Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny

Phylogeography of postglacial range expansion in Juglans mandshurica (Juglandaceae) reveals no evidence of bottleneck, loss of genetic diversity, or isolation by distance in the leading-edge populations

(2016) Wen-Ting Wang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

(2016) Polina Yu Novikova et al.   NATURE GENETICS

The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

(2016) Gurusamy Raman et al.   Frontiers in Plant Science

Comparative Analysis of the Complete Chloroplast Genomes of Five Quercus Species

(2016) Yanci Yang et al.   Frontiers in Plant Science

The complete chloroplast genome of common walnut (Juglans regia)

(2016) Yiheng Hu et al.   Mitochondrial DNA Part B-Resources

Identification, development, and application of 12 polymorphic EST-SSR markers for an endemic Chinese walnut (Juglans cathayensis L.) using next-generation sequencing technology

(2015) Meng Dang et al.   BIOCHEMICAL SYSTEMATICS AND ECOLOGY

De novo assembly and characterization of transcriptome using Illumina sequencing and development of twenty five microsatellite markers for an endemic tree Juglans hopeiensis Hu in China

(2015) Yi-Heng Hu et al.   BIOCHEMICAL SYSTEMATICS AND ECOLOGY

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

Complete chloroplast genome of the Oriental white oak:Quercus alienaBlume

(2015) Sihai Lu et al.   Mitochondrial DNA

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the GenusCitrus

(2015) Jose Carbonell-Caballero et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient Humans Influenced the Current Spatial Genetic Structure of Common Walnut Populations in Asia

(2015) Paola Pollegioni et al.   PLoS One

An improved method for chloroplast genome sequencing in non-model forest tree species

(2015) Fang K. Du et al.   Tree Genetics & Genomes

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies

(2014) Cédric Mariac et al.   Molecular Ecology Resources

Contrasts between the phylogeographic patterns of chloroplast and nuclear DNA highlight a role for pollen-mediated gene flow in preventing population divergence in an East Asian temperate tree

(2014) Wei-Ning Bai et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars,Populus balsamiferaandP. trichocarpa(Salicaceae)

(2014) Daisie I. Huang et al.   NEW PHYTOLOGIST

Pyrosequencing of the northern red oak (Quercus rubra L.) chloroplast genome reveals high quality polymorphisms for population management

(2014) Lisa W. Alexander et al.   Tree Genetics & Genomes

The genetic diversity and introgression of Juglans regia and Juglans sigillata in Tibet as revealed by SSR markers

(2014) Hua Wang et al.   Tree Genetics & Genomes

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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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 of Banana (Musa acuminata, Zingiberales): Insight into Plastid Monocotyledon Evolution

(2013) Guillaume Martin et al.   PLoS One

Plastid Genome Sequence of a Wild Woody Oil Species, Prinsepia utilis, Provides Insights into Evolutionary and Mutational Patterns of Rosaceae Chloroplast Genomes

(2013) Shuo Wang et al.   PLoS One

Complete Chloroplast Genome of Sedum sarmentosum and Chloroplast Genome Evolution in Saxifragales

(2013) Wenpan Dong et al.   PLoS One

Polymorphic chloroplast microsatellite loci in Nelumbo (Nelumbonaceae)

(2012) J. Xue et al.   AMERICAN JOURNAL OF BOTANY

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

(2012) M. Kearse et al.   BIOINFORMATICS

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

(2012) Chang Liu et al.   BMC GENOMICS

Genetic Diversity and Population Structure: Implications for Conservation of Wild Soybean (Glycine soja Sieb. et Zucc) Based on Nuclear and Chloroplast Microsatellite Variation

(2012) Shuilian He et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

Complete cpDNA genome sequence of Smilax china and phylogenetic placement of Liliales – Influences of gene partitions and taxon sampling

(2012) Juan Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Horizontal transfer of chloroplast genomes between plant species

(2012) S. Stegemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing

(2012) Diego Fajardo et al.   Tree Genetics & Genomes

Chloroplast microsatellite markers in Liriodendron tulipifera (Magnoliaceae) and cross-species amplification in L. chinense

(2011) A.-H. Yang et al.   AMERICAN JOURNAL OF BOTANY

Angiosperm phylogeny: 17 genes, 640 taxa

(2011) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

The Complete Chloroplast Genome of 17 Individuals of Pest Species Jacobaea vulgaris: SNPs, Microsatellites and Barcoding Markers for Population and Phylogenetic Studies

(2011) L. Doorduin et al.   DNA RESEARCH

Characterization of chloroplast DNA microsatellites from Saccharum spp and related species

(2011) D.M. Melotto-Passarin et al.   GENETICS AND MOLECULAR RESEARCH

West to east dispersal and subsequent rapid diversification of the mega-diverse genus Begonia (Begoniaceae) in the Malesian archipelago

(2011) D. C. Thomas et al.   JOURNAL OF BIOGEOGRAPHY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Combining chloroplast and nuclear microsatellites to investigate origin and dispersal of New World sweet potato landraces

(2011) C. ROULLIER et al.   MOLECULAR ECOLOGY

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

DNA markers identify hybrids between butternut (Juglans cinerea L.) and Japanese walnut (Juglans ailantifolia Carr.)

(2010) Peng Zhao et al.   Tree Genetics & Genomes

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

(2009) P. Librado et al.   BIOINFORMATICS

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

(2009)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale – A wild ancestor of cultivated buckwheat

(2008) Maria D Logacheva et al.   BMC PLANT BIOLOGY

Phylogeny, Species Richness, and Ecological Specialization in Cyperaceae Tribe Cariceae

(2008) Marcia J. Waterway et al.   BOTANICAL REVIEW