What can we do with 1000 plastid genomes?

Physiological Functions of Cyclic Electron Transport Around Photosystem I in Sustaining Photosynthesis and Plant Growth

(2016) Wataru Yamori et al.   Annual Review of Plant Biology

Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes

(2016) Michael R. McKain et al.   BIOINFORMATICS

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV

(2016)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Lineage-Specific Reductions of Plastid Genomes in an Orchid Tribe with Partially and Fully Mycoheterotrophic Species

(2016) Yan-Lei Feng et al.   Genome Biology and Evolution

From barcodes to genomes: extending the concept of DNA barcoding

(2016) Eric Coissac et al.   MOLECULAR ECOLOGY

Strategies for complete plastid genome sequencing

(2016) Alex D. Twyford et al.   Molecular Ecology Resources

Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia

(2016) Anna V. Williams et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution

(2016) Yanxia Sun et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Biparental chloroplast inheritance leads to rescue from cytonuclear incompatibility

(2016) Karen B. Barnard-Kubow et al.   NEW PHYTOLOGIST

Telling plant species apart with DNA: from barcodes to genomes

(2016) Peter M. Hollingsworth et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Codon Optimization to Enhance Expression Yields Insights into Chloroplast Translation

(2016) Kwang-Chul Kwon et al.   PLANT PHYSIOLOGY

The Type II NADPH Dehydrogenase Facilitates Cyclic Electron Flow, Energy-Dependent Quenching, and Chlororespiratory Metabolism during Acclimation ofChlamydomonas reinhardtiito Nitrogen Deprivation

(2016) Shai I. Saroussi et al.   PLANT PHYSIOLOGY

Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants

(2016) Susann Wicke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms

(2016) Ryan A. Folk et al.   SYSTEMATIC BIOLOGY

An Integrated Perspective on Phylogenetic Workflows

(2016) August Guang et al.   TRENDS IN ECOLOGY & EVOLUTION

Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins

(2016) Cuicui Shen et al.   Nature Communications

A new synthetic biology approach allows transfer of an entire metabolic pathway from a medicinal plant to a biomass crop

(2016) Paulina Fuentes et al.   eLife

Engineering Plastid Genomes: Methods, Tools, and Applications in Basic Research and Biotechnology

(2015) Ralph Bock   Annual Review of Plant Biology

NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss

(2015) Tracey A Ruhlman et al.   BMC PLANT BIOLOGY

The linear plastid chromosomes of maize: terminal sequences, structures, and implications for DNA replication

(2015) Delene J. Oldenburg et al.   CURRENT GENETICS

Mutation Rates in Plastid Genomes: They Are Lower than You Might Think

(2015) David Roy Smith   Genome Biology and Evolution

The Plastomes of Two Species in the Endoparasite GenusPilostyles(Apodanthaceae) Each Retain Just Five or Six Possibly Functional Genes

(2015) Sidonie Bellot et al.   Genome Biology and Evolution

Direct Estimate of the Spontaneous Mutation Rate Uncovers the Effects of Drift and Recombination in theChlamydomonas reinhardtiiPlastid Genome

(2015) Rob W. Ness et al.   MOLECULAR BIOLOGY AND EVOLUTION

Massive intracellular gene transfer during plastid genome reduction in nongreen Orobanchaceae

(2015) Natalie Cusimano et al.   NEW PHYTOLOGIST

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Predictable Alteration of Sequence Recognition by RNA Editing Factors from Arabidopsis

(2015) Peter Kindgren et al.   PLANT CELL

YCF1: A Green TIC: Response to the de Vries et al. Commentary: Figure 1.

(2015) Masato Nakai   PLANT CELL

YCF1: A Green TIC?

(2015) Jan de Vries et al.   PLANT CELL

The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene

(2015) Anna V. Williams et al.   PLoS One

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

DNA maintenance in plastids and mitochondria of plants

(2015) Delene J. Oldenburg et al.   Frontiers in Plant Science

Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: The tortoise and the hare IV

(2014) Joey Shaw et al.   AMERICAN JOURNAL OF BOTANY

Pentatricopeptide Repeat Proteins in Plants

(2014) Alice Barkan et al.   Annual Review of Plant Biology

Why are most organelle genomes transmitted maternally?

(2014) Stephan Greiner et al.   BIOESSAYS

kmacs: the k -mismatch average common substring approach to alignment-free sequence comparison

(2014) Chris-Andre Leimeister et al.   BIOINFORMATICS

Plant DNA barcoding: from gene to genome

(2014) Xiwen Li et al.   BIOLOGICAL REVIEWS

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

A precise chloroplast genome of Nelumbo nucifera (Nelumbonaceae) evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots

(2014) Zhihua Wu et al.   BMC PLANT BIOLOGY

A meta-analysis of the strength and nature of cytoplasmic genetic effects

(2014) R. Dobler et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Possible Loss of the Chloroplast Genome in the Parasitic Flowering Plant Rafflesia lagascae (Rafflesiaceae)

(2014) Jeanmaire Molina et al.   MOLECULAR BIOLOGY AND EVOLUTION

Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep?

(2014) Diana M. Percy et al.   MOLECULAR ECOLOGY

On the adaptive value of cytoplasmic genomes in plants

(2014) Dan G. Bock et al.   MOLECULAR ECOLOGY

High-accuracyde novoassembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy

(2014) Qiushi Li et al.   NEW PHYTOLOGIST

A Plastid without a Genome: Evidence from the Nonphotosynthetic Green Algal Genus Polytomella

(2014) D. R. Smith et al.   PLANT PHYSIOLOGY

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

Enzymes involved in organellar DNA replication in photosynthetic eukaryotes

(2014) Takashi Moriyama et al.   Frontiers in Plant Science

A Long PCR–Based Approach for DNA Enrichment Prior to Next-Generation Sequencing for Systematic Studies

(2014) Simon Uribe-Convers et al.   Applications in Plant Sciences

An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome

(2013) Marco Ferrarini et al.   BMC GENOMICS

Sequencing Angiosperm Plastid Genomes Made Easy: A Complete Set of Universal Primers and a Case Study on the Phylogeny of Saxifragales

(2013) Wenpan Dong et al.   Genome Biology and Evolution

Disproportional Plastome-Wide Increase of Substitution Rates and Relaxed Purifying Selection in Genes of Carnivorous Lentibulariaceae

(2013) Susann Wicke et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) S. Wicke et al.   PLANT CELL

Synthetic biology in plastids

(2013) Lars B. Scharff et al.   PLANT JOURNAL

The potential for manipulating RNA with pentatricopeptide repeat proteins

(2013) Yusuke Yagi et al.   PLANT JOURNAL

Contradiction between Plastid Gene Transcription and Function Due to Complex Posttranscriptional Splicing: An Exemplary Study of ycf15 Function and Evolution in Angiosperms

(2013) Chao Shi et al.   PLoS One

A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid Genomes

(2013) Gregory W. Stull et al.   Applications in Plant Sciences

Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA

(2012) Nolan Kane et al.   AMERICAN JOURNAL OF BOTANY

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

(2012) Chang Liu et al.   BMC GENOMICS

The Evolutionary Root of Flowering Plants

(2012) Vadim V. Goremykin et al.   SYSTEMATIC BIOLOGY

A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins

(2012) Alice Barkan et al.   PLoS Genetics

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny

(2011) Chung-Shien Wu et al.   Genome Biology and Evolution

Systematic Error in Seed Plant Phylogenomics

(2011) Bojian Zhong et al.   Genome Biology and Evolution

Rampant Gene Loss in the Underground Orchid Rhizanthella gardneri Highlights Evolutionary Constraints on Plastid Genomes

(2011) E. Delannoy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Protein-mediated protection as the predominant mechanism for defining processed mRNA termini in land plant chloroplasts

(2011) Petya Zhelyazkova et al.   NUCLEIC ACIDS RESEARCH

Chloroplast genomes of photosynthetic eukaryotes

(2011) Beverley R. Green   PLANT JOURNAL

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Expression of Plastid Genes: Organelle-Specific Elaborations on a Prokaryotic Scaffold

(2011) A. Barkan   PLANT PHYSIOLOGY

Choosing and Using a Plant DNA Barcode

(2011) Peter M. Hollingsworth et al.   PLoS One

Chloroplast RNA Metabolism

(2010) David B. Stern et al.   Annual Review of Plant Biology

Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae

(2010) Mary M. Guisinger et al.   JOURNAL OF MOLECULAR EVOLUTION

Changes in Rubisco Kinetics during the Evolution of C4 Photosynthesis in Flaveria (Asteraceae) Are Associated with Positive Selection on Genes Encoding the Enzyme

(2010) Maxim V. Kapralov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage

(2010) M. M. Guisinger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recombination and the maintenance of plant organelle genome stability

(2010) Alexandre Maréchal et al.   NEW PHYTOLOGIST

Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform

(2010) Robin A Atherton et al.   Plant Methods

Identification of Nuclear Genes Encoding Chloroplast-Localized Proteins Required for Embryo Development in Arabidopsis

(2010) N. Bryant et al.   PLANT PHYSIOLOGY

The Path from C3 to C4 Photosynthesis

(2010) U. Gowik et al.   PLANT PHYSIOLOGY

The Role of Heterologous Chloroplast Sequence Elements in Transgene Integration and Expression

(2010) T. Ruhlman et al.   PLANT PHYSIOLOGY

Mechanism of RNA stabilization and translational activation by a pentatricopeptide repeat protein

(2010) J. Prikryl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comparative approach to elucidate chloroplast genome replication

(2009) Neeraja M Krishnan et al.   BMC GENOMICS

Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?

(2009) ARON J. FAZEKAS et al.   Molecular Ecology Resources

A DNA barcode for land plants

(2009) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From chloroplasts to “cryptic” plastids: evolution of plastid genomes in parasitic plants

(2008) Kirsten Krause   CURRENT GENETICS

The pentatricopeptide repeat geneOTP51with two LAGLIDADG motifs is required for thecis-splicing of plastidycf3intron 2 inArabidopsis thaliana

(2008) Andéol Falcon de Longevialle et al.   PLANT JOURNAL