Strategies for complete plastid genome sequencing

Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor

(2016) Mario Vallejo-Marín et al.   AMERICAN JOURNAL OF BOTANY

Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasiteCytinus hypocistis(Cytinaceae)

(2016) Cristina Roquet et al.   ANNALS OF BOTANY

Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic PlantHydnora visseri(Hydnoraceae)

(2016) Julia Naumann et al.   Genome Biology and Evolution

From barcodes to genomes: extending the concept of DNA barcoding

(2016) Eric Coissac et al.   MOLECULAR ECOLOGY

The (in)complete organelle genome: exploring the use and nonuse of available technologies for characterizing mitochondrial and plastid chromosomes

(2016) Matheus Sanitá Lima et al.   Molecular Ecology Resources

Telling plant species apart with DNA: from barcodes to genomes

(2016) Peter M. Hollingsworth et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants

(2016) Susann Wicke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Will Benchtop Sequencers Resolve the Sequencing Trade-off in Plant Genetics?

(2016) Alex D. Twyford   Frontiers in Plant Science

A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae)

(2016) Simon Uribe-Convers et al.   PLoS One

Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using plastid sequences derived from next-generation sequencing

(2015) J. R. Comer et al.   AMERICAN JOURNAL OF BOTANY

Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes

(2015) Joseph F. Walker et al.   AMERICAN JOURNAL OF BOTANY

Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline

(2015) Freek T. Bakker et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris) chloroplast genome

(2015) Kai Bernd Stadermann et al.   BMC BIOINFORMATICS

Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis

(2015) William P Wysocki et al.   BMC EVOLUTIONARY BIOLOGY

Direct Estimate of the Spontaneous Mutation Rate Uncovers the Effects of Drift and Recombination in theChlamydomonas reinhardtiiPlastid Genome

(2015) Rob W. Ness et al.   MOLECULAR BIOLOGY AND EVOLUTION

Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria ?

(2015) Markus Ruhsam et al.   Molecular Ecology Resources

Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives

(2015) Jan Janouškovec et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes

(2015) David Roy Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for horizontal transfer of mitochondrial DNA to the plastid genome in a bamboo genus

(2015) Peng-Fei Ma et al.   Scientific Reports

Chloroplast genome of Aconitum barbatum var. puberulum (Ranunculaceae) derived from CCS reads using the PacBio RS platform

(2015) Xiaochen Chen et al.   Frontiers in Plant Science

Plastid Primers for Angiosperm Phylogenetics and Phylogeography

(2015) Linda M. Prince   Applications in Plant Sciences

Plann: A Command-Line Application for Annotating Plastome Sequences

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

Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach

(2015) Wiebke Sickel et al.   BMC ECOLOGY

Complete Chloroplast Genome of the Multifunctional Crop Globe Artichoke and Comparison with Other Asteraceae

(2015) Pasquale L. Curci 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

A precise chloroplast genome of Nelumbo nucifera (Nelumbonaceae) evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots

(2014) Zhihua Wu et al.   BMC PLANT BIOLOGY

A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants

(2014) Peter Civáň et al.   Genome Biology and Evolution

Variation, Evolution, and Correlation Analysis of C+G Content and Genome or Chromosome Size in Different Kingdoms and Phyla

(2014) Xiu-Qing Li et al.   PLoS One

Genome and Metagenome Sequencing: Using the Human Methyl-Binding Domain to Partition Genomic DNA Derived from Plant Tissues

(2014) Erbay Yigit et al.   Applications in Plant Sciences

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

A Long PCR–Based Approach for DNA Enrichment Prior to Next-Generation Sequencing for Systematic Studies

(2014) Simon Uribe-Convers et al.   Applications in Plant Sciences

A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae

(2014) Jennifer R. Mandel et al.   Applications in Plant Sciences

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

(2014) Gregory L. Wheeler et al.   Applications in Plant Sciences

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

(2013) Craig F. Barrett et al.   ANNALS OF BOTANY

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

Horizontal Transfer of DNA from the Mitochondrial to the Plastid Genome and Its Subsequent Evolution in Milkweeds (Apocynaceae)

(2013) Shannon C.K. Straub et al.   Genome Biology and Evolution

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

Disproportional Plastome-Wide Increase of Substitution Rates and Relaxed Purifying Selection in Genes of Carnivorous Lentibulariaceae

(2013) Susann Wicke et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke

(2013) Dan G. Bock et al.   NEW PHYTOLOGIST

Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape Family

(2013) S. Wicke et al.   PLANT CELL

Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens

(2013) Martijn Staats et al.   PLoS One

A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid Genomes

(2013) Gregory W. Stull et al.   Applications in Plant Sciences

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation

(2012) Craig F. Barrett et al.   AMERICAN JOURNAL OF BOTANY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

An Improved Chloroplast DNA Extraction Procedure for Whole Plastid Genome Sequencing

(2012) Chao Shi 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

Efficient counting of k-mers in DNA sequences using a bloom filter

(2011) Páll Melsted et al.   BMC BIOINFORMATICS

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

Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability

(2011) Petr Šmarda et al.   NEW PHYTOLOGIST

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

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

A Set of 100 Chloroplast DNA Primer Pairs to Study Population Genetics and Phylogeny in Monocotyledons

(2011) Nora Scarcelli et al.   PLoS One

High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)

(2011) Yun-Jie Zhang et al.   PLoS One

Choosing and Using a Plant DNA Barcode

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

The GC-Rich Mitochondrial and Plastid Genomes of the Green Alga Coccomyxa Give Insight into the Evolution of Organelle DNA Nucleotide Landscape

(2011) David Roy Smith et al.   PLoS One

The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae

(2010) J. S. Brouard et al.   Genome Biology and Evolution

Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines

(2010) J. B. WHITTALL et al.   MOLECULAR ECOLOGY

Recombination and the maintenance of plant organelle genome stability

(2010) Alexandre Maréchal et al.   NEW PHYTOLOGIST

Chloroplast genome sequences from total DNA for plant identification

(2010) Catherine J. Nock et al.   PLANT BIOTECHNOLOGY JOURNAL

Conservation and divergence of methylation patterning in plants and animals

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

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

(2009) Matthew Parks et al.   BMC BIOLOGY

The Complete Plastid Genome Sequence of the Secondarily Nonphotosynthetic Alga Cryptomonas paramecium: Reduction, Compaction, and Accelerated Evolutionary Rate

(2009) Natalie Donaher et al.   Genome Biology and Evolution

A DNA barcode for land plants

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

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH