- Open Access
Diatom genomes come of age
© BioMed Central Ltd 2008
- Published: 09 January 2009
The Erratum to this article has been published in Genome Biology 2010 11:401
The results of two published genome sequences from marine diatoms provide basic insights into how these remarkable organisms evolved to become one of the most successful groups of eukaryotic algae in the contemporary ocean.
- Horizontal Gene Transfer
- Long Terminal Repeat
- Long Terminal Repeat Retrotransposons
- Pennate Diatom
- Orthosilicic Acid
Comparison of the genome properties of Thalassiosira pseudonana and Phaeodactylum tricornutum genomes*
Genome size (Mb)
Number of chromosomes
Percentage of genome that is non-coding
ESTs in GenBank
A second, more surprising source of genetic variability is horizontal gene transfer (HGT). Phylogenetic analysis of P. tricornutum suggests that about 5% of the genome (587 genes) is derived from bacterial orthologs; more than half of these are shared with T. pseudonana, implying that they were acquired by diatoms early in their evolutionary history and perform essential functions [6, 7]. In particular, several genes of prokaryotic origin seem to have been recruited for metabolism of organic carbon and nitrogen, including genes involved in a urea cycle that probably evolved in the primordial heterotrophic host cell before acquisition of the secondary symbiont. The mechanism of HGT in diatoms is not understood. Viral infection is one obvious pathway; indeed, several viruses, including single-stranded RNA and single- and double-stranded DNA types, have been isolated that target specific diatoms . Virally mediated HGT can be inferred from the gene encoding a putative photo-receptor, phytochrome, that is clustered in the P. tricornutum genome with two viruses that infect brown algae . Other mechanisms proposed to facilitate acquisition of bacterial genes by HGT include phagotrophy and association with organelles or with intracellular endosymbionts or parasites. Furthermore, 22 genes in the diatoms are of chlamydial origin ; these genes were hypothesized to be derived from an ancient endosymbiosis event between chlamydiae and the ancestor of primary photosynthetic eukaryotes .
In the ocean, essential nutrients such as nitrate, phosphate and silicate are brought up to the surface from the interior by wind-driven mixing (for example, storms) or deep convection. Diatoms assimilate these nutrients very rapidly in excess of their immediate growth demands, storing the nutrients in a special compartment (a vacuole) and then using them for macromolecular biosynthesis . The genome sequences [6, 7] have revealed the unique nature of nitrogen cycling in diatoms: a catabolic urea cycle has been identified involving ornithine and citruline and potentially yielding urea and subsequently ammonia from hydrolysis of the substrate by urease. However, diatoms do not excrete inorganic nitrogen; rather the catabolic end-products of the urea cycle are themselves returned back to anabolic pathways that initially yield glutamine and glutamate (via the glutamine synthetase/glutamate synthase (GS/GOGAT) pathway) . Indeed, this efficient recycling of nutrients in diatoms was probably a major selective force for the evolution of the secondary symbiont; it prevented the original heterotrophic host cell from losing a valuable nutrient, while simultaneously photosynthesis in the newly acquired protoplast provided a steady supply of organic carbon skeletons essential for growth .
The primary mode of nutrition in diatoms is oxygenic photosynthesis. Although the core machinery for this process is highly conserved, it has been known since the mid-1970s that the affinity of diatoms for inorganic carbon is considerably higher than that of their primary carbon-fixing enzyme, Rubisco, for CO2, suggesting that diatoms must concentrate inorganic carbon in their cells . Metabolic studies on the biochemistry of photosynthesis in the related diatom Thalassiosira weissflogii suggest that a C4-like photosynthetic pathway, in which the initial product of carbon fixation is a four-carbon molecule such as malate or oxaloacetate, indeed operates in diatoms. In this model, these molecules would subsequently be translocated to the plastid and be decarboxylated, thereby increasing the local concentration of CO2 for Rubisco [19, 20]. In silico analysis of the diatom genome has revealed a complete suite of genes required for C4 metabolism [6, 21], but how the system actually operates remains unclear. Sequences of the two enzymes responsible for decarboxylation of oxaloacetate and malate suggest that the proteins are targeted to the mitochondria. If so, this would require CO2 to cross six intra-cellular membranes, from its source (the mitochondria, two membranes) to its sink (the plastid, a further four membranes); a seemingly inefficient system, as the mitochondria is clearly a major intracellular source of CO2 simply as a result of respiration. The localization of the first carboxylation step in the C4 pathway is also still unclear. Determination of the cellular localization of key enzymes and of the expression of C4-related genes in cells exposed to low levels of CO2 could resolve these issues.
The formation of the silicate-based cell wall in diatoms is one of the most interesting areas of research. Silicic acid is translocated across the plasma membrane via specific transporters and is subsequently conveyed to a silica deposition vesicle, a slightly acidic environment in which the new cell wall is completely formed before it is exported by exocytosis. Silaffins and long-chain polyamines have a role in the polymerization of silica, but the mechanism of pattern formation remains unknown. Genome analysis reveals that T. pseudonana contains three silicon transporters  and three silaffin genes . P. tricornutum, however, is an atypical diatom in that it does not have an obligate requirement of silicon for growth and exists as three distinct morphotypes: oval, triradiate and fusiform (Figure 1a). Only the oval morphotype contains a lightly silicified valve  and is the only diatom reported to take up the anionic form of silicon (silicate, or SiO(OH-)3), rather than the more commonly transported form, orthosilicic acid (Si(OH)4) . Genome sequencing  revealed genes for four silicon transporters in P. tricornutum, all with strong support from ESTs, but only one silaffin-like protein.
Iron limits primary production in three major areas of the ocean: the eastern equatorial Pacific, the subarctic Pacific and the Southern Ocean. So far, 11 iron enrichment experiments have been conducted in the open ocean, covering all three environments; these involve adding iron to the sea in order to stimulate growth of phytoplankton. In all experiments, the first major group of organisms to grow following fertilization was pennate diatoms. One major factor in the ability of diatoms to take advantage of the nutrient enrichment is the vacuole, a sort of 'food pantry', which does not, as yet, have a clear genetic marker. However, analysis of the T. pseudonana and P. tricornutum genomes has revealed the presence of several Fe acquisition and storage genes in P. tricornutum that are absent from T. pseudonana. Iron acquisition in T. pseudonana seems to work through a ferroxidase/permease pathway for Fe(II) uptake. In contrast, P. tricornutum may acquire iron through a cell-surface reductase. A recent discovery of iron storage ferritin in bloom-forming pennate diatoms contributes to their success in chronically low-iron oceanic regions . More data are required before we can be sure that this strategy can explain the success of pennate diatoms specifically in low Fe environments.
Diatoms use sophisticated mechanisms to monitor and adapt appropriately to changes in environmental stress conditions [27, 28]. The mosaic multi-lineage nature of the diatom genomes predicts interesting signaling pathways that are similar to features not only of plants and animals but also of prokaryotes. Both diatom genomes contain a bacterially derived two-component system composed of a novel domain organization of histidine kinase (sensor) and response regulator (transcriptional activators) [6, 7]. Calcium and nitric oxide were recently shown to act as important second messengers in diatom perception and transduction of stress conditions. A novel calcium-regulated protein, induced by nitric oxide (NO) and regulating cell death, has also been identified . Furthermore, a diatom alternative oxidase contains a calcium-binding EF-hand domain that is induced under iron starvation . Genetic manipulation of a chloroplast-localized protein PtNOA in diatoms has revealed the interplay between sensing chemicals cues (info-chemicals), oxidative stress and cell death through NO-based signaling .
One of the more enigmatic aspects of evolution of protists is the emergence of programmed cell death pathways. T. pseudonana has homologs to key components of programmed cell death biochemical machinery, including metacaspases, HtrA-family proteases, apoptosis-associated nuclear factors of the E2F and DP1 families, cell death suppressor proteins and a cellular apoptosis susceptibility protein . Diatom genomes contain five to six metacaspases, some of which are constitutively expressed whereas others are induced by nutrient deprivation [6, 7, 32]. However, T. pseudonana lacks homologs of important elements of metazoan apoptotic pathways, such as p53 and the Bcl-2 family of apoptosis regulators, as well as TIR adaptor proteins and AP-ATPases, both of which are abundant in Arabidopsis thaliana. These findings raise fundamental questions about whether T. pseudonana has a functional programmed cell death pathway in response to iron starvation , raising fundamental questions about how it is regulated.
Genetic transformation methods have been established for both T. pseudonana and P. tricornutum [33, 34]. Expression vectors for T. pseudonana have been developed that allow constitutive and inducible protein expression . Also recently developed was a method for growing cultures of T. pseudonana synchronously , making it possible to gain insights into cell division and other metabolic processes tightly coupled to the cell cycle, such as silification. A useful tool for reverse functional genomics has also been developed in P. tricornutum that allows high-throughput cloning and expression of a target gene . These tools are important advances that will enable insights into the molecular mechanisms of diatom biology that were not possible even 5 years ago. However, the field still lacks classical genetic techniques, such as a method for gene knockout. Perhaps with the newly available genome sequence and the growing interest in diatom genetics, these tools will soon become available.
Diatoms have inspired many biologists and engineers. Silicon-based nanotechnology is a multi-billion-dollar industry, but there is an increasing need for the efficient and cost-effective production of such devices, for example, in solar energy capture, charge separation in battery technologies, or even in separation technologies involving purification of gases or solutes in fluids. Diatoms provide an unparalleled system for studying the basic mechanism of silica nanofabrication because they can make complex, reproducible three-dimensional structures under ambient conditions. In addition, because diatoms have been such an important component of petroleum, potential genetic manipulation may lead to more efficient use of these organisms as biofuel feedstock. Indeed, the development of a model organism such as P. tricornutum, combined with system-level approaches for better understanding of how carbon is allocated to specific sinks, may ultimately provide a source of advanced, sustainable biofuels that does not compete with food production.
Diatom genomes are coming of age. These protists, long studied by marine biologists for their complexity and ecological success, are now becoming a source of information not only about the evolutionary history of eukaryotes, but as a potential source of nanodevices and energy for our future. These genome sequences [6, 7] are the beginning of a long learning process that will potentially teach us how the complex web of metabolic processes was selected by specific clades and how we can use that information to develop a sustainable world in the coming centuries.
- Smetacek V: Diatoms and the ocean carbon cycle. Protist. 1999, 150: 25-32.View ArticleGoogle Scholar
- Delwiche C: Tracing the thread of plastid diversity through the tapestry of life. Am Nat. 2000, 154: S164-S177. 10.1086/303291.View ArticleGoogle Scholar
- Cavalier-Smith T: Chloroplast evolution: secondary symbiogenesis and multiple losses. Curr Biol. 2002, 12: R62-R64. 10.1016/S0960-9822(01)00675-3.View ArticleGoogle Scholar
- Falkowski PG, Katz ME, Knoll AH, Quigg A, Raven JA, Schofield O, Taylor FJ: The evolution of modern eukaryotic phytoplankton. Science. 2004, 305: 354-360. 10.1126/science.1095964.View ArticleGoogle Scholar
- Kooistra WHCF, Gersonde R, Medlin LK, Mann DG: The origin and evolution of the diatoms: their adaptation to a planktonic existence. Evolution of Primary Producers in the Sea. Edited by: Falkowski PG, Knoll AH. 2007, New York: Academic Press, 207-249.View ArticleGoogle Scholar
- Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kröger N, Lau WW, Lane TW, Larimer FW, Lippmeier JC, Lucas S: The genome diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science. 2004, 306: 79-86. 10.1126/science.1101156.View ArticleGoogle Scholar
- Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A: The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature. 2008, doi:10.1038/nature07410.Google Scholar
- Oliver MJ, Petrov D, Ackerly D, Falkowski P, Schofield OM: The mode and tempo of genome size evolution in eukaryotes. Genome Res. 2007, 17: 594-601. 10.1101/gr.6096207.View ArticleGoogle Scholar
- The Diatom EST Database. [http://www.biologie.ens.fr/diatomics/EST3/]
- Roy SW, Penny D: A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain. Mol Biol Evol. 2007, 24: 1447-1457. 10.1093/molbev/msm048.View ArticleGoogle Scholar
- De Bodt S, Maere S, Peer Van de Y: Genome duplication and the origin of angiosperms. Trends Ecol Evol. 2005, 20: 591-597. 10.1016/j.tree.2005.07.008.View ArticleGoogle Scholar
- Nagasaki K: Dinoflagellates, diatoms and their viruses. J Microbiol. 2008, 46: 235-243. 10.1007/s12275-008-0098-y.View ArticleGoogle Scholar
- Montsant A, Allen AE, Coesel S, De Martino A, Falciatore A, Mangogna M, Siaut M, Heijde M, Jabbari K, Maheswari U, Rayko E, Vardi A, Apt KE, Berges JA, Chiovitti A, Davis AK, Thamatrakoln K, Hadi MZ, Lane TW, Lippmeier JC, Martinez D, Parker MS, Pazour GJ, Saito MA, Rokhsar DS, Armbrust EV, Bowler C: Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana. J Phycol. 2007, 43: 585-604. 10.1111/j.1529-8817.2007.00342.x.View ArticleGoogle Scholar
- Becker B, Hoef-Emden K, Melkonian M: Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes. BMC Evol Biol. 2008, 8: 203-10.1186/1471-2148-8-203.View ArticleGoogle Scholar
- Huang JL, Gogarten JP: Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?. Genome Biol. 2007, 8: 13-Google Scholar
- Allen AE, Vardi A, Bowler C: An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms. Curr Opin Plant Biol. 2006, 9: 264-273. 10.1016/j.pbi.2006.03.013.View ArticleGoogle Scholar
- Zehr JP, Falkowski PG: Pathway of ammonium in a marine diatom determined with the radiotracer 13N. J Phycol. 1988, 24: 588-591.Google Scholar
- Falkowski PG, Raven JA: Aquatic Photosynthesis. 2007, Princeton: Princeton University Press, 484-2Google Scholar
- Morris I, Mukerji D: Photosynthetic carboxylating enzymes on Phaeodactylum tricornutum : assay methods and properties. Mar Biol. 1976, 36: 199-206. 10.1007/BF00389280.View ArticleGoogle Scholar
- Reinfelder JR, Kraepiel AML, Morel FMM: Unicellular C4 photosynthesis in a marine diatom. Nature. 2000, 407: 996-999. 10.1038/35039612.View ArticleGoogle Scholar
- Kroth PG, Chiovitti A, Gruber A, Martin-Jezequel V, Mock T, Parker MS, Stanley MS, Kaplan A, Caron L, Weber T, Maheswari U, Armbrust EV, Bowler C: A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. PLoS ONE. 2008, 3: e1426-10.1371/journal.pone.0001426.View ArticleGoogle Scholar
- Thamatrakoln K, Alverson AJ, Hildebrand M: Comparative sequence analysis of diatom silicon transporters: towards a mechanistic model of silicon transport. J Phycol. 2006, 42: 822-834. 10.1111/j.1529-8817.2006.00233.x.View ArticleGoogle Scholar
- Kröger N: Prescribing diatom morphology: toward genetic engineering of biological nanomaterials. Curr Opin Chem Biol. 2007, 11: 662-669. 10.1016/j.cbpa.2007.10.009.View ArticleGoogle Scholar
- Borowitzka MA, Volcani BE: The polymorphic diatom Phaeodactylum tricornutum : ultrastructure of its morphotypes. J Phycol. 1978, 14: 10-21. 10.1111/j.1529-8817.1978.tb00625.x.View ArticleGoogle Scholar
- Del Amo Y, Brzezinski MA: The chemical form of dissolved Si taken up by marine diatoms. J Phycol. 1999, 35: 1162-1170. 10.1046/j.1529-8817.1999.3561162.x.View ArticleGoogle Scholar
- Marchetti A, Parker MS, Moccia LP, Ostlund EL, Arrieta A, Ribalet F, Murphy MEP, Maldonado MT, Armbrust EV: Ferritin is used for iron storage in bloom-forming marine pennate diatoms. Nature. 2008, doi:101038/nature07539.Google Scholar
- Falciatore A, d'Alcalà MR, Croot P, Bowler C: Perception of environmental signals by a marine diatom. Science. 2000, 288: 2363-2366. 10.1126/science.288.5475.2363.View ArticleGoogle Scholar
- Vardi A, Formiggini F, Casotti R, De Martino A, Ribalet F, Miralto A, Bowler C: A stress surveillance system based on calcium and nitric oxide in marine diatoms. PLoS Biol. 2006, 4: e60-10.1371/journal.pbio.0040060.View ArticleGoogle Scholar
- Chung CC, Hwang S-PL, Chang J: Nitric oxide as a signaling factor to upregulate the death-specific protein in a marine diatom, Skeletonema costatum, during blockage of electron flow in photosynthesis. Appl Environ Microbiol. 2008, 74: 6521-6527. 10.1128/AEM.01481-08.View ArticleGoogle Scholar
- Allen AE, LaRoche J, Maheswari U, Lommer M, Schauer N: Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation. Proc Natl Acad Sci USA. 2008, 105: 10438-10443. 10.1073/pnas.0711370105.View ArticleGoogle Scholar
- Vardi A, Bidle KD, Kwityn C, Hirsh DJ, Thompson SM, Callow JA, Falkowski P, Bowler C: A diatom gene regulating nitric oxide signaling and susceptibility to diatom-derived aldehydes. Curr Biol. 2008, 18: 1-5. 10.1016/j.cub.2008.05.037.View ArticleGoogle Scholar
- Bidle KD, Bender SJ: Iron starvation and culture age activate meta-caspases and programmed cell death in the marine diatom, Thalassiosira pseudonana. Eukaryotic Cell. 2008, 7: 223-236. 10.1128/EC.00296-07.View ArticleGoogle Scholar
- Apt KE, Kroth-Pancic PG, Grossman AR: Stable nuclear transformation of the diatom Phaeodactylum tricornutum. Mol Gen Genet. 1996, 252: 572-579.Google Scholar
- Poulsen N, Chesley PM, Kröger N: Molecular genetic manipulation of the diatom Thalassiosira pseudonana (Bacillariophyceae). J Phycol. 2006, 42: 1059-1065. 10.1111/j.1529-8817.2006.00269.x.View ArticleGoogle Scholar
- Hildebrand M, Frigeri LG, Davis AK: Synchronized growth of Thalassiosira pseudonana (Bacillariophyceae) provides novel insights into cell wall synthesis processes in relation to the cell cycle. J Phycol. 2007, 43: 730-740. 10.1111/j.1529-8817.2007.00361.x.View ArticleGoogle Scholar
- Siaut M, Heijde M, Mangogna M, Montsant A, Coesel S, Allen A, Manfredonia A, Falciatore A, Bowler C: Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum. Gene. 2007, 406: 23-25.View ArticleGoogle Scholar