Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species

Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins

(2014) Blaise Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions

(2014) Cymon J. Cox et al.   SYSTEMATIC BIOLOGY

Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes

(2013) Felix Grewe et al.   BMC EVOLUTIONARY BIOLOGY

A 20-state empirical amino-acid substitution model for green plant chloroplasts

(2013) Cymon J. Cox et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Mitochondrial Genome of the Prasinophyte Prasinoderma coloniale Reveals Two Trans-Spliced Group I Introns in the Large Subunit rRNA Gene

(2013) Jean-François Pombert et al.   PLoS One

Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates

(2012) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study

(2012) Omar Rota-Stabelli et al.   SYSTEMATIC BIOLOGY

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

(2011) Frederik Leliaert et al.   BIOESSAYS

Acoelomorph flatworms are deuterostomes related to Xenoturbella

(2011) Hervé Philippe et al.   NATURE

The GC-Rich Mitochondrial and Plastid Genomes of the Green Alga Coccomyxa Give Insight into the Evolution of Organelle DNA Nucleotide Landscape

(2011) David Roy Smith et al.   PLoS One

Nested in the Chlorellales or Independent Class? Phylogeny and Classification of the Pedinophyceae (Viridiplantae) Revealed by Molecular Phylogenetic Analyses of Complete Nuclear and Plastid-encoded rRNA Operons

(2011) Birger Marin   PROTIST

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS 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

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2010) Takuya Matsumoto et al.   PROTIST

Trans-splicing of organelle introns - a detour to continuous RNAs

(2009) Stephanie Glanz et al.   BIOESSAYS

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

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

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

The Chloroplast Genomes of the Green Algae Pedinomonas minor, Parachlorella kessleri, and Oocystis solitaria Reveal a Shared Ancestry between the Pedinomonadales and Chlorellales

(2009) M. Turmel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular Phylogeny and Classification of the Mamiellophyceae class. nov. (Chlorophyta) based on Sequence Comparisons of the Nuclear- and Plastid-encoded rRNA Operons

(2009) Birger Marin et al.   PROTIST

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

(2009) A. Z. Worden et al.   SCIENCE

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

Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylum-biased PCR approach

(2008) Manon Viprey et al.   ENVIRONMENTAL MICROBIOLOGY