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

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

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

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

An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome

(2013) Marco Ferrarini et al.   BMC GENOMICS

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

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

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

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

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

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

(2013) S. Wicke et al.   PLANT CELL

The sacred lotus genome provides insights into the evolution of flowering plants

(2013) Yun Wang et al.   PLANT JOURNAL

The Complete Chloroplast Genome of Banana (Musa acuminata, Zingiberales): Insight into Plastid Monocotyledon Evolution

(2013) Guillaume Martin 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

Comparative Chloroplast Genomes of Camellia Species

(2013) Jun-Bo Yang et al.   PLoS One

Complete Sequencing of Five Araliaceae Chloroplast Genomes and the Phylogenetic Implications

(2013) Rong Li et al.   PLoS One

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform

(2013) Erin B Fichot et al.   Microbiome

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

The Complete Chloroplast Genome of Ginkgo biloba Reveals the Mechanism of Inverted Repeat Contraction

(2012) Ching-Ping Lin et al.   Genome Biology and Evolution

Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene

(2012) E. W. Loomis et al.   GENOME RESEARCH

The limitations of draft assemblies for understanding prokaryotic adaptation and evolution

(2012) N. Ricker et al.   GENOMICS

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

Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations

(2012) Trevor J. Pugh et al.   NATURE

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

The mitochondrial genome sequence of the ciliate Paramecium caudatum reveals a shift in nucleotide composition and codon usage within the genus Paramecium

(2011) Dana Barth et al.   BMC GENOMICS

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

(2011) Shannon CK Straub et al.   BMC GENOMICS

Rampant Gene Loss in the Underground Orchid Rhizanthella gardneri Highlights Evolutionary Constraints on Plastid Genomes

(2011) E. Delannoy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times

(2011) M. d. Reis et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Multiple northern refugia for Asian sacred lotus, an aquatic plant with characteristics of ice-age endurance

(2010) Jiao-Kun Li et al.   AUSTRALIAN JOURNAL OF BOTANY

Why does biparental plastid inheritance revive in angiosperms?

(2010) Quan Zhang et al.   JOURNAL OF PLANT RESEARCH

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

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

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

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

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Episodic Evolution and Adaptation of Chloroplast Genomes in Ancestral Grasses

(2009) Bojian Zhong et al.   PLoS One

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

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

Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots

(2008) Rui-Jiang Wang et al.   BMC EVOLUTIONARY BIOLOGY

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY