Chloroplast Genome Evolution in Actinidiaceae: clpP Loss, Heterogenous Divergence and Phylogenomic Practice

Multi-locus plastid phylogenetic biogeography supports the Asian hypothesis of the temperate woody bamboos (Poaceae: Bambusoideae)

(2016) Xian-Zhi Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolutionary Stasis in Cycad Plastomes and the First Case of Plastome GC-Biased Gene Conversion

(2015) Chung-Shien Wu et al.   Genome Biology and Evolution

Exploring the Limits for Reduction of Plastid Genomes: A Case Study of the Mycoheterotrophic Orchids Epipogium aphyllum and Epipogium roseum

(2015) Mikhail I. Schelkunov et al.   Genome Biology and Evolution

Massive intracellular gene transfer during plastid genome reduction in nongreen Orobanchaceae

(2015) Natalie Cusimano et al.   NEW PHYTOLOGIST

Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots

(2015) Craig F. Barrett et al.   NEW PHYTOLOGIST

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

(2015) Cody E. Hinchliff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards

(2015) Jeffrey W. Streicher et al.   SYSTEMATIC BIOLOGY

A Comparative Analysis of Whole Plastid Genomes from the Apiales: Expansion and Contraction of the Inverted Repeat, Mitochondrial to Plastid Transfer of DNA, and Identification of Highly Divergent Noncoding Regions

(2015) Stephen R. Downie et al.   SYSTEMATIC BOTANY

Genome skimming for next-generation biodiversity analysis

(2015) Steven Dodsworth   TRENDS IN PLANT SCIENCE

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

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

Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP

(2015) Diana V. Dugas et al.   Scientific Reports

Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA inAsclepias(Apocynaceae)

(2015) Kevin Weitemier et al.   PeerJ

The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis

(2015) Xiaohong Yao et al.   PLoS One

Congruent Deep Relationships in the Grape Family (Vitaceae) Based on Sequences of Chloroplast Genomes and Mitochondrial Genes via Genome Skimming

(2015) Ning Zhang et al.   PLoS One

The relative and absolute frequencies of angiosperm sexual systems: Dioecy, monoecy, gynodioecy, and an updated online database

(2014) Susanne S. Renner   AMERICAN JOURNAL OF BOTANY

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

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

The Plastid Genome of Mycoheterotrophic Monocot Petrosavia stellaris Exhibits Both Gene Losses and Multiple Rearrangements

(2014) Maria D. Logacheva et al.   Genome Biology and Evolution

Investigating the Path of Plastid Genome Degradation in an Early-Transitional Clade of Heterotrophic Orchids, and Implications for Heterotrophic Angiosperms

(2014) Craig F. Barrett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Possible Loss of the Chloroplast Genome in the Parasitic Flowering Plant Rafflesia lagascae (Rafflesiaceae)

(2014) Jeanmaire Molina et al.   MOLECULAR BIOLOGY AND EVOLUTION

Should genes with missing data be excluded from phylogenetic analyses?

(2014) Wei Jiang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics, molecular evolution, and estimated ages of lineages from the deep phylogeny of Poaceae

(2014) Samuel S. Jones et al.   PLANT SYSTEMATICS AND EVOLUTION

Effective Extraction and Assembly Methods for Simultaneously Obtaining Plastid and Mitochondrial Genomes

(2014) Wanjun Hao et al.   PLoS One

The dynamic history of plastid genomes in the Campanulaceae sensu lato is unique among angiosperms

(2014) E. B. Knox   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)

(2014) Peng-Fei Ma et al.   SYSTEMATIC BIOLOGY

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

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

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

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

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

A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae)

(2013) Daniel B. Sloan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Three keys to the radiation of angiosperms into freezing environments

(2013) Amy E. Zanne et al.   NATURE

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

Complete Plastid Genome Sequence of the Basal Asterid Ardisia polysticta Miq. and Comparative Analyses of Asterid Plastid Genomes

(2013) Chuan Ku et al.   PLoS One

Comparative Chloroplast Genomes of Camellia Species

(2013) Jun-Bo Yang et al.   PLoS One

Complete Chloroplast Genome of Sedum sarmentosum and Chloroplast Genome Evolution in Saxifragales

(2013) Wenpan Dong et al.   PLoS One

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Recent Acceleration of Plastid Sequence and Structural Evolution Coincides with Extreme Mitochondrial Divergence in the Angiosperm Genus Silene

(2012) Daniel B. Sloan et al.   Genome Biology and Evolution

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing

(2012) Diego Fajardo et al.   Tree Genetics & Genomes

Angiosperm phylogeny: 17 genes, 640 taxa

(2011) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

Sex Chromosomes in Land Plants

(2011) Ray Ming et al.   Annual Review of Plant Biology

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

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

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

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

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

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

Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

(2011) John J. Wiens et al.   SYSTEMATIC BIOLOGY

Localized hypermutation and associated gene losses in legume chloroplast genomes

(2010) A. M. Magee et al.   GENOME RESEARCH

Complete Plastid Genome Sequences of Three Rosids (Castanea, Prunus, Theobroma): Evidence for At Least Two Independent Transfers of rpl22 to the Nucleus

(2010) R. K. Jansen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

(2009) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

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

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

(2008) M. M. Guisinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA