Contrasting Patterns of Nucleotide Substitution Rates Provide Insight into Dynamic Evolution of Plastid and Mitochondrial Genomes of Geranium

Variable presence of the inverted repeat and plastome stability inErodium

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

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

(2016) Kate Rockenbach et al.   GENETICS

Plastid–Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae

(2016) Mao-Lun Weng et al.   Genome Biology and Evolution

Coevolution between Nuclear-Encoded DNA Replication, Recombination, and Repair Genes and Plastid Genome Complexity

(2016) Jin Zhang et al.   Genome Biology and Evolution

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

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

Evolution of short inverted repeat in cupressophytes, transfer of accD to nucleus in Sciadopitys verticillata and phylogenetic position of Sciadopityaceae

(2016) Jia Li et al.   Scientific Reports

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

(2016) Kate Rockenbach et al.   GENETICS

Chloroplast Genome Evolution in Actinidiaceae: clpP Loss, Heterogenous Divergence and Phylogenomic Practice

(2016) Wen-Cai Wang et al.   PLoS One

Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement

(2016) J. Chris Blazier et al.   Scientific Reports

Complete plastome sequence of Thalictrum coreanum (Ranunculaceae) and transfer of the rpl32 gene to the nucleus in the ancestor of the subfamily Thalictroideae

(2015) Seongjun Park et al.   BMC 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

Dynamic evolution ofGeraniummitochondrial genomes through multiple horizontal and intracellular gene transfers

(2015) Seongjun Park et al.   NEW PHYTOLOGIST

Coordinated Rates of Evolution between Interacting Plastid and Nuclear Genes in Geraniaceae

(2015) Jin Zhang et al.   PLANT CELL

Miniaturized mitogenome of the parasitic plantViscum scurruloideumis extremely divergent and dynamic and has lost allnadgenes

(2015) Elizabeth Skippington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)

(2014) Saemundur Sveinsson et al.   BMC EVOLUTIONARY BIOLOGY

Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome

(2014) Karen B Barnard-Kubow et al.   BMC EVOLUTIONARY BIOLOGY

Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids

(2014) Seongjun Park et al.   BMC GENOMICS

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

Unprecedented Heterogeneity in the Synonymous Substitution Rate within a Plant Genome

(2014) Andan Zhu et al.   MOLECULAR BIOLOGY AND EVOLUTION

CDD: NCBI's conserved domain database

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

Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes

(2014) Jamal Sabir et al.   PLANT BIOTECHNOLOGY JOURNAL

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

The “fossilized” mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate

(2013) Aaron O Richardson et al.   BMC BIOLOGY

The Complete Chloroplast Genome Sequence of Cephalotaxus oliveri (Cephalotaxaceae): Evolutionary Comparison of Cephalotaxus Chloroplast DNAs and Insights into the Loss of Inverted Repeat Copies in Gymnosperms

(2013) Xuan Yi et al.   Genome Biology and Evolution

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

A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae)

(2013) Daniel B. Sloan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Potential Functional Replacement of the Plastidic Acetyl-CoA Carboxylase Subunit (accD) Gene by Recent Transfers to the Nucleus in Some Angiosperm Lineages

(2013) M. Rousseau-Gueutin et al.   PLANT PHYSIOLOGY

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

A reevaluation of dual-targeting of proteins to mitochondria and chloroplasts

(2012) Christopher Carrie et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Recent Acceleration of Plastid Sequence and Structural Evolution Coincides with Extreme Mitochondrial Divergence in the Angiosperm Genus Silene

(2012) Daniel B. Sloan et al.   Genome Biology and Evolution

Loss of Two Introns from the Magnolia tripetala Mitochondrial cox2 Gene Implicates Horizontal Gene Transfer and Gene Conversion as a Novel Mechanism of Intron Loss

(2012) N. J. Hepburn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae)

(2012) Mao-Lun Weng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates

(2012) Daniel B. Sloan et al.   PLOS BIOLOGY

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

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

Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family

(2011) E. Babiychuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The endosymbiotic origin, diversification and fate of plastids

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae

(2009) Daniel B Sloan et al.   BMC EVOLUTIONARY BIOLOGY

Discovery of the rpl10 Gene in Diverse Plant Mitochondrial Genomes and Its Probable Replacement by the Nuclear Gene for Chloroplast RPL10 in Two Lineages of Angiosperms

(2009) N. Kubo et al.   DNA RESEARCH

The Functional Transfer of Genes From the Mitochondria to the Nucleus: The Effects of Selection, Mutation, Population Size and Rate of Self-Fertilization

(2009) Yaniv Brandvain et al.   GENETICS

Comparative Analysis of Structural Diversity and Sequence Evolution in Plant Mitochondrial Genes Transferred to the Nucleus

(2009) S.-L. Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

DNA Transfer from Organelles to the Nucleus: The Idiosyncratic Genetics of Endosymbiosis

(2008) Tatjana Kleine et al.   Annual Review of Plant Biology

Identification of new protein substrates for the chloroplast ATP-dependent Clp protease supports its constitutive role inArabidopsis

(2008) Tara M. Stanne et al.   BIOCHEMICAL JOURNAL

Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species

(2008) Tomonori Hirao et al.   BMC PLANT BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

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

Substitution of the Gene for Chloroplast RPS16 Was Assisted by Generation of a Dual Targeting Signal

(2008) M. Ueda et al.   MOLECULAR BIOLOGY AND EVOLUTION

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

(2008) G DROUIN et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

CLB19, a pentatricopeptide repeat protein required for editing ofrpoAandclpPchloroplast transcripts

(2008) Anne-Laure Chateigner-Boutin et al.   PLANT JOURNAL

Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast clpP1 Gene

(2008) Per Erixon et al.   PLoS One

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

(2008) M. M. Guisinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA