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7 results on '"Allen, Andrew E."'

1. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

Author

Mock, Thomas, Otillar, Robert P, Strauss, Jan, McMullan, Mark, Paajanen, Pirita, Schmutz, Jeremy, Salamov, Asaf, Sanges, Remo, Toseland, Andrew, Ward, Ben J, Allen, Andrew E, Dupont, Christopher L, Frickenhaus, Stephan, Maumus, Florian, Veluchamy, Alaguraj, Wu, Taoyang, Barry, Kerrie W, Falciatore, Angela, Ferrante, Maria I, Fortunato, Antonio E, Glöckner, Gernot, Gruber, Ansgar, Hipkin, Rachel, Janech, Michael G, Kroth, Peter G, Leese, Florian, Lindquist, Erika A, Lyon, Barbara R, Martin, Joel, Mayer, Christoph, Parker, Micaela, Quesneville, Hadi, Raymond, James A, Uhlig, Christiane, Valas, Ruben E, Valentin, Klaus U, Worden, Alexandra Z, Armbrust, E Virginia, Clark, Matthew D, Bowler, Chris, Green, Beverley R, Moulton, Vincent, van Oosterhout, Cock, and Grigoriev, Igor V

Subjects
Diatoms, Carbon Dioxide, Iron, Gene Expression Profiling, Genomics, Ice Cover, Acclimatization, Evolution, Molecular, Phylogeny, Recombination, Genetic, Genetic Drift, Alleles, Genome, Darkness, Freezing, Oceans and Seas, Cold Temperature, Transcriptome, Mutation Rate, Evolution, Molecular, Recombination, Genetic, General Science & Technology
Abstract

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.

Published
2017

2. Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms

Author

McQuaid, Jeffrey B., Kustka, Adam B., Obornk, Miroslav, Hork, Ale, McCrow, John P., Karas, Bogumil J., Zheng, Hong, Kindeberg, Theodor, Andersson, Andreas J., Barbeau, Katherine A., and Allen, Andrew E.

Subjects
Carbonates -- Physiological aspects, Iron (Nutrient) -- Physiological aspects, Transferrin -- Physiological aspects, Diatoms -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Jeffrey B. McQuaid [1, 2]; Adam B. Kustka [3]; Miroslav Obornk [4, 5]; Ale Hork [4, 5]; John P. McCrow [1]; Bogumil J. Karas [1]; Hong Zheng [1]; Theodor [...]

Published
2018
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3. Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

Author

Allen, Andrew E., Dupont, Christopher L., Obornik, Miroslav, Horak, Ales, Nunes-Nesi, Adriano, McCrow, John P., Zheng, Hong, Johnson, Daniel A., Hu, Hanhua, Fernie, Alisdair R., and Bowler, Chris

Subjects
Phylogenetic trees -- Physiological aspects -- Research, Urea cycle -- Research, Photosynthesis -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

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 (1-4). The diatom nuclear genome contains genes with bacterial and plastid origins as well as genes of the secondary endosymbiotic host (the exosymbiont (5)) (1,6-10), 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 (12) and the precursors for long-chain polyamines required for silica precipitation during cell wall formation (11). 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., An ornithine-urea cycle (OUC) driven by mitochondrial carbamoyl phosphate synthase (CPS) was long assumed to have originated in metazoans (13-16) and is known to have facilitated key physiological and life-history [...]

Published
2011
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4. Genomic and functional adaptation in surface ocean planktonic prokaryotes

Author

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

Subjects
Marine plankton -- Identification and classification -- Genetic aspects -- Physiological aspects -- Research, Adaptation (Physiology) -- Research -- Genetic aspects -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

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 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., Molecular taxonomy and phylogeny (1) revitalized the field of marine microbiology, allowing for the first time the realization that the 'unseen' and 'unknown' majority of uncultivated microbial taxa could be [...]

Published
2010
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5. Pan genome of the phytoplankton Emiliania underpins its global distribution

Author

Read, Betsy A., Kegel, Jessica, Klute, Mary J., Kuo, Alan, Lefebvre, Stephane C., Maumus, Florian, Mayer, Christoph, Miller, John, Monier, Adam, Salamov, Asaf, Young, Jeremy, Aguilar, Maria, Claverie, Jean-Michel, Frickenhaus, Stephan, Gonzalez, Karina, Herman, Emily K., Lin, Yao-Cheng, Napier, Johnathan, Ogata, Hiroyuki, Sarno, Analissa F., Shmutz, Jeremy, Schroeder, Declan, de Vargas, Colomban, Verret, Frederic, von Dassow, Peter, Valentin, Klaus, Van de Peer, Yves, Wheeler, Glen, Allen, Andrew E., Bidle, Kay, Borodovsky, Mark, Bowler, Chris, Brownlee, Colin, Cock, Mark J., Elias, Marek, Gladyshev, Vadim N., Groth, Marco, Guda, Chittibabu, Hadaegh, Ahmad, Debora Iglesias-Rodriguez, Maria, Jenkins, Jerry, Jones, Bethan M., Lawson, Tracy, Leese, Florian, Lindquist, Erika, Lobanov, Alexei, Lomsadze, Alexandre, Malik, Shehre-Banoo, Marsh, Mary E., Mackinder, Luke, Mock, Thomas, Mueller-Roeber, Bernd, Pagarete, António, Parker, Micaela, Probert, Ian, Quesneville, Hadi, Raines, Christine, Rensing, Stefan A., Riaño-Pachón, Diego Mauricio, Richier, Sophie, Rokitta, Sebastian, Shiraiwa, Yoshihiro, Soanes, Darren M., van der Giezen, Mark, Wahlund, Thomas M., Williams, Bryony, Wilson, Willie, Wolfe, Gordon, Wurch, Louie L., Dacks, Joel B., Delwiche, Charles F., Dyhrman, Sonya T., Glöckner, Gernot, John, Uwe, Richards, Thomas, Worden, Alexandra Z., Zhang, Xiaoyu, and Grigoriev, Igor V.

Published
2013
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6. The Ectocarpus genome and the independent evolution of multicellularity in brown algae

Author

Cock, Mark J., Sterck, Lieven, Rouzé, Pierre, Scornet, Delphine, Allen, Andrew E., Amoutzias, Grigoris, Anthouard, Veronique, Artiguenave, François, Aury, Jean-Marc, Badger, Jonathan H., Beszteri, Bank, Billiau, Kenny, Bonnet, Eric, Bothwell, John H., Bowler, Chris, Boyen, Catherine, Brownlee, Colin, Carrano, Carl J., Charrier, Bénédicte, Cho, Ga Youn, Coelho, Susana M., Collén, Jonas, Corre, Erwan, Da Silva, Corinne, Delage, Ludovic, Delaroque, Nicolas, Dittami, Simon M., Doulbeau, Sylvie, Elias, Marek, Farnham, Garry, Gachon, Claire M. M., Gschloessl, Bernhard, Heesch, Svenja, Jabbari, Kamel, Jubin, Claire, Kawai, Hiroshi, Kimura, Kei, Kloareg, Bernard, Küpper, Frithjof C., Lang, Daniel, Le Bail, Aude, Leblanc, Catherine, Lerouge, Patrice, Lohr, Martin, Lopez, Pascal J., Martens, Cindy, Maumus, Florian, Michel, Gurvan, Miranda-Saavedra, Diego, Morales, Julia, Moreau, Hervé, Motomura, Taizo, Nagasato, Chikako, Napoli, Carolyn A., Nelson, David R., Nyvall-Collén, Pi, Peters, Akira F., Pommier, Cyril, Potin, Philippe, Poulain, Julie, Quesneville, Hadi, Read, Betsy, Rensing, Stefan A., Ritter, Andrés, Rousvoal, Sylvie, Samanta, Manoj, Samson, Gaelle, Schroeder, Declan C., Ségurens, Béatrice, Strittmatter, Martina, Tonon, Thierry, Tregear, James W., Valentin, Klaus, von Dassow, Peter, Yamagishi, Takahiro, Van de Peer, Yves, and Wincker, Patrick

Published
2010
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7. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author

Bowler, Chris, Allen, Andrew E., Badger, Jonathan H., Grimwood, Jane, Jabbari, Kamel, Kuo, Alan, Maheswari, Uma, Martens, Cindy, Maumus, Florian, Otillar, Robert P., Rayko, Edda, Salamov, Asaf, Vandepoele, Klaas, Beszteri, Bank, Gruber, Ansgar, Heijde, Marc, Katinka, Michael, Mock, Thomas, Valentin, Klaus, Verret, Fréderic, Berges, John A., Brownlee, Colin, Cadoret, Jean-Paul, Chiovitti, Anthony, Choi, Chang Jae, Coesel, Sacha, De Martino, Alessandra, Detter, J. Chris, Durkin, Colleen, Falciatore, Angela, Fournet, Jérome, Haruta, Miyoshi, Huysman, Marie J. J., Jenkins, Bethany D., Jiroutova, Katerina, Jorgensen, Richard E., Joubert, Yolaine, Kaplan, Aaron, Kröger, Nils, Kroth, Peter G., La Roche, Julie, Lindquist, Erica, Lommer, Markus, Martin-Jézéquel, Véronique, Lopez, Pascal J., Lucas, Susan, Mangogna, Manuela, McGinnis, Karen, Medlin, Linda K., Montsant, Anton, Secq, Marie-Pierre Oudot-Le, Napoli, Carolyn, Obornik, Miroslav, Parker, Micaela Schnitzler, Petit, Jean-Louis, Porcel, Betina M., Poulsen, Nicole, Robison, Matthew, Rychlewski, Leszek, Rynearson, Tatiana A., Schmutz, Jeremy, Shapiro, Harris, Siaut, Magali, Stanley, Michele, Sussman, Michael R., Taylor, Alison R., Vardi, Assaf, von Dassow, Peter, Vyverman, Wim, Willis, Anusuya, Wyrwicz, Lucjan S., Rokhsar, Daniel S., Weissenbach, Jean, Armbrust, E. Virginia, Green, Beverley R., Van de Peer, Yves, and Grigoriev, Igor V.

Published
2008
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