Development of Chloroplast Genomic Resources for Oryza Species Discrimination

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

(2017) Hongru Wang et al.   GENOME RESEARCH

The rice paradox: Multiple origins but single domestication in Asian rice

(2017) Jae Young Choi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Development of Chloroplast and Nuclear DNA Markers for Chinese Oaks (Quercus Subgenus Quercus) and Assessment of Their Utility as DNA Barcodes

(2017) Jia Yang et al.   Frontiers in Plant Science

Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

(2017) Chao Xu et al.   Frontiers in Plant Science

Chloroplast Genomic Resource of Paris for Species Discrimination

(2017) Yun Song et al.   Scientific Reports

Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse Oryza Species Assessed by Whole-Genome Resequencing

(2016) Wei Tong et al.   Rice

The Complete Chloroplast Genome Sequences of Three Veroniceae Species (Plantaginaceae): Comparative Analysis and Highly Divergent Regions

(2016) Kyoung Su Choi et al.   Frontiers in Plant Science

Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences

(2015) Peterson W. Wambugu et al.   Scientific Reports

Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae

(2015) Yu Song et al.   Frontiers in Plant Science

Plann: A Command-Line Application for Annotating Plastome Sequences

(2015) Daisie I. Huang et al.   Applications in Plant Sciences

ycf1, the most promising plastid DNA barcode of land plants

(2015) Wenpan Dong et al.   Scientific Reports

A chloroplast genomic strategy for designing taxon specific DNA mini-barcodes: a case study on ginsengs

(2014) Wenpan Dong et al.   BMC GENETICS

Rapid diversification of fiveOryzaAA genomes associated with rice adaptation

(2014) Qun-Jie Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing Angiosperm Plastid Genomes Made Easy: A Complete Set of Universal Primers and a Case Study on the Phylogeny of Saxifragales

(2013) Wenpan Dong et al.   Genome Biology and Evolution

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

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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Discriminating plants using the DNA barcoderbcLb: an appraisal based on a large data set

(2013) Wenpan Dong et al.   Molecular Ecology Resources

Barcoding success as a function of phylogenetic relatedness in Viburnum, a clade of woody angiosperms

(2012) Wendy L Clement et al.   BMC EVOLUTIONARY BIOLOGY

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

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

Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding

(2012) SAMUEL D. J. BROWN et al.   Molecular Ecology Resources

Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding

(2012) Wenpan Dong et al.   PLoS One

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Phylogeny and biogeography of the rice tribe (Oryzeae): Evidence from combined analysis of 20 chloroplast fragments

(2009) Liang Tang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A DNA barcode for land plants

(2009) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GenomeVx: simple web-based creation of editable circular chromosome maps

(2008) G. C. Conant et al.   BIOINFORMATICS

Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well

(2008) Aron J. Fazekas et al.   PLoS One

Analysis of 142 genes resolves the rapid diversification of the rice genus

(2008) Xin-Hui Zou et al.   GENOME BIOLOGY