Comparative Chloroplast Genomics of Dipsacales Species: Insights Into Sequence Variation, Adaptive Evolution, and Phylogenetic Relationships

Complete Chloroplast Genome of Medicinal Plant Lonicera japonica: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies

(2017) Liu He et al.   MOLECULES

One-third of the plastid genes evolved under positive selection in PACMAD grasses

(2017) Anthony Piot et al.   PLANTA

Chloroplast Genome Analysis of Resurrection Tertiary Relict Haberlea rhodopensis Highlights Genes Important for Desiccation Stress Response

(2017) Zdravka Ivanova et al.   Frontiers in Plant Science

Complete chloroplast genome sequences of Eucommia ulmoides: genome structure and evolution

(2016) Lin Wang et al.   Tree Genetics & Genomes

The complete chloroplast genome of Sinadoxa corydalifolia (Adoxaceae)

(2016) Yaling Wang et al.   Conservation Genetics Resources

The complete chloroplast genome of Kolkwitzia amabilis (Caprifoliaceae), an endangered horticultural plant in China

(2016) Guo-Qing Bai et al.   Mitochondrial DNA Part A

Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries

(2015) Hyoung Tae Kim et al.   PLoS One

Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships

(2014) Hui Huang et al.   BMC EVOLUTIONARY BIOLOGY

Complete chloroplast genome sequences of Praxelis (Eupatorium catarium Veldkamp), an important invasive species

(2014) Ying Zhang et al.   GENE

Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)

(2014) Peng-Fei Ma et al.   SYSTEMATIC BIOLOGY

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

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

The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

(2013) Jun Qian et al.   PLoS One

The Plastid Genome of Najas flexilis: Adaptation to Submersed Environments Is Accompanied by the Complete Loss of the NDH Complex in an Aquatic Angiosperm

(2013) Elena L. Peredo et al.   PLoS One

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

(2012) M. Kearse et al.   BIOINFORMATICS

Complete chloroplast genome sequence of Elodea canadensis and comparative analyses with other monocot plastid genomes

(2012) Tea Huotari et al.   GENE

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Complete Chloroplast Genome Sequence of a Major Invasive Species, Crofton Weed (Ageratina adenophora)

(2012) Xiaojun Nie et al.   PLoS One

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

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

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

High-Throughput Sequencing of Three Lemnoideae (Duckweeds) Chloroplast Genomes from Total DNA

(2011) Wenqin Wang et al.   PLoS One

An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants

(2010) S. A. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Phylogeny and biogeographic diversification of Maianthemum (Ruscaceae: Polygonatae)

(2008) Ying Meng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2008) Per Erixon et al.   PLoS One

Mitochondrial sequence data and Dipsacales phylogeny: Mixed models, partitioned Bayesian analyses, and model selection

(2007) Richard C. Winkworth et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION