Reconfiguration of the plastid genome in Lamprocapnos spectabilis: IR boundary shifting, inversion, and intraspecific variation

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

(2017) Seongjun Park et al.   Genome Biology and Evolution

TRIM5α SPRY/coiled-coil interactions optimize avid retroviral capsid recognition

(2017) Marcin D. Roganowicz et al.   PLoS Pathogens

Variable presence of the inverted repeat and plastome stability inErodium

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

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

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

Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution

(2016) Yanxia Sun et al.   MOLECULAR PHYLOGENETICS 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

The number of known plants species in the world and its annual increase

(2016) MAARTEN J.M. CHRISTENHUSZ et al.   Phytotaxa

Insight into infrageneric circumscription through complete chloroplast genome sequences of twoTrilliumspecies

(2016) Sang-Chul Kim et al.   AoB Plants

Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae)

(2016) Yuling Huang et al.   Frontiers in Plant Science

Complete plastid genome sequences of Coreanomecon hylomeconoides Nakai (Papaveraceae), a Korea endemic genus

(2016) Hoe-Won Kim et al.   Mitochondrial DNA Part B-Resources

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

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

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

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

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

(2015) Andan Zhu et al.   NEW PHYTOLOGIST

Phylogeny and Character Evolution of Papaveraceae s. l. (Ranunculales)

(2015) Sara B. Hoot et al.   SYSTEMATIC BOTANY

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

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

The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family

(2014) Guillaume E. Martin et al.   ANNALS OF BOTANY

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

A trnI_CAU Triplication Event in the Complete Chloroplast Genome of Paris verticillata M.Bieb. (Melanthiaceae, Liliales)

(2014) Hoang Dang Khoa Do 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

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

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 Genome of Ginkgo biloba Reveals the Mechanism of Inverted Repeat Contraction

(2012) Ching-Ping Lin et al.   Genome Biology and Evolution

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Evolutionary constraints on the plastid tRNA set decoding methionine and isoleucine

(2012) Sibah Alkatib et al.   NUCLEIC ACIDS RESEARCH

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Chung-Shien Wu et al.   Genome Biology and Evolution

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences

(2011) Michael J. McDonald et al.   PLOS BIOLOGY

Variable Tandem Repeats Accelerate Evolution of Coding and Regulatory Sequences

(2010) Rita Gemayel et al.   Annual Review of Genetics

Regional Context in the Alignment of Biological Sequence Pairs

(2010) Raymond Sammut et al.   JOURNAL OF MOLECULAR EVOLUTION

Complete Plastid Genome Sequences of Three Rosids (Castanea, Prunus, Theobroma): Evidence for At Least Two Independent Transfers of rpl22 to the Nucleus

(2010) R. K. Jansen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study

(2009) Fereydoun Hormozdiari et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Phylogeny and classification of Ranunculales: Evidence from four molecular loci and morphological data

(2009) Wei Wang et al.   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

Reconstructing evolution: Gene transfer from plastids to the nucleus

(2008) Ralph Bock et al.   BIOESSAYS

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

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

Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes

(2008) Dacheng Tian et al.   NATURE

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

(2008) Per Erixon et al.   PLoS One