Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates

Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids

(2018) Christopher Jackson et al.   Scientific Reports

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Non-photosynthetic Diatom Reveals Early Steps of Reductive Evolution in Plastids

(2017) Ryoma Kamikawa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Three classes of oxygen-dependent cyclase involved in chlorophyll and bacteriochlorophyll biosynthesis

(2017) Guangyu E. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2017) Richard G Dorrell et al.   eLife

Plastid genome sequences of Gymnochlora stellata, Lotharella vacuolata, and Partenskyella glossopodia reveal remarkable structural conservation among chlorarachniophyte species

(2016) Shigekatsu Suzuki et al.   JOURNAL OF PLANT RESEARCH

The Evolution of Silicon Transport in Eukaryotes

(2016) Alan O. Marron et al.   MOLECULAR 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

Evolution of the Tetrapyrrole Biosynthetic Pathway in Secondary Algae: Conservation, Redundancy and Replacement

(2016) Jaromír Cihlář et al.   PLoS One

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

Identification of the chlE gene encoding oxygen-independent Mg-protoporphyrin IX monomethyl ester cyclase in cyanobacteria

(2015) Kaori Yamanashi et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae

(2015) Heather M Hunsperger et al.   BMC EVOLUTIONARY BIOLOGY

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

Complex Ancestries of Isoprenoid Synthesis in Dinoflagellates

(2015) Bastian Bentlage et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Proposal of a Twin Aarginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes

(2015) Ryoma Kamikawa et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Molecular Phylogeny and Intricate Evolutionary History of the Three Isofunctional Enzymes Involved in the Oxidation of Protoporphyrinogen IX

(2014) Koichi Kobayashi 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

Multiple losses of photosynthesis inNitzschia(Bacillariophyceae)

(2014) Ryoma Kamikawa et al.   PHYCOLOGICAL RESEARCH

Evolution of a New Chlorophyll Metabolic Pathway Driven by the Dynamic Changes in Enzyme Promiscuous Activity

(2014) Hisashi Ito et al.   PLANT AND CELL PHYSIOLOGY

Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle

(2014) T. Nakayama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Endosymbiotic Gene Transfer in Tertiary Plastid-Containing Dinoflagellates

(2013) Fabien Burki et al.   EUKARYOTIC CELL

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape Family

(2013) S. Wicke et al.   PLANT CELL

Chlorophyll Biosynthesis Gene Evolution Indicates Photosystem Gene Duplication, Not Photosystem Merger, at the Origin of Oxygenic Photosynthesis

(2012) Filipa L. Sousa et al.   Genome Biology and Evolution

Pigment-based chloroplast types in dinoflagellates

(2012) M Zapata et al.   MARINE ECOLOGY PROGRESS SERIES

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

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Tetrapyrrole Synthesis of Photosynthetic Chromerids Is Likely Homologous to the Unusual Pathway of Apicomplexan Parasites

(2011) Luděk Kořený et al.   PLANT CELL

Identification of the 7-Hydroxymethyl ChlorophyllaReductase of the Chlorophyll Cycle inArabidopsis

(2011) Miki Meguro et al.   PLANT CELL

Isoprenoid biosynthesis in eukaryotic phototrophs: A spotlight on algae

(2011) Martin Lohr et al.   PLANT SCIENCE

Genome Evolution of a Tertiary Dinoflagellate Plastid

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

A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum

(2010) Marianne A Minge et al.   BMC EVOLUTIONARY BIOLOGY

The evolution, metabolism and functions of the apicoplast

(2010) L. Lim et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Green-colored Plastids in the Dinoflagellate Genus Lepidodinium are of Core Chlorophyte Origin

(2010) Takuya Matsumoto et al.   PROTIST

The ferredoxin-NADP+reductase/ferredoxin electron transfer system ofPlasmodium falciparum

(2009) Emanuela Balconi et al.   FEBS Journal

The Complete Plastid Genome Sequence of the Secondarily Nonphotosynthetic Alga Cryptomonas paramecium: Reduction, Compaction, and Accelerated Evolutionary Rate

(2009) Natalie Donaher et al.   Genome Biology and Evolution

Protein Targeting into Secondary Plastids

(2009) KATHRIN BOLTE et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

An Integrated Analysis of Molecular Acclimation to High Light in the Marine Diatom Phaeodactylum tricornutum

(2009) Marianne Nymark et al.   PLoS One

Identification of a Novel Vinyl Reductase Gene Essential for the Biosynthesis of Monovinyl Chlorophyll inSynechocystissp. PCC6803

(2008) Hisashi Ito et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum

(2007) Kiyotaka Takishita et al.   GENE