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Erica Lindquist

Bio: Erica Lindquist is an academic researcher from Joint Genome Institute. The author has contributed to research in topics: Genome & Thalassiosira pseudonana. The author has an hindex of 1, co-authored 1 publications receiving 1346 citations.

Papers
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Journal ArticleDOI
13 Nov 2008-Nature
TL;DR: Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms, and documents the presence of hundreds of genes from bacteria, likely to provide novel possibilities for metabolite management and for perception of environmental signals.
Abstract: 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(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). 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 (similar to 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.

1,500 citations


Cited by
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Journal ArticleDOI
13 Aug 2010-Science
TL;DR: Although microalgae are not yet produced at large scale for bulk applications, recent advances—particularly in the methods of systems biology, genetic engineering, and biorefining—present opportunities to develop this process in a sustainable and economical way within the next 10 to 15 years.
Abstract: Microalgae are considered one of the most promising feedstocks for biofuels. The productivity of these photosynthetic microorganisms in converting carbon dioxide into carbon-rich lipids, only a step or two away from biodiesel, greatly exceeds that of agricultural oleaginous crops, without competing for arable land. Worldwide, research and demonstration programs are being carried out to develop the technology needed to expand algal lipid production from a craft to a major industrial process. Although microalgae are not yet produced at large scale for bulk applications, recent advances—particularly in the methods of systems biology, genetic engineering, and biorefining—present opportunities to develop this process in a sustainable and economical way within the next 10 to 15 years.

1,712 citations

Journal ArticleDOI
TL;DR: Potential avenues of genetic engineering that may be undertaken in order to improve microalgae as a biofuel platform for the production of biohydrogen, starch-derived alcohols, diesel fuel surrogates, and/or alkanes are focused on.
Abstract: There are currently intensive global research efforts aimed at increasing and modifying the accumulation of lipids, alcohols, hydrocarbons, polysaccharides, and other energy storage compounds in photosynthetic organisms, yeast, and bacteria through genetic engineering. Many improvements have been realized, including increased lipid and carbohydrate production, improved H2 yields, and the diversion of central metabolic intermediates into fungible biofuels. Photosynthetic microorganisms are attracting considerable interest within these efforts due to their relatively high photosynthetic conversion efficiencies, diverse metabolic capabilities, superior growth rates, and ability to store or secrete energy-rich hydrocarbons. Relative to cyanobacteria, eukaryotic microalgae possess several unique metabolic attributes of relevance to biofuel production, including the accumulation of significant quantities of triacylglycerol; the synthesis of storage starch (amylopectin and amylose), which is similar to that found in higher plants; and the ability to efficiently couple photosynthetic electron transport to H2 production. Although the application of genetic engineering to improve energy production phenotypes in eukaryotic microalgae is in its infancy, significant advances in the development of genetic manipulation tools have recently been achieved with microalgal model systems and are being used to manipulate central carbon metabolism in these organisms. It is likely that many of these advances can be extended to industrially relevant organisms. This review is focused on potential avenues of genetic engineering that may be undertaken in order to improve microalgae as a biofuel platform for the production of biohydrogen, starch-derived alcohols, diesel fuel surrogates, and/or alkanes.

1,079 citations

Journal ArticleDOI
Patrick J. Keeling1, Patrick J. Keeling2, Fabien Burki1, Heather M. Wilcox3, Bassem Allam4, Eric E. Allen5, Linda A. Amaral-Zettler6, Linda A. Amaral-Zettler7, E. Virginia Armbrust8, John M. Archibald9, John M. Archibald2, Arvind K. Bharti10, Callum J. Bell10, Bank Beszteri11, Kay D. Bidle12, Connor Cameron10, Lisa Campbell13, David A. Caron14, Rose Ann Cattolico8, Jackie L. Collier4, Kathryn J. Coyne15, Simon K. Davy16, Phillipe Deschamps17, Sonya T. Dyhrman18, Bente Edvardsen19, Ruth D. Gates20, Christopher J. Gobler4, Spencer J. Greenwood21, Stephanie Guida10, Jennifer L. Jacobi10, Kjetill S. Jakobsen19, Erick R. James1, Bethany D. Jenkins22, Uwe John11, Matthew D. Johnson23, Andrew R. Juhl18, Anja Kamp24, Anja Kamp25, Laura A. Katz26, Ronald P. Kiene27, Alexander Kudryavtsev28, Alexander Kudryavtsev29, Brian S. Leander1, Senjie Lin30, Connie Lovejoy31, Denis H. Lynn1, Denis H. Lynn32, Adrian Marchetti33, George B. McManus30, Aurora M. Nedelcu34, Susanne Menden-Deuer22, Cristina Miceli35, Thomas Mock36, Marina Montresor37, Mary Ann Moran38, Shauna A. Murray39, Govind Nadathur40, Satoshi Nagai, Peter B. Ngam10, Brian Palenik5, Jan Pawlowski29, Giulio Petroni41, Gwenael Piganeau42, Matthew C. Posewitz43, Karin Rengefors44, Giovanna Romano37, Mary E. Rumpho30, Tatiana A. Rynearson22, Kelly B. Schilling10, Declan C. Schroeder, Alastair G. B. Simpson9, Alastair G. B. Simpson2, Claudio H. Slamovits9, Claudio H. Slamovits2, David Roy Smith45, G. Jason Smith46, Sarah R. Smith5, Heidi M. Sosik23, Peter Stief25, Edward C. Theriot47, Scott N. Twary48, Pooja E. Umale10, Daniel Vaulot49, Boris Wawrik50, Glen L. Wheeler51, William H. Wilson52, Yan Xu53, Adriana Zingone37, Alexandra Z. Worden3, Alexandra Z. Worden2 
University of British Columbia1, Canadian Institute for Advanced Research2, Monterey Bay Aquarium Research Institute3, Stony Brook University4, University of California, San Diego5, Brown University6, Marine Biological Laboratory7, University of Washington8, Dalhousie University9, National Center for Genome Resources10, Alfred Wegener Institute for Polar and Marine Research11, Rutgers University12, Texas A&M University13, University of Southern California14, University of Delaware15, Victoria University of Wellington16, University of Paris-Sud17, Columbia University18, University of Oslo19, University of Hawaii at Manoa20, University of Prince Edward Island21, University of Rhode Island22, Woods Hole Oceanographic Institution23, Jacobs University Bremen24, Max Planck Society25, Smith College26, University of South Alabama27, Saint Petersburg State University28, University of Geneva29, University of Connecticut30, Laval University31, University of Guelph32, University of North Carolina at Chapel Hill33, University of New Brunswick34, University of Camerino35, University of East Anglia36, Stazione Zoologica Anton Dohrn37, University of Georgia38, University of Technology, Sydney39, University of Puerto Rico40, University of Pisa41, Centre national de la recherche scientifique42, Colorado School of Mines43, Lund University44, University of Western Ontario45, California State University46, University of Texas at Austin47, Los Alamos National Laboratory48, Pierre-and-Marie-Curie University49, University of Oklahoma50, Plymouth Marine Laboratory51, Bigelow Laboratory For Ocean Sciences52, Princeton University53
TL;DR: In this paper, the authors describe a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans and their biology, evolution, and ecology.
Abstract: Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.

852 citations

Journal ArticleDOI
13 May 2009-Nature
TL;DR: Marine diatoms rose to prominence about 100 million years ago and today generate most of the organic matter that serves as food for life in the sea.
Abstract: Marine diatoms rose to prominence about 100 million years ago and today generate most of the organic matter that serves as food for life in the sea. They exist in a dilute world where compounds essential for growth are recycled and shared, and they greatly influence global climate, atmospheric carbon dioxide concentration and marine ecosystem function. How these essential organisms will respond to the rapidly changing conditions in today's oceans is critical for the health of the environment and is being uncovered by studies of their genomes.

809 citations

Journal ArticleDOI
TL;DR: Deciphering the languages of diatoms and bacteria and how they interact will inform the understanding of the role these organisms have in shaping the ocean and how these interactions may change in future oceans.
Abstract: SUMMARY Diatoms and bacteria have cooccurred in common habitats for hundreds of millions of years, thus fostering specific associations and interactions with global biogeochemical consequences. Diatoms are responsible for one-fifth of the photosynthesis on Earth, while bacteria remineralize a large portion of this fixed carbon in the oceans. Through their coexistence, diatoms and bacteria cycle nutrients between oxidized and reduced states, impacting bioavailability and ultimately feeding higher trophic levels. Here we present an overview of how diatoms and bacteria interact and the implications of these interactions. We emphasize that heterotrophic bacteria in the oceans that are consistently associated with diatoms are confined to two phyla. These consistent bacterial associations result from encounter mechanisms that occur within a microscale environment surrounding a diatom cell. We review signaling mechanisms that occur in this microenvironment to pave the way for specific interactions. Finally, we discuss known interactions between diatoms and bacteria and exciting new directions and research opportunities in this field. Throughout the review, we emphasize new technological advances that will help in the discovery of new interactions. Deciphering the languages of diatoms and bacteria and how they interact will inform our understanding of the role these organisms have in shaping the ocean and how these interactions may change in future oceans.

750 citations