Lost and Found: Return of the Inverted Repeat in the Legume Clade Defined by Its Absence

Passiflora plastome sequencing reveals widespread genomic rearrangements

(2018) Samar O. Rabah et al.   Journal of Systematics and Evolution

Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies

(2017) Erika N. Schwarz et al.   JOURNAL OF MOLECULAR EVOLUTION

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny – The Legume Phylogeny Working Group (LPWG)

(2017) Nasim Azani et al.   TAXON

Variable presence of the inverted repeat and plastome stability inErodium

(2016) John C. Blazier et al.   ANNALS OF BOTANY

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

GinkgoandWelwitschiaMitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution

(2016) Wenhu Guo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes

(2016) Mao-Lun Weng et al.   NEW PHYTOLOGIST

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Patterns of phylogenetic incongruence in Medicago found among six loci

(2016) Filipe de Sousa et al.   PLANT SYSTEMATICS AND EVOLUTION

Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat

(2015) M. J. Sanderson et al.   AMERICAN JOURNAL OF BOTANY

Filling in the gaps of the papilionoid legume phylogeny: The enigmatic Amazonian genus Petaladenium is a new branch of the early-diverging Amburaneae clade

(2015) Domingos Cardoso et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates

(2015) Andan Zhu et al.   NEW PHYTOLOGIST

Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots

(2015) Craig F. Barrett et al.   NEW PHYTOLOGIST

Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP

(2015) Diana V. Dugas et al.   Scientific Reports

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Two Distinct Plastid Genome Configurations and Unprecedented Intraspecies Length Variation in the accD Coding Region in Medicago truncatula

(2014) C. Gurdon et al.   DNA RESEARCH

The dynamic history of plastid genomes in the Campanulaceae sensu lato is unique among angiosperms

(2014) E. B. Knox   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstruction of the Ancestral Plastid Genome in Geraniaceae Reveals a Correlation between Genome Rearrangements, Repeats, and Nucleotide Substitution Rates

(2013) Mao-Lun Weng 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

Balanced Gene Losses, Duplications and Intensive Rearrangements Led to an Unusual Regularly Sized Genome in Arbutus unedo Chloroplasts

(2013) Fernando Martínez-Alberola et al.   PLoS One

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); Comparative evolutionary analyses with other three asterids

(2012) Dong-Keun Yi et al.   MOLECULES AND CELLS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Complete Chloroplast Genome Sequences of Important Oilseed Crop Sesamum indicum L

(2012) Dong-Keun Yi et al.   PLoS One

Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing

(2012) Diego Fajardo et al.   Tree Genetics & Genomes

Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae)

(2011) J. Chris Blazier et al.   PLANT MOLECULAR BIOLOGY

High-Throughput Sequencing of Three Lemnoideae (Duckweeds) Chloroplast Genomes from Total DNA

(2011) Wenqin Wang et al.   PLoS One

Localized hypermutation and associated gene losses in legume chloroplast genomes

(2010) A. M. Magee et al.   GENOME RESEARCH

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

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Microhomology-mediated and nonhomologous repair of a double-strand break in the chloroplast genome of Arabidopsis

(2010) T. Kwon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications

(2009) Young-Kyu Kim et al.   MOLECULES AND CELLS

Whirly proteins maintain plastid genome stability in Arabidopsis

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

Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots

(2008) Rui-Jiang Wang et al.   BMC EVOLUTIONARY BIOLOGY

Extensive Rearrangements in the Chloroplast Genome of Trachelium caeruleum Are Associated with Repeats and tRNA Genes

(2008) Rosemarie C. Haberle et al.   JOURNAL OF MOLECULAR EVOLUTION

Extensive Reorganization of the Plastid Genome of Trifolium subterraneum (Fabaceae) Is Associated with Numerous Repeated Sequences and Novel DNA Insertions

(2008) Zhengqiu Cai et al.   JOURNAL OF MOLECULAR EVOLUTION

The Reticulate History of Medicago (Fabaceae)

(2008) Iván J. Maureira-Butler et al.   SYSTEMATIC BIOLOGY

Phylogeny and Historical Biogeography of Geraniaceae in Relation to Climate Changes and Pollination Ecology

(2008) Omar Fiz et al.   SYSTEMATIC BOTANY