Fragaria mitogenomes evolve rapidly in structure but slowly in sequence and incur frequent multinucleotide mutations mediated by microinversions

Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives

(2021) Shuang Wu et al.   BMC PLANT BIOLOGY

Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)

(2021) Qin Qiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Can Green Algal Plastid Genome Size Be Explained by DNA Repair Mechanisms?

(2020) David Roy Smith   Genome Biology and Evolution

The Tempo and Mode of Angiosperm Mitochondrial Genome Divergence Inferred from Intraspecific Variation in Arabidopsis thaliana

(2020) Zhiqiang Wu et al.   G3-Genes Genomes Genetics

Comparative Analysis of the Mitochondrial Genomes of Nicotiana tabacum: Hints Toward the Key Factors Closely Related to the Cytoplasmic Male Sterility Mechanism

(2020) Ruyi Wang et al.   Frontiers in Genetics

Episodic and guanine–cytosine‐biased bursts of intragenomic and interspecific synonymous divergence in Ajugoideae (Lamiaceae) mitogenomes

(2020) Fang Liu et al.   NEW PHYTOLOGIST

MSH1is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes

(2020) Zhiqiang Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracing the diploid ancestry of the cultivated octoploid strawberry

(2020) Chao Feng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nucleotide substitution rates of diatom plastid encoded protein genes are positively correlated with genome architecture

(2020) Yan Ren et al.   Scientific Reports

Origin and evolution of the octoploid strawberry genome

(2019) Patrick P. Edger et al.   NATURE GENETICS

Molecular evolution in large steps - Codon substitutions under positive selection

(2019) Qingjian Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The alternative reality of plant mitochondrial DNA: One ring does not rule them all

(2019) Alexander Kozik et al.   PLoS Genetics

The mitogenome of Norway spruce and a reappraisal of mitochondrial recombination in plants

(2019) Alexis R Sullivan et al.   Genome Biology and Evolution

Characterization of 20 complete plastomes from the tribe Laureae (Lauraceae) and distribution of small inversions

(2019) Sangjin Jo et al.   PLoS One

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana

(2018) Mao-Lun Weng et al.   GENETICS

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Repeats of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution

(2018) Emily L. Wynn et al.   G3-Genes Genomes Genetics

A New Perspective on Polyploid Fragaria (Strawberry) Genome Composition Based on Large-Scale, Multi-Locus Phylogenetic Analysis

(2017) Yilong Yang et al.   Genome Biology 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

Plant organellar DNA polymerases are replicative and translesion DNA synthesis polymerases

(2017) Noe Baruch-Torres et al.   NUCLEIC ACIDS RESEARCH

Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages

(2016) Dennis V. Lavrov et al.   Genome Biology and Evolution

GinkgoandWelwitschiaMitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution

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

The mutational hazard hypothesis of organelle genome evolution: 10 years on

(2016) David Roy Smith   MOLECULAR ECOLOGY

Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns

(2016) Wenhu Guo et al.   NEW PHYTOLOGIST

Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species

(2015) Rajanikanth Govindarajulu et al.   AMERICAN JOURNAL OF BOTANY

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

(2015) Ryan R. Wick et al.   BIOINFORMATICS

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

(2015) David Roy Smith   Genome Biology and Evolution

Are Synonymous Substitutions in Flowering Plant Mitochondria Neutral?

(2015) Emily L. Wynn et al.   JOURNAL OF MOLECULAR EVOLUTION

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

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

The massive mitochondrial genome of the angiospermSilene noctiflorais evolving by gain or loss of entire chromosomes

(2015) Zhiqiang Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fragaria : A genus with deep historical roots and ripe for evolutionary and ecological insights

(2014) Aaron Liston et al.   AMERICAN JOURNAL OF BOTANY

History of Plastid DNA Insertions Reveals Weak Deletion and AT Mutation Biases in Angiosperm Mitochondrial Genomes

(2014) Daniel B. Sloan et al.   Genome Biology and Evolution

Evolutionary Origins and Dynamics of Octoploid Strawberry Subgenomes Revealed by Dense Targeted Capture Linkage Maps

(2014) Jacob A. Tennessen et al.   Genome Biology and Evolution

Genes and Junk in Plant Mitochondria—Repair Mechanisms and Selection

(2014) Alan C. Christensen   Genome Biology and Evolution

Unprecedented Heterogeneity in the Synonymous Substitution Rate within a Plant Genome

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

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

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

Plant Mitochondrial Genome Evolution Can Be Explained by DNA Repair Mechanisms

(2013) Alan C. Christensen   Genome Biology and Evolution

One ring to rule them all? Genome sequencing provides new insights into the ‘master circle’ model of plant mitochondrial DNA structure

(2013) Daniel B. Sloan   NEW PHYTOLOGIST

Highly rearranged and size-variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers

(2013) Chung-Shien Wu et al.   PLANT BIOTECHNOLOGY JOURNAL

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

(2012) M. Kearse et al.   BIOINFORMATICS

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

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

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

The intriguing evolutionary dynamics of plant mitochondrial DNA

(2011) Nicolas Galtier   BMC BIOLOGY

Pervasive Multinucleotide Mutational Events in Eukaryotes

(2011) Daniel R. Schrider et al.   CURRENT BIOLOGY

Structural and Content Diversity of Mitochondrial Genome in Beet: A Comparative Genomic Analysis

(2011) A. Darracq et al.   Genome Biology and Evolution

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

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

A Reevaluation of Rice Mitochondrial Evolution Based on the Complete Sequence of Male-Fertile and Male-Sterile Mitochondrial Genomes

(2011) S. Bentolila et al.   PLANT PHYSIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Testing for Selection on Synonymous Sites in Plant Mitochondrial DNA: The Role of Codon Bias and RNA Editing

(2010) Daniel B. Sloan et al.   JOURNAL OF MOLECULAR EVOLUTION

Insights into the Evolution of Mitochondrial Genome Size from Complete Sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae)

(2010) A. J. Alverson 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

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria

(2009) J.-Q. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA

(2009) Thomas Borsch et al.   PLANT SYSTEMATICS AND EVOLUTION

Parallel Rate Heterogeneity in Chloroplast and Mitochondrial Genomes of Brazil Nut Trees (Lecythidaceae) Is Consistent with Lineage Effects

(2008) D. F. Soria-Hernanz 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

Angiosperm mitochondrial genomes and mutations

(2007) Tomohiko Kubo et al.   MITOCHONDRION