Applications of next-generation sequencing to unravelling the evolutionary history of algae

Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea

(2013) Huan Qiu et al.   CURRENT BIOLOGY

Chloroplast genome of one brown seaweed, Saccharina japonica (Laminariales, Phaeophyta): Its structural features and phylogenetic analyses with other photosynthetic plastids

(2013) Xiuliang Wang et al.   Marine Genomics

Pan genome of the phytoplankton Emiliania underpins its global distribution

(2013) Betsy A. Read et al.   NATURE

Evolution of Red Algal Plastid Genomes: Ancient Architectures, Introns, Horizontal Gene Transfer, and Taxonomic Utility of Plastid Markers

(2013) Jan Janouškovec et al.   PLoS One

The Plastid Genome of the Red Macroalga Grateloupia taiwanensis (Halymeniaceae)

(2013) Michael S. DePriest 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 Revised Classification of Eukaryotes

(2012) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

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

Algae's complex origins

(2012) Sven B. Gould   NATURE

Complete Sequences of the Mitochondrial DNA of the Wild Gracilariopsis lemaneiformis and Two Mutagenic Cultivated Breeds (Gracilariaceae, Rhodophyta)

(2012) Lei Zhang et al.   PLoS One

Possible Role of Horizontal Gene Transfer in the Colonization of Sea Ice by Algae

(2012) James A. Raymond et al.   PLoS One

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

The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins

(2012) F. Burki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants

(2012) D. C. Price et al.   SCIENCE

Single cell genome analysis supports a link between phagotrophy and primary plastid endosymbiosis

(2012) Debashish Bhattacharya et al.   Scientific Reports

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

(2012) Adrian M. Altenhoff et al.   PLoS Computational Biology

The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

(2012) Guillaume Blanc et al.   GENOME BIOLOGY

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

(2012) Markus Lommer et al.   GENOME BIOLOGY

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Decoding algal genomes: tracing back the history of photosynthetic life on Earth

(2011) Leïla Tirichine et al.   PLANT JOURNAL

The Bryopsis hypnoides Plastid Genome: Multimeric Forms and Complete Nucleotide Sequence

(2011) Fang Lü et al.   PLoS One

Plastid 16S rRNA Gene Diversity among Eukaryotic Picophytoplankton Sorted by Flow Cytometry from the South Pacific Ocean

(2011) Xiao Li Shi et al.   PLoS One

Red and Green Algal Origin of Diatom Membrane Transporters: Insights into Environmental Adaptation and Cell Evolution

(2011) Cheong Xin Chan et al.   PLoS One

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

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

Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists

(2011) H. S. Yoon et al.   SCIENCE

Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

(2010) Heroen Verbruggen et al.   BMC EVOLUTIONARY BIOLOGY

The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae

(2010) J. S. Brouard et al.   Genome Biology and Evolution

Diversity of active marine picoeukaryotes in the Eastern Mediterranean Sea unveiled using photosystem-II psbA transcripts

(2010) Dikla Man-Aharonovich et al.   ISME Journal

Differential Gene Retention in Plastids of Common Recent Origin

(2010) A. Reyes-Prieto et al.   MOLECULAR BIOLOGY AND EVOLUTION

Endosymbiotic Gene Transfer and Transcriptional Regulation of Transferred Genes in Paulinella chromatophora

(2010) E. C. M. Nowack 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

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011

(2010) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

TheChlorella variabilisNC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex

(2010) Guillaume Blanc et al.   PLANT CELL

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton

(2010) M. L. Cuvelier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri

(2010) S. E. Prochnik et al.   SCIENCE

Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life

(2010) Laura Wegener Parfrey et al.   SYSTEMATIC BIOLOGY

A single origin of the photosynthetic organelle in different Paulinella lineages

(2009) Hwan Su Yoon et al.   BMC EVOLUTIONARY BIOLOGY

Another acquisition of a primary photosynthetic organelle is underway in Paulinella chromatophora

(2009) Takuro Nakayama et al.   CURRENT BIOLOGY

A multivariate statistical evaluation of the “acolla-complex” of Corythionella species, including a description of C. darwini n. sp. (Rhizopoda: Filosea or Rhizaria: Cercozoa)

(2009) Kenneth H. Nicholls   EUROPEAN JOURNAL OF PROTISTOLOGY

Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates

(2009) Fabien Burki et al.   Genome Biology and Evolution

A molecular method for identification of the morphologically plastic invasive algal genera Eucheuma and Kappaphycus (Rhodophyta, Gigartinales) in Hawaii

(2009) Kimberly Y. Conklin et al.   JOURNAL OF APPLIED PHYCOLOGY

Signal Conflicts in the Phylogeny of the Primary Photosynthetic Eukaryotes

(2009) P. Deschamps et al.   MOLECULAR BIOLOGY AND EVOLUTION

The microbial ocean from genomes to biomes

(2009) Edward F. DeLong   NATURE

Single-molecule sequencing of an individual human genome

(2009) Dmitry Pushkarev et al.   NATURE BIOTECHNOLOGY

Molecular Phylogeny and Description of the Novel Katablepharid Roombia truncata gen. et sp. nov., and Establishment of the Hacrobia Taxon nov

(2009) Noriko Okamoto et al.   PLoS One

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

(2009) A. Z. Worden et al.   SCIENCE

Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms

(2009) A. Moustafa et al.   SCIENCE

Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes

(2008) F. Burki et al.   Biology Letters

Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): Unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer

(2008) Jean-Simon Brouard et al.   BMC GENOMICS

Chromatophore Genome Sequence of Paulinella Sheds Light on Acquisition of Photosynthesis by Eukaryotes

(2008) Eva C.M. Nowack et al.   CURRENT BIOLOGY

Metagenomic retrieval of a ribosomal DNA repeat array from an uncultured marine alveolate

(2008) Ramon Massana et al.   ENVIRONMENTAL MICROBIOLOGY

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

(2008) Chris Bowler et al.   NATURE

EEF2 Analysis Challenges the Monophyly of Archaeplastida and Chromalveolata

(2008) Eunsoo Kim et al.   PLoS One

Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures

(2008) J. Korlach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Picoeukaryotic sequences in the Sargasso Sea metagenome

(2008) Gwenael Piganeau et al.   GENOME BIOLOGY