A Review of the Prevalence, Utility, and Caveats of Using Chloroplast Simple Sequence Repeats for Studies of Plant Biology

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

Another Look at the Root of the Angiosperms Reveals a Familiar Tale

(2014) Bryan T. Drew et al.   SYSTEMATIC BIOLOGY

20,000 species and five key markers: The status of molecular bryophyte phylogenetics

(2014) M. Stech et al.   Phytotaxa

De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba

(2013) Susana L Torales et al.   BMC GENOMICS

Farmers’ Varietal Identification in a Reference Sample of Local Phaseolus Species in the Sierra Juárez, Oaxaca, Mexico

(2013) Daniela Soleri et al.   ECONOMIC BOTANY

The complete chloroplast genome of Origanum vulgare L. (Lamiaceae)

(2013) Brigitte Lukas et al.   GENE

The Complete Chloroplast Genome Sequence of Cephalotaxus oliveri (Cephalotaxaceae): Evolutionary Comparison of Cephalotaxus Chloroplast DNAs and Insights into the Loss of Inverted Repeat Copies in Gymnosperms

(2013) Xuan Yi et al.   Genome Biology and Evolution

Chloroplast genome analysis of Australian eucalypts – Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae)

(2013) Michael J. Bayly et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

(2013) Jun Qian et al.   PLoS One

Complete Chloroplast Genome Sequences of Mongolia Medicine Artemisia frigida and Phylogenetic Relationships with Other Plants

(2013) Yue Liu et al.   PLoS One

Complete Plastid Genome Sequencing of Trochodendraceae Reveals a Significant Expansion of the Inverted Repeat and Suggests a Paleogene Divergence between the Two Extant Species

(2013) Yan-xia Sun et al.   PLoS One

Impact of Geography and Climate on the Genetic Differentiation of the Subtropical Pine Pinus yunnanensis

(2013) Baosheng Wang et al.   PLoS One

Complete chloroplast genome sequence of Magnolia grandiflora and comparative analysis with related species

(2013) XiWen Li et al.   Science China-Life Sciences

Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree

(2013) Hannah McPherson et al.   BMC ECOLOGY

Variable length chloroplast markers for population genetic studies in Acmispon (Fabaceae)

(2012) Gregory L. Wheeler et al.   AMERICAN JOURNAL OF BOTANY

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

(2012) Tea Huotari et al.   GENE

The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); Comparative evolutionary analyses with other three asterids

(2012) Dong-Keun Yi et al.   MOLECULES AND CELLS

Systematic position ofPinus henryi(Pinaceae) as revealed by multiple evidence

(2012) Zhan-Lin Liu et al.   NORDIC JOURNAL OF BOTANY

Spread of herbicide-resistant weedy rice (red rice, Oryza sativa L.) after 5 years of Clearfield rice cultivation in Italy

(2012) M. Busconi et al.   PLANT BIOLOGY

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

(2012) Wenpan Dong et al.   PLoS One

Complete Chloroplast Genome Sequences of Important Oilseed Crop Sesamum indicum L

(2012) Dong-Keun Yi et al.   PLoS One

Always Look on Both Sides: Phylogenetic Information Conveyed by Simple Sequence Repeat Allele Sequences

(2012) Stéphanie Barthe et al.   PLoS One

Complete sequence of the chloroplast genome from pear (Pyrus pyrifolia): genome structure and comparative analysis

(2012) Shingo Terakami et al.   Tree Genetics & Genomes

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

Genome-wide analysis of plastome sequence variation and development of plastidial CAPS markers in common potato and related Solanum species

(2011) Daniela Gargano et al.   GENETIC RESOURCES AND CROP EVOLUTION

Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics

(2011) Dai-Yong Kuang et al.   GENOME

Evidence for the equal resilience of Triodia spp. (Poaceae), from different functional groups, to frequent fire dating back to the late Pleistocene

(2011) G Armstrong   HEREDITY

Contrasting Patterns of Pollen and Seed Flow Influence the Spatial Genetic Structure of Sweet Vernal Grass (Anthoxanthum odoratum) Populations

(2011) Joanna R. Freeland et al.   JOURNAL OF HEREDITY

Current trends in microsatellite genotyping

(2011) E. GUICHOUX et al.   Molecular Ecology Resources

Elucidating Polyploidization of Bermudagrasses as Assessed by Organelle and Nuclear DNA Markers

(2011) Osman Gulsen et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Choosing and Using a Plant DNA Barcode

(2011) Peter M. Hollingsworth et al.   PLoS One

Genome-Wide Distribution and Organization of Microsatellites in Plants: An Insight into Marker Development in Brachypodium

(2011) Humira Sonah et al.   PLoS One

Asymmetrical Gene Flow in a Hybrid Zone of Hawaiian Schiedea (Caryophyllaceae) Species with Contrasting Mating Systems

(2011) Lisa E. Wallace et al.   PLoS One

Phylogeographic structure of jack pine (Pinus banksiana ; Pinaceae) supports the existence of a coastal glacial refugium in northeastern North America

(2010) Julie Godbout et al.   AMERICAN JOURNAL OF BOTANY

Improving sequencing quality from PCR products containing long mononucleotide repeats

(2010) Aron Fazekas et al.   BIOTECHNIQUES

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites

(2010) R J Haasl et al.   HEREDITY

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Cost-Effective, Species-Specific Microsatellite Development for the Endangered Dwarf Bulrush (Typha minima) Using Next-Generation Sequencing Technology

(2010) D. Csencsics et al.   JOURNAL OF HEREDITY

Phylogeographic inferences from chloroplast DNA: quantifying the effects of mutations in repetitive and non-repetitive sequences

(2010) NICOLE VACHON et al.   Molecular Ecology Resources

Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

(2010) Shilin Chen et al.   PLoS One

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

Beans in Europe: origin and structure of the European landraces of Phaseolus vulgaris L.

(2010) S. A. Angioi et al.   THEORETICAL AND APPLIED GENETICS

Chloroplast diversity in a putative hybrid swarm of Ponderosae (Pinaceae)

(2009) Bryan K. Epperson et al.   AMERICAN JOURNAL OF BOTANY

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

A frameshift mutation of the chloroplast matK coding region is associated with chlorophyll deficiency in the Cryptomeria japonica virescent mutant Wogon-Sugi

(2009) Tomonori Hirao et al.   CURRENT GENETICS

Genetic variability of Italian southern Scots pine (Pinus sylvestris L.) populations: the rear edge of the range

(2009) Marta Scalfi et al.   EUROPEAN JOURNAL OF FOREST RESEARCH

Patterns of seed dispersal and pollen flow inQuercus garryana(Fagaceae) following post-glacial climatic changes

(2009) Travis D. Marsico et al.   JOURNAL OF BIOGEOGRAPHY

Genetic diversity and phylogeographic analysis ofPinus leiophylla: a post-glacial range expansion

(2009) Abril Rodríguez-Banderas et al.   JOURNAL OF BIOGEOGRAPHY

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

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

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

A DNA barcode for land plants

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

Single nucleotide sequence analysis: a cost- and time-effective protocol for the analysis of microsatellite- and indel-rich chloroplast DNA regions

(2007) DANIELA GUICKING et al.   Molecular Ecology Resources