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Frédéric Verret

Bio: Frédéric Verret is an academic researcher from Foundation for Research & Technology – Hellas. The author has contributed to research in topics: Diatom & Mutant. The author has an hindex of 11, co-authored 15 publications receiving 2742 citations. Previous affiliations of Frédéric Verret include University of the Algarve & University of Essex.

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

Journal ArticleDOI
TL;DR: It is demonstrated that AtHMA4 is localized at the plasma membrane and expressed in tissues surrounding the root vascular vessels and plays a role in metal loading in the xylem.

505 citations

Journal ArticleDOI
Betsy A. Read1, Jessica Kegel2, Mary J. Klute3, Alan Kuo4, Stephane C. Lefebvre5, Florian Maumus6, Christoph Mayer7, John P. Miller8, Adam Monier9, Asaf Salamov4, Jeremy R. Young10, María Aguilar3, Jean-Michel Claverie11, Stephan Frickenhaus2, Karina Gonzalez12, Emily K. Herman3, Yao-Cheng Lin13, Johnathan A. Napier14, Hiroyuki Ogata11, Analissa F. Sarno1, Jeremy Shmutz4, Declan C. Schroeder, Colomban de Vargas15, Frédéric Verret16, Peter von Dassow17, Klaus Valentin2, Yves Van de Peer13, Glen L. Wheeler18, Joel B. Dacks3, Charles F. Delwiche8, Sonya T. Dyhrman19, Sonya T. Dyhrman2, Sonya T. Dyhrman20, Gernot Glöckner21, Uwe John2, Thomas A. Richards22, Alexandra Z. Worden9, Xiaoyu Zhang1, Igor V. Grigoriev23, Andrew E. Allen24, Kay D. Bidle11, Kay D. Bidle25, Mark Borodovsky11, Chris Bowler15, Colin Brownlee26, Colin Brownlee1, J. Mark Cock12, Marek Eliáš27, Vadim N. Gladyshev28, Marco Groth1, Chittibabu Guda, Ahmad R. Hadaegh29, M. D. Iglesias-Rodriguez30, Jerry Jenkins16, Bethan M. Jones31, Tracy Lawson32, Florian Leese33, Erika Lindquist34, Alexei Lobanov27, Alexandre Lomsadze25, Shehre-Banoo Malik35, Mary E. Marsh36, Luke C. M. Mackinder15, Thomas Mock11, Bernd Mueller-Roeber37, António Pagarete38, Micaela S. Parker39, Ian Probert11, Hadi Quesneville15, Christine A. Raines31, Stefan A. Rensing2, Stefan A. Rensing15, Diego Mauricio Riaño-Pachón40, Sophie Richier41, Sophie Richier40, Sebastian D. Rokitta42, Yoshihiro Shiraiwa43, Darren M. Soanes42, Mark van der Giezen39, Thomas M. Wahlund41, Bryony A. P. Williams44, Willie Wilson43, Gordon Wolfe41, Louie L. Wurch40, Louie L. Wurch42 
11 Jul 2013-Nature
TL;DR: Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires, and reveals a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome.
Abstract: Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.

430 citations

Journal ArticleDOI
TL;DR: A mutant of AtHMA3 altered in the P‐ATPase phosphorylation domain did not complement Δycf1, suggesting that metal transport rather than chelation is involved, and a role in the influx of cadmium into the vacuolar compartment is confirmed.

189 citations

Journal ArticleDOI
TL;DR: The assessment of the roles of Ca(2+) channel genes in diverse physiological, developmental and life history processes represents a major challenge for future studies.
Abstract: Contents Summary 23 I. Introduction 24 II. Physiological features of Ca2+ channel activity ineukaryotic photoautotrophs 25 III. Expansion, loss and horizontal gene transfer of Ca2+-permeable channels in photoautotrophs 28 IV. Conclusions 36 Acknowledgements 37 References 37 Summary Much of our current knowledge on the mechanisms by which Ca2+ signals are generated in photosynthetic eukaryotes comes from studies of a relatively small number of model species, particularly green plants and algae, revealing some common features and notable differences between ‘plant’ and ‘animal’ systems. Physiological studies from a broad range of algal cell types have revealed the occurrence of animal-like signalling properties, including fast action potentials and fast propagating cytosolic Ca2+ waves. Genomic studies are beginning to reveal the widespread occurrence of conserved channel types likely to be involved in Ca2+ signalling. However, certain widespread ‘ancient’ channel types appear to have been lost by certain groups, such as the embryophytes. More recent channel gene loss is also evident from comparisons of more closely related algal species. The underlying processes that have given rise to the current distributions of Ca2+ channel types include widespread retention of ancient Ca2+ channel genes, horizontal gene transfer (including symbiotic gene transfer and acquisition of bacterial genes), gene loss and gene expansion within taxa. The assessment of the roles of Ca2+ channel genes in diverse physiological, developmental and life history processes represents a major challenge for future studies.

142 citations


Cited by
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

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: The dominant fluxes of Zn in the soil-root-shoot continuum are described, including Zn inputs to soils, the plant availability of soluble Zn(2+) at the root surface, and plant uptake and accumulation of ZN.
Abstract: Zinc (Zn) is an essential component of thousands of proteins in plants, although it is toxic in excess. In this review, the dominant fluxes of Zn in the soil-root-shoot continuum are described, including Zn inputs to soils, the plant availability of soluble Zn(2+) at the root surface, and plant uptake and accumulation of Zn. Knowledge of these fluxes can inform agronomic and genetic strategies to address the widespread problem of Zn-limited crop growth. Substantial within-species genetic variation in Zn composition is being used to alleviate human dietary Zn deficiencies through biofortification. Intriguingly, a meta-analysis of data from an extensive literature survey indicates that a small proportion of the genetic variation in shoot Zn concentration can be attributed to evolutionary processes whose effects manifest above the family level. Remarkable insights into the evolutionary potential of plants to respond to elevated soil Zn have recently been made through detailed anatomical, physiological, chemical, genetic and molecular characterizations of the brassicaceous Zn hyperaccumulators Thlaspi caerulescens and Arabidopsis halleri.

1,691 citations

Journal ArticleDOI
TL;DR: In this paper, the authors review aspects of soil science, plant physiology and genetics underpinning crop bio-fortification strategies, as well as agronomic and genetic approaches currently taken to biofortify food crops with the mineral elements most commonly lacking in human diets: iron (Fe), zinc (Zn), copper (Cu), calcium (Ca), magnesium (Mg), iodine (I) and selenium (Se).
Abstract: Summary The diets of over two-thirds of the world's population lack one or more essential mineral elements. This can be remedied through dietary diversification, mineral supplementation, food fortification, or increasing the concentrations and/or bioavailability of mineral elements in produce (biofortification). This article reviews aspects of soil science, plant physiology and genetics underpinning crop biofortification strategies, as well as agronomic and genetic approaches currently taken to biofortify food crops with the mineral elements most commonly lacking in human diets: iron (Fe), zinc (Zn), copper (Cu), calcium (Ca), magnesium (Mg), iodine (I) and selenium (Se). Two complementary approaches have been successfully adopted to increase the concentrations of bioavailable mineral elements in food crops. First, agronomic approaches optimizing the application of mineral fertilizers and/or improving the solubilization and mobilization of mineral elements in the soil have been implemented. Secondly, crops have been developed with: increased abilities to acquire mineral elements and accumulate them in edible tissues; increased concentrations of ‘promoter’ substances, such as ascorbate, β-carotene and cysteine-rich polypeptides which stimulate the absorption of essential mineral elements by the gut; and reduced concentrations of ‘antinutrients’, such as oxalate, polyphenolics or phytate, which interfere with their absorption. These approaches are addressing mineral malnutrition in humans globally.

1,677 citations