the panel B (Fig. Skeletonema costatum, and Porphyridium cruentum. For saltwater invertebrates, shrimp, such as Mysidopsis bahia and Penaeus duorarum, are used for acute and chronic assays for reproduction, mortality, and growth. 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). An important class of low-molecular-weight antioxidants, present in microalgae, are antioxidant vitamins. Lewis WM. To extract the nuclear genome, blastn (v2.2.30) [33] search against chloroplast and mitochondrial genomes was done in the DB. 2014;5:375. https://doi.org/10.3389/fmicb.2014.00375. Batch cultures for toxicity tests have often been criticized—for good reasons. YA performed genome analysis, and HI performed transcriptome analysis. Is the origin of diatoms related to the end-Permian mass extinction? This work was funded by Grants-in-Aid for Scientific Research (KAKENHI) 17H06399 and Grant for Basic Science Research Projects from the Sumitomo Foundation to AO, and Science and Technology Research Partnership for sustainable Development to SN. The endpoint is generally the inhibition of their growth (USEPA, 1996; OECD, 2002; OEHHA, 2004). For the genome size estimation, we used KmerGenie that could estimate the best k-mer length for genome de novo assembly [34]. 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. 17.4) of physiological response may have a … By conducting transcriptome analysis, we analyzed changes in gene expression corresponding to the changes of conditions to elucidate the molecular mechanism of harmful algal bloom. Much effort has been devoted to the physiological response of marine diatoms to ambient P change, however, the whole-genome molecular mechanisms are poorly understood.
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