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). https://doi.org/10.1093/bioinformatics/btu638. Google Scholar. Spatial differences—among latitudes or between neritic shelf waters and the open oceanic systems— probably also attest to the functional differentiation of the phytoplankton. Morphological and genetic variation within the diatom Skeletonema costatum (Bacillariophyta): evidence for a new species, Skeletonema pseudocostatum. We conducted transcriptome analysis with two biological replicates. Nevertheless, the apparent functional and morphological correlations have scarcely been quantified. In the highly stratified, tropical oceans, dominance passes quickly from diatoms to Emiliana and to the large Ceratium spp. These tests focus on development and growth during the first 30–90 days of development from the egg. The addition of NO3 results in gln II transcription being induced to express the GS II isoform, which catalyzes assimilation of NH4 that has been made available by reduction of NO3 and NO2 by NaR and NiR. 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). 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. Next to the common antioxidant components that are found in other plants, some microalgae produce specific types of antioxidants such as the phycobiliproteins, for example, phycocyanin and phycoerythrin in rhodophytes and cyanobacteria (Huang et al., 2007), dimethylsulfide/dimethylsulfoxide (Sunda et al., 2002), and sulfated polysaccharides (Tannin-Spitz et al., 2005). Kajitani R, Toshimoto K, Noguchi H, et al. 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). Differentially expressed genes related to Oxidation reduction process and Response to cytokinin on the venn diagram. Genome annotations. A total of 31,964 protein-coding genes were predicted in the S. obliquus AS-6-11 genome (Table 2).The predicted gene number of S. obliquus AS-6-11 genome is dramatically higher than the other Scenedesmus strains (Table 1).According to the Non-redundant protein (NR), SWISS-PROT, and Pfam protein families databases, 19,847, 13,099, and 13,612 proteins … Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom. Such approaches are being developed to study the molecular basis for biogeochemical changes (e.g., Parker and Armbrust, 2005) and variability in acceleration/adaptation of N uptake and new production rates in simulated upwelling studies. NH4 assimilation occurs by the action of GS and GOGAT (Wheeler, 1983; Falkowski, 1983). Since then, a wide variety of aspects of EOC have been intensively studied. 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 . Medlin LK, Elwood HJ, Stickel S, Sogin ML. For saltwater invertebrates, shrimp, such as Mysidopsis bahia and Penaeus duorarum, are used for acute and chronic assays for reproduction, mortality, and growth. Amount of solar energy per unit area on a surface (units: μE m-2 sec-1, where E is an Einstein, a mole of photons).. irradiance of 1.6×10 16 quanta/s⋅cm 2 (Yan et al. This work has been supported partly by funding from King Abdullah University of Science and Technology (KAUST) to TG. b The number of genes in the orthologous gene groups. 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). 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. 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). Phenolics are efficient antioxidant molecules and exhibit a wide range of chemical structures and polarities. marinoi is an important primary producer in the N Atlantic and a valuable food source for zooplankton. J Comput Biol. The dominant species of harmful algal blooms in Japan is the diatom, Skeletonema costatum (Sc). 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. (2010) screened microalgae for polyphenol content and antioxidant activity and found large variations between species. GENOME ANNOUNCEMENT. Some of those problems could be solved with the design of continuous-flow toxicity tests (Chen et al., 1997), although other problems could appear, such as the dilution of the cellular density. Copyright © 2020 Elsevier B.V. or its licensors or contributors. Mar Ecol Prog Ser. Early life-stage tests may also be conducted. Part of Nishikawa T, Hori Y, Nagai S, Miyahara K, Nakamura Y, Harada K, Tada K, Imai I. In the different nutrients condition, down-regulation of oxidative stress pathway was observed in N-depletion and lower irradiance. (2016) studied the bioactivity of five north Atlantic marine diatoms, Attheya longicornis, Chaetoceros socialis, Chaetoceros furcellatus, Skeletonema marinoi, and Porosira glacialis with different light and temperature treatments. 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. The genes that related to proliferation were significantly enriched in the orthologous gene group found in the red tide causing diatoms. The detailed morphology of the siliceous frustule (cell wall) varies with the availability of silica; however, a ring of 6–14 strutted marginal processes is present, with one labiate process also present along with one subcentral strutted process (Hasle and Syvertsen, 1997). (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. Nevertheless, 48-h spore germination success and length of gametophyte germ tubes of the giant kelp Macrocystis pyrifera have been developed as marine standardized toxicity tests (OEHHA, 2004), and, in Australia and New Zealand, assays related to the fertilization of Hormosira banksii, and the germination and growth of Ecklonia radiata have also been standardized (ANZECC and ARMCANZ, 2000). Organisms used include algae such as the freshwater algae, Pseudokirchneriella subcapitata, Anabaena flos-aquae, Microcystis aeriginosa, and Navicula peliculosa and the saltwater algae, Chlorella spp., Chlorococcum spp., Dunaliella tertiolecta, Isochrysis galbana, Nitzchia closterium. Molecular genetic techniques are beginning to be applied to the study of nitrogen cycling processes in marine systems (for review see Zehr and Ward, 2002; Chapter 30 by Zehr and Jenkins, this volume), where species- and group-specific information on the physiological/biochemical responses of marine microbes can be obtained (e.g., Cooksey 1998; Zehr and Voytek, 1999). 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. 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. In a recent report, Imai et al. (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 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). The pathway of oxidative stress response and response to cytokinin were taken from the KEGG database. This indicates that the high light shift-up (Fig. These bacteria were lethal against Karenia mikimotoi, Fibrocapsa japonica, and Heterosigma akashiwo. For aquatic systems, plants, invertebrates and vertebrates are tested. a Venn diagram of sharing pattern of orthologous gene groups. 2005;41:140–50. Description: Centric diatom, chain forming, two chloroplasts per cell. For the evaluation of repeat sequences, RepeatMasker (version 4.0.6) was used. Marinobacter sp. Because of this specific role of GSII in diatoms assimilating NH4 derived from NO3 assimilation rather than NH4 taken up directly from the environment, quantification of GS II gene expression (i.e., gln II mRNA) promises to be a useful indication (or proxy) of new production by phytoplankton (Takabayashi et al., 2005). Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Phycologia. Toxicity of substances is often underestimated when those protocols are used, as part of the toxicants can be removed from the media by adsorption to vial walls or the surfaces of living or dead cells. Effects of temperature and irradiance on growth of strains belonging to seven Skeletonema species isolate from Dokai Bay, southern Japan. In contrast, the valve diameter of resting spores is similar to the vegetative cells, but setae are absent (Reinke, 1984). Based on 16S rRNA gene sequence identity, the closest type species is Marinobacter algicola strain DG893, which had also been isolated from a laboratory culture of eukaryotic … Measures of effect include growth (as a percent of control) and cell numbers are usually reported as EC50s or IC50s. In the same manner, the number of conserved genes among the species tested could be calculated from the digit in the same figure and table. The valve face diameter for the genus is 2–38 μm. One strain, 41-DBG2, produced lethal substances that affected K. brevis and another related species, Gymnodinium mikimotoi (now Karenia mikimotoi). (XLSX 502 kb). It can be regarded as a toxic species since it produces a toxin that causes diarrohetic shellfish poisoning. PubMed 1). We therefore investigated gene expression profiles of oxidative stress pathway and cytokinin pathway including non differentially expressed genes. consists of a series of genetically and morphologically distinct species [13,14,15,16]. strain MCTG268 was isolated from a laboratory culture of the marine diatom Skeletonema costatum (CCAP 1077/1C) by enrichment with naphthalene as the sole carbon source. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 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. 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). (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). (B) Dinophyceae, Ceratium furca, a worldwide dinoflagellate with a solitary or paired life-form, length between 70 and 200 μm and in width between 30 and 50 μm. Measures of effect for algae are based on growth and the tests are normally run for periods of time that include many generations. 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. Cell division and Mitotic nuclear division were also shown from the common genes for harmful algal bloom. 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). These sequence raw reads were deposited to DDBJ DRA sequence read archive (ID:DRA007346). Few gene and protein sequences for nitrate reductase (NaR) have been well characterized from eukaryotic algae. 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. The genome size of Sc was larger than other diatoms, so that we checked if the reason for the larger-sized genome is due to repeat sequences. Tests on aquatic plants are required for most herbicide registrations with the U.S. EPA (CFR, 2004) and in Europe (European Commission, 1994). Thus the EC50s reported are similar to those that would be expected from chronic studies in other organisms. PubMed Imai (1997) examined several strains of Alteromonas sp. All sequence data are deposited in DDBJ (accession number is DRA007346). https://doi.org/10.1093/bioinformatics/btn548. Organic extracts of Skeletonema costatum were tested against the pathogenic bacteria Proteus mirabilis, Proteus vulgaris, Proteus aeruginosa, Salmonella paratyphi B, S. aureus, and Vibrio cholerae with in vitro assessment. Growth-related genes, such as cytokinin-related genes were also found in the common genes for the red tide from orthologs in four species (Figs. 1999;38:437–95. Then, we performed a blastp search using these seven genes against gene models of S. costatum, T. pseudonana, P. tricornutum, V. brassicaformis as a query with the threshold of e-value: 1e - 5. However, in coastal upwelling areas, since phytoplankton communities are dominated by the eukaryotic diatoms, sequences are required for genes for N assimilation by this eukaryotic group, and these are limited at the present time (see below and Armbrust et al., 2004). Numerous studies and observations have been made regarding the interaction between algaecidal bacteria and bloom-forming species. 143 genes were extracted as highly expressed genes at high temperatures with FC > 2. PubMed Central Estuar Coasts. A novel death-specific gene, ScDSP , was obtained from a death stage subtraction cDNA library of the diatom Skeletonema costatum . The authors proposed a novel approach of using this natural flora for preventing and controlling blooms by co-culturing macroalgae in the vicinity of aquaculture sites, or the establishment/restoration of macroalgal bed along the coast in order to seed the water with algaecidal bacteria. Test organisms include fathead minnow, bluegill, brook trout, flagfish, and sheepshead minnow. Red to green color represents log gene expression of ROS, SOD, RBO, and other genes involved in the pathway (a), and LOG, IPT, UGT, CKX, ARR, AK, AHK, CYP735A1, CYP735A2, and other genes involved in the pathway (b). 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.As results, we found that both evolutionary genomic and comparative transcriptomic studies revealed genes for oxidative stress response and response to … 5a). High levels of vitamin C or ascorbic acid have been reported in Chlorella sp. (2002) reported finding algaecidal bacteria growing on the surface of macroalgae such as Ulva sp. The example of the freshwater crustacean Daphnia pulex is significant. Basic local alignment search tool. Seraspe et al. AO and SN conceived the project, designed the content, and organized the manuscript. 2014;30(1):31–7. A. thaliana ID was then converted to RefSeq protein ID using BioMart to perform gene enrichment analysis by DAVID. in The Biology of Diatoms, ed. 2014;5:375. https://doi.org/10.3389/fmicb.2014.00375. For the genome quality in terms of gene model estimation we have performed BUSCO analysis, which assesses genome assembly with benchmarking universal single-copy orthologs. To extract the nuclear genome, blastn (v2.2.30)  search against chloroplast and mitochondrial genomes was done in the DB. Antibacterial activity was tested against S. aureus, MRSA, E. coli, P. aeruginosa and Enterococcus faecalis. 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. The full length of ScDSP cDNA was 921 bp in length, containing a 699-bp open reading frame encoding 232 amino acids and two stretches of 66 and 156 bp in the 5′ and 3′ untranslated regions, respectively. A heat map on the expression level of Sc under the conditions of light and darkness representing 251 genes was identified (Fig. The freshwater macrophyte Lemna spp. From screening studies, it has been shown that crude extracts of the diatom S. marinoi, cultured under phosphate and nitrogen starvation, displayed antibacterial activity against S. aureus with extracts at a concentration of 50 μg/mL (Lauritano et al., 2016). 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). Science. We conducted gene set enrichment analysis to clarify what functional categories are comprised of the Sc-specific genes and the common diatom genes related to the harmful algal bloom. Away from the epicenters of the upwelling areas and where, indeed, the water is less mixed but still charged with nutrients, such dinoflagellate taxa as Dinophysis, Gonyaulax and Gymnodinium catenatum provide prominent markers of the (R-S) transition between stressed and disturbed conditions. KM and TG conducted library construction and sequencing experiment using Illumina sequencer and data processing from raw data to qualified sequences. A. thaliana was chosen as they are most closely related to diatoms. 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. 2005;41:151–76. 251 genes were extracted as highly expressed genes at lighter condition with FC > 2. Size (cell): Diameter = 2-21um Distribution: Cosmopolitan in coastal waters excluding polar regions. Li et al. Article DIVERSITY IN THE GENUS SKELETONEMA (BACILLARIOPHYCEAE). Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Preliminary considerations of the types of phytoplankton characterizing the various subdivisions of the sea (Fig. BMC Genomics. However, most reports from coastal Japan described blooms of the species S. costatum, which was the first described in the genus, and until recently it was believed that only S. costatum and S. tropicum appear in Japanese coastal waters. A heat map on the expression level of Sc under poor nitrogen conditions and normal conditions were shown. 4). b Differentially expressed genes among Sc culture samples for different light conditions. Although phenolics are well-studied antioxidant components in higher plants, the acknowledgment of their presence in microalgae is fairly recent. From the k-mer analysis, genome size of Sc is estimated as 51,364,529 bp and Platanus (46.9 Mb) and SOAPdenovo2 (52.7 Mb) showed close genome size. Short read sequences were mapped to the assembled genome using HISAT2 (v2.1)  with default settings, and then expression frequencies were calculated using HTseq (v0.10.0) against the estimated gene model (CDS). Skeletonema costatum is a major bloom-forming species widely distributed around the world. ScienceDirect ® is a registered trademark of Elsevier B.V. ScienceDirect ® is a registered trademark of Elsevier B.V. URL: https://www.sciencedirect.com/science/article/pii/B0122268652003278, URL: https://www.sciencedirect.com/science/article/pii/B9780128009499000097, URL: https://www.sciencedirect.com/science/article/pii/B9780123725226000177, URL: https://www.sciencedirect.com/science/article/pii/B9780128114056000128, URL: https://www.sciencedirect.com/science/article/pii/B9780128007761000030, URL: https://www.sciencedirect.com/science/article/pii/B0122268652003394, URL: https://www.sciencedirect.com/science/article/pii/B9781845691523500078, URL: https://www.sciencedirect.com/science/article/pii/B9780123743671000562, URL: https://www.sciencedirect.com/science/article/pii/B9780128007761000364, URL: https://www.sciencedirect.com/science/article/pii/B9780128007761000078, Frances Wilkerson, Richard C. Dugdale, in, Nitrogen in the Marine Environment (Second Edition), Berges, 1997; Berges and Harrison, 1995; Berges, Hildebrand and Dahlin (2000) and Hildebrand (2005), Robertson and Alberte, 1996; Robertson and Tartar, 2006; Robertson, Anticancer, Antiviral, Antibacterial, and Antifungal Properties in Microalgae, Microalgae in Health and Disease Prevention, Mitigation of effects of harmful algal blooms, Ecotoxicological Risk Assessment of Pesticides in the Environment, Hayes' Handbook of Pesticide Toxicology (Third Edition), Cristiano V.M. BMC Genomics 19, 765 (2018). Many phenolics show good thermal stability. Front Microbiol. genome, we evaluated the assembled genomes by WGS , Platanus , Allpaths-LG , SOAPdenovo 2 , and SPAdes . However, these genetic diversities of silicate-related genes might reflect the complexity of diatom structures. 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. However, it is not a legal authority for statutory or regulatory purposes. Basically, the current standard microalgal bioassays for substances and effluents involve batch cultures of 50 mL in borosilicate flasks with an initial cellular density of 104 cells mL−1, continuous light, temperatures of 20 ± 1 °C and 72 h incubation, with four total cellular density counts (day 0, 1, 2, and 3). Bioinformatics. Poulsen and Kroger (2005) also showed that NaR expression was inducible in transgenic Cylindrotheca fusiformis when cells were given NO3.
2020 skeletonema costatum genome