Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)

The Carboxy Terminus of YCF1 Contains a Motif Conserved throughout >500 Myr of Streptophyte Evolution

(2017) Jan de Vries et al.   Genome Biology and Evolution

Phylogenetic position of the coral symbiont Ostreobium (Ulvophyceae) inferred from chloroplast genome data

(2017) Heroen Verbruggen et al.   JOURNAL OF PHYCOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae

(2017) Monique Turmel et al.   Scientific Reports

Plastomes of the green algae Hydrodictyon reticulatum and Pediastrum duplex (Sphaeropleales, Chlorophyceae)

(2017) Hilary A. McManus et al.   PeerJ

Taxonomic revision of Halimeda (Bryopsidales, Chlorophyta) in south-western Australia

(2016) Ma. Chiela M. Cremen et al.   AUSTRALIAN SYSTEMATIC BOTANY

Evolutionary Dynamics of Chloroplast Genomes in Low Light: A Case Study of the Endolithic Green AlgaOstreobium quekettii

(2016) Vanessa R. Marcelino et al.   Genome Biology and Evolution

Mitochondrion-to-Chloroplast DNA Transfers and Intragenomic Proliferation of Chloroplast Group II Introns inGloeotilopsisGreen Algae (Ulotrichales, Ulvophyceae)

(2016) Monique Turmel et al.   Genome Biology and Evolution

Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss

(2016) Pavel Avdeyev et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genome Stability and Evolution: Attempting a Holistic View

(2016) Ingo Schubert et al.   TRENDS IN PLANT SCIENCE

Comparative Chloroplast Genome Analyses of Streptophyte Green Algae Uncover Major Structural Alterations in the Klebsormidiophyceae, Coleochaetophyceae and Zygnematophyceae

(2016) Claude Lemieux et al.   Frontiers in Plant Science

Proliferation of group II introns in the chloroplast genome of the green algaOedocladium carolinianum(Chlorophyceae)

(2016) Jean-Simon Brouard et al.   PeerJ

Chloroplast Phylogenomic Inference of Green Algae Relationships

(2016) Linhua Sun et al.   Scientific Reports

Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.

(2016) Frederik Leliaert et al.   Scientific Reports

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin

(2015) Frederik Leliaert et al.   BMC GENOMICS

Dynamic Evolution of the Chloroplast Genome in the Green Algal Classes Pedinophyceae and Trebouxiophyceae

(2015) Monique Turmel et al.   Genome Biology and Evolution

The plastid genome of the red algaLaurencia

(2015) Heroen Verbruggen et al.   JOURNAL OF PHYCOLOGY

Evolution of group II introns

(2015) Steven Zimmerly et al.   Mobile DNA

Complete Chloroplast Genome of the Wollemi Pine (Wollemia nobilis): Structure and Evolution

(2015) Jia-Yee S. Yap et al.   PLoS One

The Complete Chloroplast and Mitochondrial Genomes of the Green Macroalga Ulva sp. UNA00071828 (Ulvophyceae, Chlorophyta)

(2015) James T. Melton et al.   PLoS One

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae

(2014) Claude Lemieux et al.   BMC EVOLUTIONARY BIOLOGY

Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants

(2014) Peter Civáň et al.   Genome Biology and Evolution

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Inclusion of chloroplast genes that have undergone expansion misleads phylogenetic reconstruction in the Chlorophyta

(2013) Phil M. Novis et al.   AMERICAN JOURNAL OF BOTANY

Genome reduction as the dominant mode of evolution

(2013) Yuri I. Wolf et al.   BIOESSAYS

Is ftsH the Key to Plastid Longevity in Sacoglossan Slugs?

(2013) Jan de Vries et al.   Genome Biology and Evolution

Tracing the Evolution of Streptophyte Algae and Their Mitochondrial Genome

(2013) Monique Turmel et al.   Genome Biology and Evolution

Reverse Transcription of Spliced psbA mRNA in Chlamydomonas spp. and Its Possible Role in Evolutionary Intron Loss

(2013) Obed W. Odom et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets

(2013) Marc Lohse et al.   NUCLEIC ACIDS RESEARCH

UniMoG--a unifying framework for genomic distance calculation and sorting based on DCJ

(2012) R. Hilker et al.   BIOINFORMATICS

Phylogeny and Molecular Evolution of the Green Algae

(2012) Frederik Leliaert et al.   CRITICAL REVIEWS IN PLANT SCIENCES

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Horizontal gene transfer in the evolution of photosynthetic eukaryotes

(2012) Jinling HUANG et al.   Journal of Systematics and Evolution

Psb30 is a photosystem II reaction center subunit and is required for optimal growth in high light in Chlamydomonas reinhardtii

(2011) Natsuko Inoue-Kashino et al.   JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY

The Role of Reverse Transcriptase in Intron Gain and Loss Mechanisms

(2011) Noa E. Cohen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chloroplast genomes of photosynthetic eukaryotes

(2011) Beverley R. Green   PLANT JOURNAL

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

(2011) Fang Lü et al.   PLoS One

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

The evolution of chloroplast genome structure in ferns

(2010) Paul G. Wolf et al.   GENOME

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

Genome comparison and context analysis reveals putative mobile forms of restriction–modification systems and related rearrangements

(2010) Yoshikazu Furuta et al.   NUCLEIC ACIDS RESEARCH

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

The endosymbiotic origin, diversification and fate of plastids

(2010) P. J. Keeling   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA

(2009) David Smith et al.   BMC GENOMICS

Deletional Bias across the Three Domains of Life

(2009) Chih-Horng Kuo et al.   Genome Biology and Evolution

ANALYSIS OF A PLASTID MULTIGENE DATA SET AND THE PHYLOGENETIC POSITION OF THE MARINE MACROALGACAULERPA FILIFORMIS(CHLOROPHYTA)

(2009) G. C. Zuccarello et al.   JOURNAL OF PHYCOLOGY

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

Genome streamlining and the elemental costs of growth

(2009) Dag O. Hessen et al.   TRENDS IN ECOLOGY & EVOLUTION

Plastid Evolution

(2008) Sven B. Gould et al.   Annual Review of Plant Biology

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

The Chloroplast Genomes of the Green Algae Pyramimonas, Monomastix, and Pycnococcus Shed New light on the Evolutionary History of Prasinophytes and the Origin of the Secondary Chloroplasts of Euglenids

(2008) Monique Turmel et al.   MOLECULAR BIOLOGY AND EVOLUTION

A multi-locus time-calibrated phylogeny of the siphonous green algae

(2008) Heroen Verbruggen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION