Andrew E Allen

Publications of Andrew E Allen

• Leveraging metabolomics for functional investigations in sequenced marine diatoms.

  Authors: Alisdair R Fernie, Toshihiro Obata, Andrew E Allen, Wagner L Araújo, Chris Bowler

  Trends in plant science. 03/2012;

  Recent years have witnessed the genomic decoding of a wide range of photosynthetic organisms from the model plant Arabidopsis thaliana and the complex genomes of important crop species toRecent years have witnessed the genomic decoding of a wide range of photosynthetic organisms from the model plant Arabidopsis thaliana and the complex genomes of important crop species to single-celled marine phytoplankton. The comparative sequencing of green, red and brown algae has provided considerable insight into a number of important questions concerning their evolution, physiology and metabolism. The combinatorial application of metabolomics has further deepened our understanding both of the function of individual genes and of metabolic processes. Here we discuss the power of utilising metabolomics in conjunction with sequencing data to gain greater insight into the metabolic hierarchies underpinning the function of individual organisms, using unicellular marine diatoms as a case study to exemplify the advantages of this approach.

• Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability.

  Authors: Adrian Marchetti, David M Schruth, Colleen A Durkin, Micaela S Parker, Robin B Kodner, Chris T Berthiaume, Rhonda Morales, Andrew E Allen, E Virginia Armbrust

  Proceedings of the National Academy of Sciences of the United States of America. 02/2012; 109(6):E317-25.

  In vast expanses of the oceans, growth of large phytoplankton such as diatoms is limited by iron availability. Diatoms respond almost immediately to the delivery of iron and rapidly compose theIn vast expanses of the oceans, growth of large phytoplankton such as diatoms is limited by iron availability. Diatoms respond almost immediately to the delivery of iron and rapidly compose the majority of phytoplankton biomass. The molecular bases underlying the subsistence of diatoms in iron-poor waters and the plankton community dynamics that follow iron resupply remain largely unknown. Here we use comparative metatranscriptomics to identify changes in gene expression associated with iron-stimulated growth of diatoms and other eukaryotic plankton. A microcosm iron-enrichment experiment using mixed-layer waters from the northeastern Pacific Ocean resulted in increased proportions of diatom transcripts and reduced proportions of transcripts from most other taxa within 98 h after iron addition. Hundreds of diatom genes were differentially expressed in the iron-enriched community compared with the iron-limited community; transcripts of diatom genes required for synthesis of photosynthesis and chlorophyll components, nitrate assimilation and the urea cycle, and synthesis of carbohydrate storage compounds were significantly overrepresented. Transcripts of genes encoding rhodopsins in eukaryotic phytoplankton were significantly underrepresented following iron enrichment, suggesting rhodopsins help cells cope with low-iron conditions. Oceanic diatoms appear to display a distinctive transcriptional response to iron enrichment that allows chemical reduction of available nitrogen and carbon sources along with a continued dependence on iron-free photosynthetic proteins rather than substituting for iron-containing functional equivalents present within their gene repertoire. This ability of diatoms to divert their newly acquired iron toward nitrate assimilation may underlie why diatoms consistently dominate iron enrichments in high-nitrate, low-chlorophyll regions.

• Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic.

  Authors: Lisa Zeigler Allen, Eric E Allen, Jonathan H Badger, John P McCrow, Ian T Paulsen, Liam Dh Elbourne, Mathangi Thiagarajan, Doug B Rusch, Kenneth H Nealson, Shannon J Williamson, J Craig Venter, Andrew E Allen

  The ISME journal. 01/2012;

  Metagenomic data sets were generated from samples collected along a coastal to open ocean transect between Southern California Bight and California Current waters during a seasonal upwelling event,Metagenomic data sets were generated from samples collected along a coastal to open ocean transect between Southern California Bight and California Current waters during a seasonal upwelling event, providing an opportunity to examine the impact of episodic pulses of cold nutrient-rich water into surface ocean microbial communities. The data set consists of ∼5.8 million predicted proteins across seven sites, from three different size classes: 0.1-0.8, 0.8-3.0 and 3.0-200.0 μm. Taxonomic and metabolic analyses suggest that sequences from the 0.1-0.8 μm size class correlated with their position along the upwelling mosaic. However, taxonomic profiles of bacteria from the larger size classes (0.8-200 μm) were less constrained by habitat and characterized by an increase in Cyanobacteria, Bacteroidetes, Flavobacteria and double-stranded DNA viral sequences. Functional annotation of transmembrane proteins indicate that sites comprised of organisms with small genomes have an enrichment of transporters with substrate specificities for amino acids, iron and cadmium, whereas organisms with larger genomes have a higher percentage of transporters for ammonium and potassium. Eukaryotic-type glutamine synthetase (GS) II proteins were identified and taxonomically classified as viral, most closely related to the GSII in Mimivirus, suggesting that marine Mimivirus-like particles may have played a role in the transfer of GSII gene functions. Additionally, a Planctomycete bloom was sampled from one upwelling site providing a rare opportunity to assess the genomic composition of a marine Planctomycete population. The significant correlations observed between genomic properties, community structure and nutrient availability provide insights into habitat-driven dynamics among oligotrophic versus upwelled marine waters adjoining each other spatially.

• Evolution and functional diversification of fructose bisphosphate aldolase genes in photosynthetic marine diatoms.

  Authors: Andrew E Allen, Ahmed Moustafa, Anton Montsant, Angelika Eckert, Peter G Kroth, Chris Bowler

  Molecular biology and evolution. 09/2011; 29(1):367-79.

  Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked throughDiatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked through common, although not necessarily monophyletic, acquisition of plastid endosymbionts of red as well as most likely green algal origin. There is also strong evidence for a relatively high level of lineage-specific bacterial gene acquisition within chromalveolates. Therefore, analyses of gene content and derivation in chromalveolate taxa have indicated particularly diverse origins of their overall gene repertoire. As a single group of functionally related enzymes spanning two distinct gene families, fructose 1,6-bisphosphate aldolases (FBAs) illustrate the influence on core biochemical pathways of specific evolutionary associations among diatoms and other chromalveolates with various plastid-bearing and bacterial endosymbionts. Protein localization and activity, gene expression, and phylogenetic analyses indicate that the pennate diatom Phaeodactylum tricornutum contains five FBA genes with very little overall functional overlap. Three P. tricornutum FBAs, one class I and two class II, are plastid localized, and each appears to have a distinct evolutionary origin as well as function. Class I plastid FBA appears to have been acquired by chromalveolates from a red algal endosymbiont, whereas one copy of class II plastid FBA is likely to have originated from an ancient green algal endosymbiont. The other copy appears to be the result of a chromalveolate-specific gene duplication. Plastid FBA I and chromalveolate-specific class II plastid FBA are localized in the pyrenoid region of the chloroplast where they are associated with β-carbonic anhydrase, which is known to play a significant role in regulation of the diatom carbon concentrating mechanism. The two pyrenoid-associated FBAs are distinguished by contrasting gene expression profiles under nutrient limiting compared with optimal CO(2) fixation conditions, suggestive of a distinct specialized function for each. Cytosolically localized FBAs in P. tricornutum likely play a role in glycolysis and cytoskeleton function and seem to have originated from the stramenopile host cell and from diatom-specific bacterial gene transfer, respectively.

• Genomes of uncultured eukaryotes: sorting FACS from fiction.

  Authors: Alexandra Z Worden, Christopher Dupont, Andrew E Allen

  Genome biology. 06/2011; 12(6):117.

  A recent study explores the genome content of uncultured unicellular marine eukaryotes and provides insights about interactions between uncultured eukaryotes and other biological entities.

• Evolution and metabolic significance of the urea cycle in photosynthetic diatoms.

  Authors: Andrew E Allen, Christopher L Dupont, Miroslav Oborník, Aleš Horák, Adriano Nunes-Nesi, John P McCrow, Hong Zheng, Daniel A Johnson, Hanhua Hu, Alisdair R Fernie, Chris Bowler

  Nature. 05/2011; 473(7346):203-7.

  Diatoms dominate the biomass of phytoplankton in nutrient-rich conditions and form the basis of some of the world's most productive marine food webs. The diatom nuclear genome contains genes withDiatoms dominate the biomass of phytoplankton in nutrient-rich conditions and form the basis of some of the world's most productive marine food webs. The diatom nuclear genome contains genes with bacterial and plastid origins as well as genes of the secondary endosymbiotic host (the exosymbiont), yet little is known about the relative contribution of each gene group to diatom metabolism. Here we show that the exosymbiont-derived ornithine-urea cycle, which is similar to that of metazoans but is absent in green algae and plants, facilitates rapid recovery from prolonged nitrogen limitation. RNA-interference-mediated knockdown of a mitochondrial carbamoyl phosphate synthase impairs the response of nitrogen-limited diatoms to nitrogen addition. Metabolomic analyses indicate that intermediates in the ornithine-urea cycle are particularly depleted and that both the tricarboxylic acid cycle and the glutamine synthetase/glutamate synthase cycles are linked directly with the ornithine-urea cycle. Several other depleted metabolites are generated from ornithine-urea cycle intermediates by the products of genes laterally acquired from bacteria. This metabolic coupling of bacterial- and exosymbiont-derived proteins seems to be fundamental to diatom physiology because the compounds affected include the major diatom osmolyte proline and the precursors for long-chain polyamines required for silica precipitation during cell wall formation. So far, the ornithine-urea cycle is only known for its essential role in the removal of fixed nitrogen in metazoans. In diatoms, this cycle serves as a distribution and repackaging hub for inorganic carbon and nitrogen and contributes significantly to the metabolic response of diatoms to episodic nitrogen availability. The diatom ornithine-urea cycle therefore represents a key pathway for anaplerotic carbon fixation into nitrogenous compounds that are essential for diatom growth and for the contribution of diatoms to marine productivity.

• Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana.

  Authors: Masaaki Tachibana, Andrew E Allen, Sae Kikutani, Yuri Endo, Chris Bowler, Yusuke Matsuda

  Photosynthesis research. 03/2011; 109(1-3):205-21.

  It is believed that intracellular carbonic anhydrases (CAs) are essential components of carbon concentrating mechanisms in microalgae. In this study, putative CA-encoding genes were identified in theIt is believed that intracellular carbonic anhydrases (CAs) are essential components of carbon concentrating mechanisms in microalgae. In this study, putative CA-encoding genes were identified in the genome sequences of the marine diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. Subsequently, the subcellular localizations of the encoded proteins were determined. Nine and thirteen CA sequences were found in the genomes of P. tricornutum and T. pseudonana, respectively. Two of the β-CA genes in P. tricornutum corresponded to ptca1 and ptca2 identified previously. Immunostaining transmission electron microscopy of a PtCA1:YFP fusion expressed in the cells of P. tricornutum clearly showed the localization of PtCA1 within the central part of the pyrenoid structure in the chloroplast. Besides these two β-CA genes, P. tricornutum likely contains five α- and two γ-CA genes, whereas T. pseudonana has three α-, five γ-, four δ-, and one ζ-CA genes. Semi-quantitative reverse transcription PCR performed on mRNA from the two diatoms grown in changing light and CO(2) conditions revealed that levels of six putative α- and γ-CA mRNAs in P. tricornutum did not change between cells grown in air-level CO(2) and 5% CO(2). However, mRNA levels of one putative α-CA gene, CA-VII in P. tricornutum, were reduced in the dark compared to that in the light. In T. pseudonana, mRNA accumulation levels of putative α-CA (CA-1), ζ-CA (CA-3) and δ-CA (CA-7) were analyzed and all levels found to be significantly reduced when cells were grown in 0.16% CO(2). Intercellular localizations of eight putative CAs were analyzed by expressing GFP fusion in P. tricornutum and T. pseudonana. In P. tricornutum, CA-I and II localized in the periplastidial compartment, CA-III, VI, VII were found in the chloroplast endoplasmic reticulum, and CA-VIII was localized in the mitochondria. On the other hand, T. pseudonana CA-1 localized in the stroma and CA-3 was found in the periplasm. These results suggest that CAs are constitutively present in the four chloroplastic membrane systems in P. tricornutum and that CO(2) responsive CAs occur in the pyrenoid of P. tricornutum, and in the stroma and periplasm of T. pseudonana.

• Efficiency of the CO2-concentrating mechanism of diatoms.

  Authors: Brian M Hopkinson, Christopher L Dupont, Andrew E Allen, François M M Morel

  Proceedings of the National Academy of Sciences of the United States of America. 02/2011; 108(10):3830-7.

  Diatoms are responsible for a large fraction of CO(2) export to deep seawater, a process responsible for low modern-day CO(2) concentrations in surface seawater and the atmosphere. Like otherDiatoms are responsible for a large fraction of CO(2) export to deep seawater, a process responsible for low modern-day CO(2) concentrations in surface seawater and the atmosphere. Like other photosynthetic organisms, diatoms have adapted to these low ambient concentrations by operating a CO(2) concentrating mechanism (CCM) to elevate the concentration of CO(2) at the site of fixation. We used mass spectrometric measurements of passive and active cellular carbon fluxes and model simulations of these fluxes to better understand the stoichiometric and energetic efficiency and the physiological architecture of the diatom CCM. The membranes of diatoms are highly permeable to CO(2), resulting in a large diffusive exchange of CO(2) between the cell and external milieu. An active transport of carbon from the cytoplasm into the chloroplast is the main driver of the diatom CCM. Only one-third of this carbon flux is fixed photosynthetically, and the rest is lost by CO(2) diffusion back to the cytoplasm. Both the passive influx of CO(2) from the external medium and the recycling of the CO(2) leaking out of the chloroplast are achieved by the activity of a carbonic anhydrase enzyme combined with the maintenance of a low concentration of HCO(3)(-) in the cytoplasm. To achieve the CO(2) concentration necessary to saturate carbon fixation, the CO(2) is most likely concentrated within the pyrenoid, an organelle within the chloroplast where the CO(2)-fixating enzyme is located.

• Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana.

  Authors: Trina M Norden-Krichmar, Andrew E Allen, Terry Gaasterland, Mark Hildebrand

  PloS one. 01/2011; 6(8):e22870.

  This study presents the first characterization of endogenous small RNAs in a diatom, Thalassiosira pseudonana. Small RNAs act as transcriptional and translational regulators, controlling specificThis study presents the first characterization of endogenous small RNAs in a diatom, Thalassiosira pseudonana. Small RNAs act as transcriptional and translational regulators, controlling specific target genes involved in various cellular functions. Diatoms are unicellular photosynthetic organisms that play major roles in environmental processes, such as food webs and global carbon fixation. Small RNA cDNA libraries were constructed for exponentially growing T. pseudonana, and then subjected to highly parallel pyrosequencing (454) and sequencing-by-ligation (Applied Biosystems SOLiD). From the computational analysis of approximately 300,000 sequences in the 454 library and over 17 million sequences in the SOLiD libraries, there exists evidence of a core set of small RNA genes including: novel microRNAs, repeat-associated short interfering RNAs, and endogenous short interfering RNAs. The diatom genome contains elements similar to plant small RNA systems, such as the RNAi machinery, a high percentage of short interfering RNAs originating from protein-coding and repetitive regions of the genome, and putative binding sites of the small RNAs occurring primarily in the coding section of the predicted targets. The characterization of the small RNA transcriptome of T. pseudonana establishes the possibility of a wide range of gene regulatory mechanisms in diatoms.

• iTree: A high-throughput phylogenomic pipeline

  Authors: Ahmed Moustafa, Debashish Bhattacharya, Andrew E. Allen

  Biomedical Engineering Conference (CIBEC), 2010 5th Cairo International; 12/2010

  Phylogenomics, conventionally defined as the intersection of phylogenetics and genomics, has become a key instrument in a wide spectrum of biological studies, including resolution of complexPhylogenomics, conventionally defined as the intersection of phylogenetics and genomics, has become a key instrument in a wide spectrum of biological studies, including resolution of complex evolutionary relationships, assignment of taxonomic affiliation, prediction of protein molecular functions, and tracing horizontal gene transfer event. Here, we introduce an open-source phylogenomic pipeline, iTree, which automates the execution of phylogenetic analyses under multithreaded and grid-computing environments, providing a scalable high-throughput platform for performing genome-wide evolutionary analyses. Furthermore, we describe the results of two applications of using iTree: (1) taxonomic assignment of 16S ribosomal RNA sequences from human oral metagenomic samples and (2) detection of horizontal gene transfer in microbial genomes.

• Genomic and functional adaptation in surface ocean planktonic prokaryotes.

  Authors: Shibu Yooseph, Kenneth H Nealson, Douglas B Rusch, John P McCrow, Christopher L Dupont, Maria Kim, Justin Johnson, Robert Montgomery, Steve Ferriera, Karen Beeson, Shannon J Williamson, Andrey Tovchigrechko, Andrew E Allen, Lisa A Zeigler, Granger Sutton, Eric Eisenstadt, Yu-Hui Rogers, Robert Friedman, Marvin Frazier, J Craig Venter

  Nature. 11/2010; 468(7320):60-6.

  The understanding of marine microbial ecology and metabolism has been hampered by the paucity of sequenced reference genomes. To this end, we report the sequencing of 137 diverse marine isolatesThe understanding of marine microbial ecology and metabolism has been hampered by the paucity of sequenced reference genomes. To this end, we report the sequencing of 137 diverse marine isolates collected from around the world. We analysed these sequences, along with previously published marine prokaryotic genomes, in the context of marine metagenomic data, to gain insights into the ecology of the surface ocean prokaryotic picoplankton (0.1-3.0 μm size range). The results suggest that the sequenced genomes define two microbial groups: one composed of only a few taxa that are nearly always abundant in picoplanktonic communities, and the other consisting of many microbial taxa that are rarely abundant. The genomic content of the second group suggests that these microbes are capable of slow growth and survival in energy-limited environments, and rapid growth in energy-rich environments. By contrast, the abundant and cosmopolitan picoplanktonic prokaryotes for which there is genomic representation have smaller genomes, are probably capable of only slow growth and seem to be relatively unable to sense or rapidly acclimate to energy-rich conditions. Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass.

• The voyage of the microbial eukaryote.

  Authors: Alexandra Z Worden, Andrew E Allen

  Current opinion in microbiology. 10/2010; 13(5):652-60.

  Although genome data from unicellular marine eukaryotes is sparse, sequences from several supergroups have initiated an era of genome-enabled research aimed at understanding gene function, evolution,Although genome data from unicellular marine eukaryotes is sparse, sequences from several supergroups have initiated an era of genome-enabled research aimed at understanding gene function, evolution, and adaptation in non-traditional model protists. Trends in genomic content within and between different lineages are emerging, including phylogenetically anomalous patterns, sometimes resulting from horizontal gene transfer. Some such genes have nutrient uptake and metabolism roles suggesting that bacterial and eukaryotic microbes have similar cellular-mineral-environmental constraints. Many 'accessory genome' components are of unknown function, but low gene copy numbers combined with small genomes make protists ideal for systems biology. Cultured and uncultured protists are providing insights to ecology, ancestral features and the role of cooption in development of complex traits. Various protists harbor features important in sexuality and multicellularity once believed to have originated in metazoans or other multicellular taxa.

• Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton.

  Authors: Marie L Cuvelier, Andrew E Allen, Adam Monier, John P McCrow, Monique Messié, Susannah G Tringe, Tanja Woyke, Rory M Welsh, Thomas Ishoey, Jae-Hyeok Lee [......] Mikel Latasa, Cédric Guigand, Kurt R Buck, Jason Hilton, Mathangi Thiagarajan, Elisabet Caler, Betsy Read, Roger S Lasken, Francisco P Chavez, Alexandra Z Worden

  Proceedings of the National Academy of Sciences of the United States of America. 08/2010; 107(33):14679-84.

  Among eukaryotes, four major phytoplankton lineages are responsible for marine photosynthesis; prymnesiophytes, alveolates, stramenopiles, and prasinophytes. Contributions by individual taxa,Among eukaryotes, four major phytoplankton lineages are responsible for marine photosynthesis; prymnesiophytes, alveolates, stramenopiles, and prasinophytes. Contributions by individual taxa, however, are not well known, and genomes have been analyzed from only the latter two lineages. Tiny "picoplanktonic" members of the prymnesiophyte lineage have long been inferred to be ecologically important but remain poorly characterized. Here, we examine pico-prymnesiophyte evolutionary history and ecology using cultivation-independent methods. 18S rRNA gene analysis showed pico-prymnesiophytes belonged to broadly distributed uncultivated taxa. Therefore, we used targeted metagenomics to analyze uncultured pico-prymnesiophytes sorted by flow cytometry from subtropical North Atlantic waters. The data reveal a composite nuclear-encoded gene repertoire with strong green-lineage affiliations, which contrasts with the evolutionary history indicated by the plastid genome. Measured pico-prymnesiophyte growth rates were rapid in this region, resulting in primary production contributions similar to the cyanobacterium Prochlorococcus. On average, pico-prymnesiophytes formed 25% of global picophytoplankton biomass, with differing contributions in five biogeographical provinces spanning tropical to subpolar systems. Elements likely contributing to success include high gene density and genes potentially involved in defense and nutrient uptake. Our findings have implications reaching beyond pico-prymnesiophytes, to the prasinophytes and stramenopiles. For example, prevalence of putative Ni-containing superoxide dismutases (SODs), instead of Fe-containing SODs, seems to be a common adaptation among eukaryotic phytoplankton for reducing Fe quotas in low-Fe modern oceans. Moreover, highly mosaic gene repertoires, although compositionally distinct for each major eukaryotic lineage, now seem to be an underlying facet of successful marine phytoplankton.

• The Ectocarpus genome and the independent evolution of multicellularity in brown algae.

  Authors: J Mark Cock, Lieven Sterck, Pierre Rouzé, Delphine Scornet, Andrew E Allen, Grigoris Amoutzias, Veronique Anthouard, François Artiguenave, Jean-Marc Aury, Jonathan H Badger [......] Declan C Schroeder, Béatrice Ségurens, Martina Strittmatter, Thierry Tonon, James W Tregear, Klaus Valentin, Peter von Dassow, Takahiro Yamagishi, Yves Van de Peer, Patrick Wincker

  Nature. 06/2010; 465(7298):617-21.

  Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominantBrown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further.

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• Oceanographic and biogeochemical insights from diatom genomes.

  Authors: Chris Bowler, Assaf Vardi, Andrew E Allen

  Annual review of marine science. 01/2010; 2:333-65.

  Diatoms are the most successful group of eukaryotic phytoplankton in the modern ocean and have risen to dominance relatively quickly over the last 100 million years. Recently completed whole genomeDiatoms are the most successful group of eukaryotic phytoplankton in the modern ocean and have risen to dominance relatively quickly over the last 100 million years. Recently completed whole genome sequences from two species of diatom, Thalassiosira pseudonana and Phaeodactylum tricornutum, have revealed a wealth of information about the evolutionary origins and metabolic adaptations that have led to their ecological success. A major finding is that they have incorporated genes both from their endosymbiotic ancestors and by horizontal gene transfer from marine bacteria. This unique melting pot of genes encodes novel capacities for metabolic management, for example, allowing the integration of a urea cycle into a photosynthetic cell. In this review we show how genome-enabled approaches are being leveraged to explore major phenomena of oceanographic and biogeochemical relevance, such as nutrient assimilation and life histories in diatoms. We also discuss how diatoms may be affected by climate change-induced alterations in ocean processes.

• Digital expression profiling of novel diatom transcripts provides insight into their biological functions.

  Authors: Uma Maheswari, Kamel Jabbari, Jean-Louis Petit, Betina M Porcel, Andrew E Allen, Jean-Paul Cadoret, Alessandra De Martino, Marc Heijde, Raymond Kaas, Julie La Roche, Pascal J Lopez, Véronique Martin-Jézéquel, Agnès Meichenin, Thomas Mock, Micaela Schnitzler Parker, Assaf Vardi, E Virginia Armbrust, Jean Weissenbach, Michaël Katinka, Chris Bowler

  Genome biology. 01/2010; 11(8):R85.

  Diatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available.Diatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available. Notwithstanding, our knowledge of diatom biology remains limited because only around half of their genes can be ascribed a function based onhomology-based methods. High throughput tools are needed, therefore, to associate functions with diatom-specific genes. We have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity. The digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance.

• Potential impact of stress activated retrotransposons on genome evolution in a marine diatom.

  Authors: Florian Maumus, Andrew E Allen, Corinne Mhiri, Hanhua Hu, Kamel Jabbari, Assaf Vardi, Marie Angele Grandbastien, Chris Bowler

  BMC genomics. 12/2009; 10(1):624.

  ABSTRACT: BACKGROUND: Transposable elements (TEs) are mobile DNA sequences present in the genomes of most organisms. They have been extensively studied in animals, fungi, and plants, and have beenABSTRACT: BACKGROUND: Transposable elements (TEs) are mobile DNA sequences present in the genomes of most organisms. They have been extensively studied in animals, fungi, and plants, and have been shown to have important functions in genome dynamics and species evolution. Recent genomic data can now enlarge the identification and study of TEs to other branches of the eukaryotic tree of life. Diatoms, which belong to the heterokont group, are unicellular eukaryotic algae responsible for around 40% of marine primary productivity. The genomes of a centric diatom, Thalassiosira pseudonana, and a pennate diatom, Phaeodactylum tricornutum, that likely diverged around 90 Mya, have recently become available. RESULTS: In the present work, we establish that LTR retrotransposons (LTR-RTs) are the most abundant TEs inhabiting these genomes, with a much higher presence in the P. tricornutum genome. We show that the LTR-RTs found in diatoms form two new phylogenetic lineages that appear to be diatom specific and are also found in environmental samples taken from different oceans. Comparative expression analysis in P. tricornutum cells cultured under 16 different conditions demonstrate high levels of transcriptional activity of LTR retrotransposons in response to nitrate limitation and upon exposure to diatom-derived reactive aldehydes, which are known to induce stress responses and cell death. Regulatory aspects of P. tricornutum retrotransposon transcription also include the occurrence of nitrate limitation sensitive cis-regulatory components within LTR elements and cytosine methylation dynamics. Differential insertion patterns in different P. tricornutum accessions isolated from around the world infer the role of LTR-RTs in generating intraspecific genetic variability. CONCLUSION: Based on these findings we propose that LTR-RTs may have been important for promoting genome rearrangements in diatoms.

• Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.

  Authors: Alexandra Z Worden, Jae-Hyeok Lee, Thomas Mock, Pierre Rouzé, Melinda P Simmons, Andrea L Aerts, Andrew E Allen, Marie L Cuvelier, Evelyne Derelle, Meredith V Everett [......] Jeremy Schmutz, Eve Toulza, Tania Wyss, Alexander Zelensky, Kemin Zhou, E Virginia Armbrust, Debashish Bhattacharya, Ursula W. Goodenough, Yves Van de Peer, Igor V Grigoriev

  Science (New York, N.Y.). 05/2009; 324(5924):268-72.

  Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging fromPicoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.

• The Phaeodactylum genome reveals the evolutionary history of diatom genomes.

  Authors: Chris Bowler, Andrew E Allen, Jonathan H Badger, Jane Grimwood, Kamel Jabbari, Alan Kuo, Uma Maheswari, Cindy Martens, Florian Maumus, Robert P Otillar [......] Peter von Dassow, Wim Vyverman, Anusuya Willis, Lucjan S Wyrwicz, Daniel S Rokhsar, Jean Weissenbach, E Virginia Armbrust, Beverley R Green, Yves Van de Peer, Igor V Grigoriev

  Nature. 11/2008;

  Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth.Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes ( approximately 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

• Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation.

  Authors: Andrew E Allen, Julie LaRoche, Uma Maheswari, Markus Lommer, Nicolas Schauer, Pascal J Lopez, Giovanni Finazzi, Alisdair R Fernie, Chris Bowler

  Proceedings of the National Academy of Sciences of the United States of America. 07/2008; 105(30):10438-43.

  Marine primary productivity is iron (Fe)-limited in vast regions of the contemporary oceans, most notably the high nutrient low chlorophyll (HNLC) regions. Diatoms often form large blooms upon theMarine primary productivity is iron (Fe)-limited in vast regions of the contemporary oceans, most notably the high nutrient low chlorophyll (HNLC) regions. Diatoms often form large blooms upon the relief of Fe limitation in HNLC regions despite their prebloom low cell density. Although Fe plays an important role in controlling diatom distribution, the mechanisms of Fe uptake and adaptation to low iron availability are largely unknown. Through a combination of nontargeted transcriptomic and metabolomic approaches, we have explored the biochemical strategies preferred by Phaeo dactylum tricornutum at growth-limiting levels of dissolved Fe. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport, and nitrate assimilation, were down-regulated. Our results show that this retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electrons by mitochondrial alternative oxidase (AOX) and non-photochemical quenching (NPQ), and augmented Fe-independent oxidative stress responses. Iron limitation leads to the elevated expression of at least three gene clusters absent from the Thalassiosira pseudonana genome that encode for components of iron capture and uptake mechanisms.