Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome

Identification of Highly Divergent Diatom-Derived Chloroplasts in Dinoflagellates, Including a Description of Durinskia kwazulunatalensis sp. nov. (Peridiniales, Dinophyceae)

(2017) Norico Yamada et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

(2017) Thomas Mock et al.   NATURE

Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells

(2017) Jean-François Mangot et al.   Scientific Reports

Pan-transcriptomic analysis identifies coordinated and orthologous functional modules in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum

(2016) Justin Ashworth et al.   Marine Genomics

Functional Relationship between a Dinoflagellate Host and Its Diatom Endosymbiont

(2016) Elisabeth Hehenberger et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts)

(2016) Romain Derelle et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Evolution of Silicon Transport in Eukaryotes

(2016) Alan O. Marron et al.   MOLECULAR BIOLOGY AND EVOLUTION

Progressive and Biased Divergent Evolution Underpins the Origin and Diversification of Peridinin Dinoflagellate Plastids

(2016) Richard G. Dorrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore ofPaulinella chromatophora

(2016) Eva C. M. Nowack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis

(2016) Raphaël Méheust et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista

(2016) Fabien Burki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite

(2016) Tatiana Yurchenko et al.   Open Biology

Addressing various compartments of the diatom model organism Phaeodactylum tricornutum via sub-cellular marker proteins

(2016) Xiaojuan Liu et al.   Algal Research-Biomass Biofuels and Bioproducts

Heterokont Predator Develorapax marinus gen. et sp. nov. – A Model of the Ochrophyte Ancestor

(2016) Vladimir V. Aleoshin et al.   Frontiers in Microbiology

Sequencing of the complete genome of an araphid pennate diatom Synedra acus subsp. radians from Lake Baikal

(2015) Y. P. Galachyants et al.   Doklady Biochemistry and Biophysics

A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway

(2015) Mark A. Miller et al.   Evolutionary Bioinformatics

Dual Organellar Targeting of Aminoacyl-tRNA Synthetases in Diatoms and Cryptophytes

(2015) Gillian H. Gile et al.   Genome Biology and Evolution

Evidence of ancient genome reduction in red algae (Rhodophyta)

(2015) Huan Qiu et al.   JOURNAL OF PHYCOLOGY

Phylogenomic analysis of Emiliania huxleyi provides evidence for haptophyte–stramenopile association and a chimeric haptophyte nuclear genome

(2015) John J. Miller et al.   Marine Genomics

MitoFates: Improved Prediction of Mitochondrial Targeting Sequences and Their Cleavage Sites

(2015) Yoshinori Fukasawa et al.   MOLECULAR & CELLULAR PROTEOMICS

Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista

(2015) Thomas Cavalier-Smith et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling

(2015) Edward C. Theriot et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Endosymbiotic origin and differential loss of eukaryotic genes

(2015) Chuan Ku et al.   NATURE

The role of pyruvate hub enzymes in supplying carbon precursors for fatty acid synthesis in photosynthetic microalgae

(2015) Nastassia Shtaida et al.   PHOTOSYNTHESIS RESEARCH

Oil Accumulation by the Oleaginous DiatomFistulifera solarisas Revealed by the Genome and Transcriptome

(2015) Tsuyoshi Tanaka et al.   PLANT CELL

Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage

(2015) Ansgar Gruber et al.   PLANT JOURNAL

Dual protein trafficking to secretory and non-secretory cell compartments: Clear or double vision?

(2015) Brad W. Porter et al.   PLANT SCIENCE

Integration of plastids with their hosts: Lessons learned from dinoflagellates

(2015) Richard G. Dorrell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrastructure and Membrane Traffic During Cell Division in the Marine Pennate Diatom Phaeodactylum tricornutum

(2015) Atsuko Tanaka et al.   PROTIST

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte?

(2015) Tereza Ševčíková et al.   Scientific Reports

Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae)

(2015) Blake T. Hovde et al.   PLoS Genetics

Identification of two novel type 1 peroxisomal targeting signals in Arabidopsis thaliana

(2014) Rigoberto A. Ramirez et al.   ACTA HISTOCHEMICA

A dual-targeted aminoacyl-tRNA synthetase inPlasmodium falciparumcharges cytosolic and apicoplast tRNACys

(2014) James S. Pham et al.   BIOCHEMICAL JOURNAL

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models

(2014) Nahill H Matari et al.   BMC EVOLUTIONARY BIOLOGY

Serial Gene Losses and Foreign DNA Underlie Size and Sequence Variation in the Plastid Genomes of Diatoms

(2014) Elizabeth C. Ruck et al.   Genome Biology and Evolution

Transcriptomic Insights into the Life History of Bolidophytes, the Sister Lineage to Diatoms

(2014) Colton R. Kessenich et al.   JOURNAL OF PHYCOLOGY

The evolution of photosynthesis in chromist algae through serial endosymbioses

(2014) John W. Stiller et al.   Nature Communications

Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista

(2014) Akinori Yabuki et al.   Scientific Reports

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

Nannochloropsis Genomes Reveal Evolution of Microalgal Oleaginous Traits

(2014) Dongmei Wang et al.   PLoS Genetics

Data access for the 1,000 Plants (1KP) project

(2014) Naim Matasci et al.   GigaScience

Plant amino acid-derived vitamins: biosynthesis and function

(2013) Javier A. Miret et al.   AMINO ACIDS

Pan genome of the phytoplankton Emiliania underpins its global distribution

(2013) Betsy A. Read et al.   NATURE

Green Targeting Predictor and Ambiguous Targeting Predictor 2: the pitfalls of plant protein targeting prediction and of transient protein expression in heterologous systems

(2013) Janina Fuss et al.   NEW PHYTOLOGIST

The First Symbiont-Free Genome Sequence of Marine Red Alga, Susabi-nori (Pyropia yezoensis)

(2013) Yoji Nakamura et al.   PLoS One

Proteomic Amino-Termini Profiling Reveals Targeting Information for Protein Import into Complex Plastids

(2013) Pitter F. Huesgen et al.   PLoS One

Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

(2013) J. Collen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote

(2013) G. Schonknecht et al.   SCIENCE

The CCAP KnowledgeBase: linking protistan and cyanobacterial biological resources with taxonomic and molecular data

(2013) Claire M.M. Gachon et al.   SYSTEMATICS AND BIODIVERSITY

Assessing the bacterial contribution to the plastid proteome

(2013) Huan Qiu et al.   TRENDS IN PLANT SCIENCE

Erratum: Corrigendum: Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropsis gaditana

(2013) Randor Radakovits et al.   Nature Communications

Genome of the red alga Porphyridium purpureum

(2013) Debashish Bhattacharya et al.   Nature Communications

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Loss of Nucleosomal DNA Condensation Coincides with Appearance of a Novel Nuclear Protein in Dinoflagellates

(2012) Sebastian G. Gornik et al.   CURRENT BIOLOGY

Global distribution of a wild alga revealed by targeted metagenomics

(2012) Alexandra Z. Worden et al.   CURRENT BIOLOGY

Reevaluating the Green Contribution to Diatom Genomes

(2012) Philippe Deschamps et al.   Genome Biology and Evolution

Dual Targeting and Retrograde Translocation: Regulators of Plant Nuclear Gene Expression Can Be Sequestered by Plastids

(2012) Kirsten Krause et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Dual targeting of aminoacyl-tRNA synthetases to the mitochondrion and complex plastid in chlorarachniophytes

(2012) Y. Hirakawa et al.   JOURNAL OF CELL SCIENCE

What makes a chloroplast? Reconstructing the establishment of photosynthetic symbioses

(2012) R. G. Dorrell et al.   JOURNAL OF CELL SCIENCE

Ancient Gene Paralogy May Mislead Inference of Plastid Phylogeny

(2012) Huan Qiu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

(2012) Bruce A. Curtis et al.   NATURE

Acquisition, Conservation, and Loss of Dual-Targeted Proteins in Land Plants

(2012) L. Xu et al.   PLANT PHYSIOLOGY

Trafficking of protein into the recently established photosynthetic organelles of Paulinella chromatophora

(2012) E. C. M. Nowack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional remodeling of RNA processing in replacement chloroplasts by pathways retained from their predecessors

(2012) R. G. Dorrell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unicellular Cyanobacterium Symbiotic with a Single-Celled Eukaryotic Alga

(2012) A. W. Thompson et al.   SCIENCE

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

New haptophyte lineages and multiple independent colonizations of freshwater ecosystems

(2012) Marianne Simon et al.   Environmental Microbiology Reports

Comparative analysis of diatom genomes reveals substantial differences in the organization of carbon partitioning pathways

(2012) Sarah R. Smith et al.   Algal Research-Biomass Biofuels and Bioproducts

Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation

(2012) Markus Lommer et al.   GENOME BIOLOGY

Into the deep: New discoveries at the base of the green plant phylogeny

(2011) Frederik Leliaert et al.   BIOESSAYS

Chlorophyll-binding proteins revisited - a multigenic family of light-harvesting and stress proteins from a brown algal perspective

(2011) Simon M Dittami et al.   BMC EVOLUTIONARY BIOLOGY

Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids

(2011) Shinichiro Maruyama et al.   BMC EVOLUTIONARY BIOLOGY

Red and Green Algal Monophyly and Extensive Gene Sharing Found in a Rich Repertoire of Red Algal Genes

(2011) Cheong Xin Chan et al.   CURRENT BIOLOGY

Do Red and Green Make Brown?: Perspectives on Plastid Acquisitions within Chromalveolates

(2011) Richard G. Dorrell et al.   EUKARYOTIC CELL

Red and Problematic Green Phylogenetic Signals among Thousands of Nuclear Genes from the Photosynthetic and Apicomplexa-Related Chromera velia

(2011) Christian Woehle et al.   Genome Biology and Evolution

The Thylakoid Membrane Proteome of Two Marine Diatoms Outlines Both Diatom-Specific and Species-Specific Features of the Photosynthetic Machinery

(2011) Irina Grouneva et al.   JOURNAL OF PROTEOME RESEARCH

Chloroplast genomes of photosynthetic eukaryotes

(2011) Beverley R. Green   PLANT JOURNAL

Estimating the timing of early eukaryotic diversification with multigene molecular clocks

(2011) L. W. Parfrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life

(2011) E. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics

(2011) C. J. Gobler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic Analyses of a Combined Data Set Suggest that the Attheya Lineage is the Closest Living Relative of the Pennate Diatoms (Bacillariophyceae)

(2011) Ulf Sorhannus et al.   PROTIST

Supermatrix Data Highlight the Phylogenetic Relationships of Photosynthetic Stramenopiles

(2011) Eun Chan Yang et al.   PROTIST

A Method for Inferring the Rate of Evolution of Homologous Characters that Can Potentially Improve Phylogenetic Inference, Resolve Deep Divergence and Correct Systematic Biases

(2011) Carla A. Cummins et al.   SYSTEMATIC BIOLOGY

A structural phylogenetic map for chloroplast photosynthesis

(2011) John F. Allen et al.   TRENDS IN PLANT SCIENCE

ANALYSES OF THE COMPLETE CHLOROPLAST GENOME SEQUENCES OF TWO MEMBERS OF THE PELAGOPHYCEAE: AUREOCOCCUS ANOPHAGEFFERENS CCMP1984 AND AUREOUMBRA LAGUNENSIS CCMP15071

(2010) Han Chuan Ong et al.   JOURNAL OF PHYCOLOGY

Phylogenomic Evidence for Separate Acquisition of Plastids in Cryptophytes, Haptophytes, and Stramenopiles

(2010) D. Baurain et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2010) J. Mark Cock et al.   NATURE

Carotenoid biosynthesis in diatoms

(2010) Martine Bertrand   PHOTOSYNTHESIS RESEARCH

The Complete Plastid Genomes of the Two ‘Dinotoms’ Durinskia baltica and Kryptoperidinium foliaceum

(2010) Behzad Imanian et al.   PLoS One

A Molecular Genetic Timescale for the Diversification of Autotrophic Stramenopiles (Ochrophyta): Substantive Underestimation of Putative Fossil Ages

(2010) Joseph W. Brown et al.   PLoS One

A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids

(2010) J. Janouskovec et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oceanographic and Biogeochemical Insights from Diatom Genomes

(2009) Chris Bowler et al.   Annual Review of Marine Science

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids

(2009) Gildas Le Corguillé et al.   BMC EVOLUTIONARY BIOLOGY

Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

(2009) John W Stiller et al.   BMC GENOMICS

Eukaryotic and Eubacterial Contributions to the Establishment of Plastid Proteome Estimated by Large-Scale Phylogenetic Analyses

(2009) K. Suzuki et al.   MOLECULAR BIOLOGY AND EVOLUTION

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms

(2009) A. Moustafa et al.   SCIENCE

Iron–sulfur cluster biosynthesis

(2008) Sibali Bandyopadhyay et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

HECTAR: A method to predict subcellular targeting in heterokonts

(2008) Bernhard Gschloessl et al.   BMC BIOINFORMATICS

Ancient Recruitment by Chromists of Green Algal Genes Encoding Enzymes for Carotenoid Biosynthesis

(2008) R. Frommolt et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

(2008) Chris Bowler et al.   NATURE

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

Physiological and Transcriptomic Evidence for a Close Coupling between Chloroplast Ontogeny and Cell Cycle Progression in the Pennate Diatom Seminavis robusta

(2008) J. Gillard et al.   PLANT PHYSIOLOGY

A Model for Carbohydrate Metabolism in the Diatom Phaeodactylum tricornutum Deduced from Comparative Whole Genome Analysis

(2008) Peter G. Kroth et al.   PLoS One

Evolutionary Origins and Functions of the Carotenoid Biosynthetic Pathway in Marine Diatoms

(2008) Sacha Coesel et al.   PLoS One

Testing Congruence in Phylogenomic Analysis

(2008) Jessica W. Leigh et al.   SYSTEMATIC BIOLOGY