Unprecedented Heterogeneity in the Synonymous Substitution Rate within a Plant Genome

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

Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes

(2013) Felix Grewe et al.   BMC EVOLUTIONARY BIOLOGY

The genome and transcriptome of perennial ryegrass mitochondria

(2013) Md Islam et al.   BMC GENOMICS

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

(2013) S. A. Shabalina et al.   NUCLEIC ACIDS RESEARCH

Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae)

(2012) Chi-Chun Huang et al.   GENE

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

Evidence of non-random mutation rates suggests an evolutionary risk management strategy

(2012) Iñigo Martincorena et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia pinnata

(2012) Stephen H. Kazakoff et al.   PLoS One

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

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

Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes

(2011) Jeffrey P Mower et al.   BMC BIOLOGY

Factors that Contribute to Variation in Evolutionary Rate among Arabidopsis Genes

(2011) L. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extensive Loss of RNA Editing Sites in Rapidly Evolving Silene Mitochondrial Genomes: Selection vs. Retroprocessing as the Driving Force

(2010) D. B. Sloan et al.   GENETICS

Localized hypermutation and associated gene losses in legume chloroplast genomes

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

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

Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algae

(2009) Jeffrey P Mower et al.   BMC EVOLUTIONARY BIOLOGY

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

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

Strong Evidence for Lineage and Sequence Specificity of Substitution Rates and Patterns in Drosophila

(2009) N. D. Singh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments

(2009) J. P. Mower   NUCLEIC ACIDS RESEARCH

Hotspots of Biased Nucleotide Substitutions in Human Genes

(2009) Jonas Berglund et al.   PLOS BIOLOGY

Measuring the prevalence of regional mutation rates: an analysis of silent substitutions in mammals, fungi, and insects

(2008) Aleah K Fox et al.   BMC EVOLUTIONARY BIOLOGY

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

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

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

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