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

Evolutionary Stasis in Cycad Plastomes and the First Case of Plastome GC-Biased Gene Conversion

(2015) Chung-Shien Wu et al.   Genome Biology and Evolution

A Comparative Analysis of Whole Plastid Genomes from the Apiales: Expansion and Contraction of the Inverted Repeat, Mitochondrial to Plastid Transfer of DNA, and Identification of Highly Divergent Noncoding Regions

(2015) Stephen R. Downie et al.   SYSTEMATIC BOTANY

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

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

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

Predominant and Substoichiometric Isomers of the Plastid Genome Coexist within Juniperus Plants and Have Shifted Multiple Times during Cupressophyte Evolution

(2014) Wenhu Guo et al.   Genome Biology and Evolution

Unprecedented Heterogeneity in the Synonymous Substitution Rate within a Plant Genome

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

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

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

Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species

(2013) Yan-xia Sun et al.   PLoS One

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

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

Complete Chloroplast Genome Sequences of Important Oilseed Crop Sesamum indicum L

(2012) Dong-Keun Yi 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

Comparative Chloroplast Genomes of Pinaceae: Insights into the Mechanism of Diversified Genomic Organizations

(2011) Chung-Shien Wu 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

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

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

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

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

Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: Selection toward a lower-cost strategy

(2009) Chung-Shien Wu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

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

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

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

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