Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data

Plastid DNA fingerprinting of the rare Fritillaria moggridgei (Liliaceae) reveals population differentiation and genetic isolation within the Fritillaria tubiformis complex

(2018) MARCO MUCCIARELLI et al.   Phytotaxa

The Complete Chloroplast Genome of Chinese Bayberry (Morella rubra, Myricaceae): Implications for Understanding the Evolution of Fagales

(2017) Lu-Xian Liu et al.   Frontiers in Plant Science

Development of Microsatellite Loci in Mediterranean Sarsaparilla (Smilax aspera; Smilacaceae) Using Transcriptome Data

(2017) Zhe-Chen Qi et al.   Applications in Plant Sciences

The complete chloroplast genome sequence of tung tree (Vernicia fordii): Organization and phylogenetic relationships with other angiosperms

(2017) Ze Li et al.   Scientific Reports

The influence of habitat on the evolution of plants: a case study across Saxifragales

(2016) Rafael Rubio de Casas et al.   ANNALS OF BOTANY

A New Resource for the Development of SSR Markers: Millions of Loci from a Thousand Plant Transcriptomes

(2016) Richard G. J. Hodel et al.   Applications in Plant Sciences

Multiple glacial refugia for cool-temperate deciduous trees in northern East Asia: the Mongolian oak as a case study

(2015) Yan-Fei Zeng et al.   MOLECULAR ECOLOGY

Identifying differentially expressed genes under heat stress and developing molecular markers in orchardgrass (Dactylis glomerataL.) through transcriptome analysis

(2015) L. K. Huang et al.   Molecular Ecology Resources

Phylogeny, divergence times, and historical biogeography of the angiosperm family Saxifragaceae

(2015) Jia-bin Deng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Development of Chloroplast Microsatellite Markers and Analysis of Chloroplast Diversity in Chinese Jujube (Ziziphus jujuba Mill.) and Wild Jujube (Ziziphus acidojujuba Mill.)

(2015) Jian Huang et al.   PLoS One

Understanding population structure and historical demography in a conservation context: Population genetics of the endangered Kirengeshoma palmata (Hydrangeaceae)

(2014) Na Yuan et al.   AMERICAN JOURNAL OF BOTANY

Why are most organelle genomes transmitted maternally?

(2014) Stephan Greiner et al.   BIOESSAYS

Plant DNA barcoding: from gene to genome

(2014) Xiwen Li et al.   BIOLOGICAL REVIEWS

Comparative transcriptome analysis of eggplant (Solanum melongena L.) and turkey berry (Solanum torvum Sw.): phylogenomics and disease resistance analysis

(2014) Xu Yang et al.   BMC GENOMICS

Spatial and temporal distributions of major tree taxa in eastern continental Asia during the last 22,000 years

(2014) Xianyong Cao et al.   HOLOCENE

Genetic Structure and Hierarchical Population Divergence History of Acer mono var. mono in South and Northeast China

(2014) Chunping Liu et al.   PLoS One

Development of 12 Chloroplast Microsatellite Markers in Vigna unguiculata (Fabaceae) and Amplification in Phaseolus vulgaris

(2014) Lei Pan et al.   Applications in Plant Sciences

Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach

(2013) D. E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

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

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

Complete Chloroplast Genome of Chionographis japonica (Willd.) Maxim. (Melanthiaceae): Comparative Genomics and Evaluation of Universal Primers for Liliales

(2013) Sarah S. Bodin et al.   PLANT MOLECULAR BIOLOGY REPORTER

SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing

(2013) Iratxe Montes et al.   PLoS One

New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species

(2012) Kerstin Diekmann et al.   ANNALS OF BOTANY

Mutational Dynamics of Aroid Chloroplast Genomes

(2012) Ibrar Ahmed et al.   Genome Biology and Evolution

Evolutionary history of almond tree domestication in the Mediterranean basin

(2012) M. Delplancke et al.   MOLECULAR ECOLOGY

Recommendations for utilizing and reporting population genetic analyses: the reproducibility of genetic clustering using the programstructure

(2012) Kimberly J. Gilbert et al.   MOLECULAR ECOLOGY

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Wenpan Dong et al.   PLoS One

Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences

(2011) Juan E. Zalapa 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

Plant molecular phylogeography in China and adjacent regions: Tracing the genetic imprints of Quaternary climate and environmental change in the world’s most diverse temperate flora

(2011) Ying-Xiong Qiu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Forest tree genomics: growing resources and applications

(2011) David B. Neale et al.   NATURE REVIEWS GENETICS

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

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison

(2010) Roberto Mariotti et al.   BMC PLANT BIOLOGY

Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae

(2010) Mary M. Guisinger et al.   JOURNAL OF MOLECULAR EVOLUTION

Genome-enabled development of DNA markers for ecology, evolution and conservation

(2010) ROBERT C. THOMSON et al.   MOLECULAR ECOLOGY

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Nuclear and chloroplast DNA phylogeography reveal two refuge areas with asymmetrical gene flow in a temperate walnut tree from East Asia

(2010) Wei-Ning Bai et al.   NEW PHYTOLOGIST

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

(2010) M. J. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) P. Librado et al.   BIOINFORMATICS

Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species

(2009) DANIEL EBERT et al.   Molecular Ecology Resources

Episodic Evolution and Adaptation of Chloroplast Genomes in Ancestral Grasses

(2009) Bojian Zhong et al.   PLoS One

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

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

Phylogeography of a marsh herb Sagittaria trifolia (Alismataceae) in China inferred from cpDNA atpB–rbcL intergenic spacers

(2008) Jin-Ming Chen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

(2008) G DROUIN et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design

(2007) BRANT C. FAIRCLOTH   Molecular Ecology Resources

genepop’007: a complete re-implementation of the genepop software for Windows and Linux

(2007) FRANÇOIS ROUSSET   Molecular Ecology Resources