The Phaeodactylum genome reveals the evolutionary history of diatom genomes.

PubWeight™: 6.70‹?› | Rank: Top 1%

🔗 View Article (PMID 18923393)

Published in Nature on October 15, 2008

Authors

Chris Bowler1, Andrew E Allen, Jonathan H Badger, Jane Grimwood, Kamel Jabbari, Alan Kuo, Uma Maheswari, Cindy Martens, Florian Maumus, Robert P Otillar, Edda Rayko, Asaf Salamov, Klaas Vandepoele, Bank Beszteri, Ansgar Gruber, Marc Heijde, Michael Katinka, Thomas Mock, Klaus Valentin, Fréderic Verret, John A Berges, Colin Brownlee, Jean-Paul Cadoret, Anthony Chiovitti, Chang Jae Choi, Sacha Coesel, Alessandra De Martino, J Chris Detter, Colleen Durkin, Angela Falciatore, Jérome Fournet, Miyoshi Haruta, Marie J J Huysman, Bethany D Jenkins, Katerina Jiroutova, Richard E Jorgensen, Yolaine Joubert, Aaron Kaplan, Nils Kröger, Peter G Kroth, Julie La Roche, Erica Lindquist, Markus Lommer, Véronique Martin-Jézéquel, Pascal J Lopez, Susan Lucas, Manuela Mangogna, Karen McGinnis, Linda K Medlin, Anton Montsant, Marie-Pierre Oudot-Le Secq, Carolyn Napoli, Miroslav Obornik, Micaela Schnitzler Parker, Jean-Louis Petit, Betina M Porcel, Nicole Poulsen, Matthew Robison, Leszek Rychlewski, Tatiana A Rynearson, Jeremy Schmutz, Harris Shapiro, Magali Siaut, Michele Stanley, Michael R Sussman, Alison R Taylor, Assaf Vardi, 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

Author Affiliations

1: CNRS UMR8186, Department of Biology, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France. cbowler@biologie.ens.fr

Articles citing this

(truncated to the top 100)

The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res (2011) 3.26

Genetic engineering of algae for enhanced biofuel production. Eukaryot Cell (2010) 2.97

The life of diatoms in the world's oceans. Nature (2009) 2.81

Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet (2011) 2.54

Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PLoS Biol (2011) 2.38

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol (2010) 2.36

Interactions between diatoms and bacteria. Microbiol Mol Biol Rev (2012) 2.23

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol (2014) 2.18

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature (2012) 2.15

Genome evolution in filamentous plant pathogens: why bigger can be better. Nat Rev Microbiol (2012) 1.93

Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana. Nat Commun (2012) 1.83

The response of diatom central carbon metabolism to nitrogen starvation is different from that of green algae and higher plants. Plant Physiol (2011) 1.79

Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. Proc Natl Acad Sci U S A (2011) 1.76

Gene silencing in the marine diatom Phaeodactylum tricornutum. Nucleic Acids Res (2009) 1.67

Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nat Commun (2014) 1.66

An integrated analysis of molecular acclimation to high light in the marine diatom Phaeodactylum tricornutum. PLoS One (2009) 1.63

Diatoms respire nitrate to survive dark and anoxic conditions. Proc Natl Acad Sci U S A (2011) 1.52

Trans-kingdom horizontal DNA transfer from bacteria to yeast is highly plastic due to natural polymorphisms in auxiliary nonessential recipient genes. PLoS One (2013) 1.44

Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation. Biotechnol Biofuels (2013) 1.40

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation. PLoS Genet (2016) 1.40

Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presence. PLoS One (2010) 1.40

The making of a photosynthetic animal. J Exp Biol (2011) 1.37

Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite. Genome Biol (2011) 1.36

Possible role of horizontal gene transfer in the colonization of sea ice by algae. PLoS One (2012) 1.31

Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation. Genome Biol (2012) 1.27

Sirtuin/Sir2 phylogeny, evolutionary considerations and structural conservation. Mol Cells (2009) 1.27

Genome-wide transcriptome analyses of silicon metabolism in Phaeodactylum tricornutum reveal the multilevel regulation of silicic acid transporters. PLoS One (2009) 1.27

Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. PLoS Genet (2012) 1.25

Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum. Biotechnol Biofuels (2012) 1.21

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME J (2012) 1.20

The relevance of marine chemical ecology to plankton and ecosystem function: an emerging field. Mar Drugs (2011) 1.16

Evolution of saxitoxin synthesis in cyanobacteria and dinoflagellates. Mol Biol Evol (2012) 1.16

Eukaryotic algal phytochromes span the visible spectrum. Proc Natl Acad Sci U S A (2014) 1.16

Red and problematic green phylogenetic signals among thousands of nuclear genes from the photosynthetic and apicomplexa-related Chromera velia. Genome Biol Evol (2011) 1.15

Diatom PtCPF1 is a new cryptochrome/photolyase family member with DNA repair and transcription regulation activity. EMBO Rep (2009) 1.15

The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage. J Biol Chem (2011) 1.14

Gene regulation of carbon fixation, storage, and utilization in the diatom Phaeodactylum tricornutum acclimated to light/dark cycles. Plant Physiol (2012) 1.14

Microbial oceanography in a sea of opportunity. Nature (2009) 1.14

Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling. Genome Biol (2010) 1.12

Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids. BMC Evol Biol (2009) 1.12

Iron utilization in marine cyanobacteria and eukaryotic algae. Front Microbiol (2012) 1.11

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage. Genome Biol (2012) 1.10

Update of the Diatom EST Database: a new tool for digital transcriptomics. Nucleic Acids Res (2008) 1.10

Do red and green make brown?: perspectives on plastid acquisitions within chromalveolates. Eukaryot Cell (2011) 1.09

Auxin metabolism and function in the multicellular brown alga Ectocarpus siliculosus. Plant Physiol (2010) 1.09

The others: our biased perspective of eukaryotic genomes. Trends Ecol Evol (2014) 1.08

Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes. BMC Evol Biol (2010) 1.08

Identification and Characterisation CRN Effectors in Phytophthora capsici Shows Modularity and Functional Diversity. PLoS One (2013) 1.07

Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environ Microbiol (2011) 1.06

Re-evaluating the green versus red signal in eukaryotes with secondary plastid of red algal origin. Genome Biol Evol (2012) 1.05

Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes. PLoS One (2013) 1.05

Red and green algal origin of diatom membrane transporters: insights into environmental adaptation and cell evolution. PLoS One (2011) 1.05

AUREOCHROME1a-mediated induction of the diatom-specific cyclin dsCYC2 controls the onset of cell division in diatoms (Phaeodactylum tricornutum). Plant Cell (2013) 1.05

Complete sequence of the mitochondrial genome of a diatom alga Synedra acus and comparative analysis of diatom mitochondrial genomes. Curr Genet (2010) 1.04

Metabolic engineering of Phaeodactylum tricornutum for the enhanced accumulation of omega-3 long chain polyunsaturated fatty acids. Metab Eng (2013) 1.04

Chitin in diatoms and its association with the cell wall. Eukaryot Cell (2009) 1.04

Flavonoids: a metabolic network mediating plants adaptation to their real estate. Front Plant Sci (2014) 1.04

An expressed sequence tag analysis of the intertidal brown seaweeds Fucus serratus (L.) and F. vesiculosus (L.) (Heterokontophyta, Phaeophyceae) in response to abiotic stressors. Mar Biotechnol (NY) (2009) 1.03

sxtA-based quantitative molecular assay to identify saxitoxin-producing harmful algal blooms in marine waters. Appl Environ Microbiol (2011) 1.03

Hydroxyapatite-mediated separation of double-stranded DNA, single-stranded DNA, and RNA genomes from natural viral assemblages. Appl Environ Microbiol (2010) 1.03

Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta). BMC Evol Biol (2010) 1.03

Diatom plastids depend on nucleotide import from the cytosol. Proc Natl Acad Sci U S A (2009) 1.03

Digital expression profiling of novel diatom transcripts provides insight into their biological functions. Genome Biol (2010) 1.03

RNA-mediated silencing in Algae: biological roles and tools for analysis of gene function. Eukaryot Cell (2011) 1.02

The halogenated metabolism of brown algae (Phaeophyta), its biological importance and its environmental significance. Mar Drugs (2010) 1.02

Establishment of a genetic transformation system for the marine pennate diatom Fistulifera sp. strain JPCC DA0580--a high triglyceride producer. Mar Biotechnol (NY) (2012) 1.01

Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic. Proc Natl Acad Sci U S A (2012) 1.01

Membrane glycerolipid remodeling triggered by nitrogen and phosphorus starvation in Phaeodactylum tricornutum. Plant Physiol (2014) 1.00

The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella. BMC Evol Biol (2011) 1.00

The ins and outs of algal metal transport. Biochim Biophys Acta (2012) 1.00

First evidence for the existence of pennate diatom viruses. ISME J (2012) 1.00

Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC Genomics (2009) 1.00

Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis. BMC Genomics (2011) 0.99

Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean. Plant Cell (2016) 0.99

Dynamic response of the transcriptome of a psychrophilic diatom, Chaetoceros neogracile, to high irradiance. Planta (2009) 0.99

Structural and evolutionary divergence of eukaryotic protein kinases in Apicomplexa. BMC Evol Biol (2011) 0.98

Whole-cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum. J Exp Bot (2015) 0.98

Distribution and phylogeny of the blue light receptors aureochromes in eukaryotes. Planta (2009) 0.98

Physiological and transcriptomic evidence for a close coupling between chloroplast ontogeny and cell cycle progression in the pennate diatom Seminavis robusta. Plant Physiol (2008) 0.98

Molecular and photosynthetic responses to prolonged darkness and subsequent acclimation to re-illumination in the diatom Phaeodactylum tricornutum. PLoS One (2013) 0.97

Energetic coupling between plastids and mitochondria drives CO2 assimilation in diatoms. Nature (2015) 0.97

Dynamics and innovations within oomycete genomes: insights into biology, pathology, and evolution. Eukaryot Cell (2012) 0.97

A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes. BMC Genomics (2010) 0.97

Methylcrotonyl-CoA Carboxylase Regulates Triacylglycerol Accumulation in the Model Diatom Phaeodactylum tricornutum. Plant Cell (2014) 0.96

A rooted net of life. Biol Direct (2011) 0.96

A fast Na+/Ca2+-based action potential in a marine diatom. PLoS One (2009) 0.96

The mixed lineage nature of nitrogen transport and assimilation in marine eukaryotic phytoplankton: a case study of micromonas. Mol Biol Evol (2010) 0.96

Proteomic analysis of the marine diatom Thalassiosira pseudonana upon exposure to benzo(a)pyrene. BMC Genomics (2011) 0.96

Blue light is essential for high light acclimation and photoprotection in the diatom Phaeodactylum tricornutum. J Exp Bot (2012) 0.96

Evolution and functional diversification of fructose bisphosphate aldolase genes in photosynthetic marine diatoms. Mol Biol Evol (2011) 0.95

Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus. BMC Genomics (2010) 0.95

Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana. Proc Natl Acad Sci U S A (2013) 0.95

Designer diatom episomes delivered by bacterial conjugation. Nat Commun (2015) 0.95

A comparative genome analysis of PME and PMEI families reveals the evolution of pectin metabolism in plant cell walls. PLoS One (2013) 0.95

Recent transfer of an iron-regulated gene from the plastid to the nuclear genome in an oceanic diatom adapted to chronic iron limitation. BMC Genomics (2010) 0.94

Nitrate Storage and Dissimilatory Nitrate Reduction by Eukaryotic Microbes. Front Microbiol (2015) 0.93

Host-specific adaptation governs the interaction of the marine diatom, Pseudo-nitzschia and their microbiota. ISME J (2013) 0.93

Biosynthesis of fucoxanthin and diadinoxanthin and function of initial pathway genes in Phaeodactylum tricornutum. J Exp Bot (2012) 0.92

Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana. PLoS One (2011) 0.92

High light acclimation in the secondary plastids containing diatom Phaeodactylum tricornutum is triggered by the redox state of the plastoquinone pool. Plant Physiol (2012) 0.92

Articles by these authors

Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15

A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63

Enterotypes of the human gut microbiome. Nature (2011) 24.36

Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science (2002) 20.59

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48

The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36

Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature (2004) 20.20

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature (2007) 18.04

Genome sequence of the palaeopolyploid soybean. Nature (2010) 17.82

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06

The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62

Prepublication data sharing. Nature (2009) 12.24

Mutations in PCSK9 cause autosomal dominant hypercholesterolemia. Nat Genet (2003) 11.67

Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res (2011) 11.32

The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (2007) 11.15

The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science (2002) 11.11

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03

Genome evolution in yeasts. Nature (2004) 10.50

Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. Science (2005) 10.46

The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science (2004) 9.97

Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science (2007) 9.79

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18

Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38

Reactive oxygen species produced by NADPH oxidase regulate plant cell growth. Nature (2003) 8.30

The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (2007) 8.12

The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet (2010) 8.07

The amphioxus genome and the evolution of the chordate karyotype. Nature (2008) 8.03

Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res (2008) 8.01

3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics (2003) 7.99

The European database on small subunit ribosomal RNA. Nucleic Acids Res (2002) 7.80

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods (2007) 7.73

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature (2007) 7.42

Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol (2005) 7.19

ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature (2008) 6.81

Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science (2006) 6.74

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature (2008) 6.69

The ecoresponsive genome of Daphnia pulex. Science (2011) 6.55

PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res (2002) 6.43

Comparative genomics of multidrug resistance in Acinetobacter baumannii. PLoS Genet (2006) 6.32

An abundance of bidirectional promoters in the human genome. Genome Res (2004) 5.90

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics (2010) 5.70

Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science (2009) 5.64

A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One (2007) 5.62

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol (2011) 5.60

The Trichoplax genome and the nature of placozoans. Nature (2008) 5.56