Plastid Transcript Editing across Dinoflagellate Lineages Shows Lineage-Specific Application but Conserved Trends

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

Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum

(2017) Yi Jin Liew et al.   PLoS Genetics

Deep Transcriptome Sequencing of Two Green Algae, Chara vulgaris and Chlamydomonas reinhardtii, Provides No Evidence of Organellar RNA Editing

(2017) A. Cahoon et al.   Genes

metaSNV: A tool for metagenomic strain level analysis

(2017) Paul Igor Costea et al.   PLoS One

MOCAT2: a metagenomic assembly, annotation and profiling framework

(2016) Jens Roat Kultima et al.   BIOINFORMATICS

Identification of Sequences EncodingSymbiodinium minutumMitochondrial Proteins

(2016) Erin R. Butterfield et al.   Genome Biology and Evolution

Diversity of transcripts and transcript processing forms in plastids of the dinoflagellate alga Karenia mikimotoi

(2016) Richard G. Dorrell et al.   PLANT MOLECULAR BIOLOGY

Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics

(2016) Jan Janouškovec et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcripts in the Plasmodium Apicoplast Undergo Cleavage at tRNAs and Editing, and Include Antisense Sequences

(2016) R. Ellen R. Nisbet et al.   PROTIST

The Unexpected Diversity of Plant Organelle RNA Editosomes

(2016) Tao Sun et al.   TRENDS IN PLANT SCIENCE

RNA editing in plants: Machinery and flexibility of site recognition

(2015) Toshiharu Shikanai   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates

(2015) Gregory S. Gavelis et al.   BMC GENOMICS

Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding

(2015) Noan Le Bescot et al.   ENVIRONMENTAL MICROBIOLOGY

Plastid Genome-Based Phylogeny Pinpointed the Origin of the Green-Colored Plastid in the Dinoflagellate Lepidodinium chlorophorum

(2015) Ryoma Kamikawa et al.   Genome Biology and Evolution

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes

(2015) David Roy Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis

(2015) S. Lin et al.   SCIENCE

Subcellular Investigation of Photosynthesis-Driven Carbon Assimilation in the Symbiotic Reef Coral Pocillopora damicornis

(2015) Christophe Kopp et al.   mBio

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

(2015) Tereza Ševčíková et al.   Scientific Reports

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles

(2014) Blake T Hovde et al.   BMC GENOMICS

Massive Gene Transfer and Extensive RNA Editing of a Symbiotic Dinoflagellate Plastid Genome

(2014) Sutada Mungpakdee et al.   Genome Biology and Evolution

Genome-Wide Transcript Profiling Reveals the Coevolution of Plastid Gene Sequences and Transcript Processing Pathways in the Fucoxanthin Dinoflagellate Karlodinium veneficum

(2014) Elisabeth Richardson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyteSelaginella uncinata

(2014) Bastian Oldenkott et al.   RNA

Massive outbreaks of Noctiluca scintillans blooms in the Arabian Sea due to spread of hypoxia

(2014) Helga do Rosário Gomes et al.   Nature Communications

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

Evolution of Chloroplast Transcript Processing in Plasmodium and Its Chromerid Algal Relatives

(2014) Richard G. Dorrell et al.   PLoS Genetics

RNA Editing in Plants and Its Evolution

(2013) Mizuki Takenaka et al.   Annual Review of Genetics

Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure

(2013) Eiichi Shoguchi et al.   CURRENT BIOLOGY

Split Photosystem Protein, Linear-Mapping Topology, and Growth of Structural Complexity in the Plastid Genome of Chromera velia

(2013) Jan Janouškovec et al.   MOLECULAR BIOLOGY AND EVOLUTION

Subcellular localization of minicircle DNA in the dinoflagellateAmphidinium massartii

(2013) Satomi Owari et al.   PHYCOLOGICAL RESEARCH

Evolutionary Origin of RNA Editing

(2012) Michael W. Gray   BIOCHEMISTRY

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

The Revised Classification of Eukaryotes

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

A Tertiary Plastid Gains RNA Editing in Its New Host

(2012) Christopher J. Jackson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Polyuridylylation and processing of transcripts from multiple gene minicircles in chloroplasts of the dinoflagellate Amphidinium carterae

(2012) Adrian C. Barbrook et al.   PLANT MOLECULAR BIOLOGY

Genome Fragmentation Is Not Confined to the Peridinin Plastid in Dinoflagellates

(2012) Mari Espelund et al.   PLoS One

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

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

The Mitochondrial Genome and Transcriptome of the Basal Dinoflagellate Hematodinium sp.: Character Evolution within the Highly Derived Mitochondrial Genomes of Dinoflagellates

(2011) C. J. Jackson et al.   Genome Biology and Evolution

How a neutral evolutionary ratchet can build cellular complexity

(2011) Julius Lukeš et al.   IUBMB LIFE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Genome Evolution of a Tertiary Dinoflagellate Plastid

(2011) Tove M. Gabrielsen et al.   PLoS One

Functions and Regulation of RNA Editing by ADAR Deaminases

(2010) Kazuko Nishikura   Annual Review of Biochemistry

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

(2010) Behzad Imanian et al.   PLoS One

Dinoflagellate Phylogeny as Inferred from Heat Shock Protein 90 and Ribosomal Gene Sequences

(2010) Mona Hoppenrath 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

Irremediable Complexity?

(2010) M. W. Gray et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Identification of transcribed and persistent variants of the psbA gene carried by plastid minicircles in a dinoflagellate

(2009) Satoko Iida et al.   CURRENT GENETICS

Substitutional editing of Heterocapsa triquetra chloroplast transcripts and a folding model for its divergent chloroplast 16S rRNA

(2009) Yunkun Dang et al.   GENE

Long Transcripts from Dinoflagellate Chloroplast Minicircles Suggest “Rolling Circle” Transcription

(2009) Yunkun Dang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The replication of plastid minicircles involves rolling circle intermediates

(2009) Siu Kai Leung et al.   NUCLEIC ACIDS RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH