The Highly Reduced Plastome of MycoheterotrophicSciaphila(Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection

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

Ancient Gondwana break-up explains the distribution of the mycoheterotrophic family Corsiaceae (Liliales)

(2015) Constantijn B. Mennes et al.   JOURNAL OF BIOGEOGRAPHY

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

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

Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes

(2014) Jamal Sabir et al.   PLANT BIOTECHNOLOGY JOURNAL

A Plastid without a Genome: Evidence from the Nonphotosynthetic Green Algal Genus Polytomella

(2014) D. R. Smith et al.   PLANT PHYSIOLOGY

Superiority of a mechanistic codon substitution model even for protein sequences in Phylogenetic analysis

(2013) Sanzo Miyazawa   BMC EVOLUTIONARY BIOLOGY

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

New insights in the long-debated evolutionary history of Triuridaceae (Pandanales)

(2013) Constantijn B. Mennes et al.   MOLECULAR PHYLOGENETICS 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

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

(2013) S. Wicke et al.   PLANT CELL

Potential Functional Replacement of the Plastidic Acetyl-CoA Carboxylase Subunit (accD) Gene by Recent Transfers to the Nucleus in Some Angiosperm Lineages

(2013) M. Rousseau-Gueutin et al.   PLANT PHYSIOLOGY

Complete Chloroplast Genome Sequence of Holoparasite Cistanche deserticola (Orobanchaceae) Reveals Gene Loss and Horizontal Gene Transfer from Its Host Haloxylon ammodendron (Chenopodiaceae)

(2013) Xi Li et al.   PLoS One

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

Plastid genomes and deep relationships among the commelinid monocot angiosperms

(2012) Craig F. Barrett et al.   CLADISTICS

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Molecular phylogenetics: principles and practice

(2012) Ziheng Yang et al.   NATURE REVIEWS GENETICS

Evolutionary constraints on the plastid tRNA set decoding methionine and isoleucine

(2012) Sibah Alkatib et al.   NUCLEIC ACIDS RESEARCH

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase

(2012) P. Zhelyazkova et al.   PLANT CELL

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

(2011) Shannon CK Straub et al.   BMC GENOMICS

Sequencing and Analysis of Plastid Genome in Mycoheterotrophic Orchid Neottia nidus-avis

(2011) Maria D. Logacheva et al.   Genome Biology and Evolution

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

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

raxmlGUI: a graphical front-end for RAxML

(2011) Daniele Silvestro et al.   ORGANISMS DIVERSITY & EVOLUTION

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

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1

(2010) Thomas J. Givnish et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Inference of phylogenetic relationships among the subfamilies of grasses (Poaceae: Poales) using meso-scale exemplar-based sampling of the plastid genome

(2010) Jeffery M. Saarela et al.   Botany

Localized hypermutation and associated gene losses in legume chloroplast genomes

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

Evolution of mycoheterotrophy in plants: a phylogenetic perspective

(2010) Vincent Merckx et al.   NEW PHYTOLOGIST

Recombination and the maintenance of plant organelle genome stability

(2010) Alexandre Maréchal et al.   NEW PHYTOLOGIST

Plastid ndh genes in plant evolution

(2010) Mercedes Martín et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

An organellar maturase associates with multiple group II introns

(2010) R. Zoschke 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

Bias and conflict in phylogenetic inference of myco-heterotrophic plants: a case study in Thismiaceae

(2009) Vincent Merckx et al.   CLADISTICS

Parallel Loss of Plastid Introns and Their Maturase in the Genus Cuscuta

(2009) Joel R. McNeal et al.   PLoS One

From chloroplasts to “cryptic” plastids: evolution of plastid genomes in parasitic plants

(2008) Kirsten Krause   CURRENT GENETICS

How well do we understand the overall backbone of cycad phylogeny? New insights from a large, multigene plastid data set

(2008) Jessie M. Zgurski et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Superwobbling facilitates translation with reduced tRNA sets

(2008) Marcelo Rogalski et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH

Functional Gene Losses Occur with Minimal Size Reduction in the Plastid Genome of the Parasitic Liverwort Aneura mirabilis

(2007) N. J. Wickett et al.   MOLECULAR BIOLOGY AND EVOLUTION