On the brink: the highly reduced plastomes of nonphotosynthetic Ericaceae

Plastomes on the edge: the evolutionary breakdown of mycoheterotroph plastid genomes

(2017) Sean W. Graham et al.   NEW PHYTOLOGIST

A few-gene plastid phylogenetic framework for mycoheterotrophic monocots

(2016) Vivienne K.Y. Lam et al.   AMERICAN JOURNAL OF BOTANY

The loss of photosynthetic pathways in the plastid and nuclear genomes of the non-photosynthetic mycoheterotrophic eudicot Monotropa hypopitys

(2016) Nikolai V. Ravin et al.   BMC PLANT BIOLOGY

Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales

(2016) Sidonie Bellot et al.   Genome Biology and Evolution

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

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

Lineage-Specific Reductions of Plastid Genomes in an Orchid Tribe with Partially and Fully Mycoheterotrophic Species

(2016) Yan-Lei Feng et al.   Genome Biology and Evolution

The elusive predisposition to mycoheterotrophy in Ericaceae

(2016) Félix Lallemand et al.   NEW PHYTOLOGIST

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

Phylogenetic relationships at the base of Ericaceae: Implications for vegetative and mycorrhizal evolution

(2016) John V. Freudenstein et al.   TAXON

Comparative analysis of plastid genomes of non-photosynthetic Ericaceae and their photosynthetic relatives

(2016) Maria D. Logacheva et al.   Scientific Reports

The complete chloroplast genome of parasitic flowering plant Monotropa hypopitys: extensive gene losses and size reduction

(2016) Eugene V. Gruzdev et al.   Mitochondrial DNA Part B-Resources

The Plastomes of Two Species in the Endoparasite GenusPilostyles(Apodanthaceae) Each Retain Just Five or Six Possibly Functional Genes

(2015) Sidonie Bellot et al.   Genome Biology and Evolution

Plastome Evolution in Hemiparasitic Mistletoes

(2015) Gitte Petersen et al.   Genome Biology and Evolution

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

(2015) Vivienne K.Y. Lam 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

Mycorrhizal ecology and evolution: the past, the present, and the future

(2015) Marcel G. A. van der Heijden et al.   NEW PHYTOLOGIST

YCF1: A Green TIC?

(2015) Jan de Vries et al.   PLANT CELL

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

(2015) Xiaohong Yao et al.   PLoS One

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

RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

(2014) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

Plastid genome evolution across the genus Cuscuta (Convolvulaceae): two clades within subgenus Grammica exhibit extensive gene loss

(2013) Thomas Braukmann et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2013) S. Wicke et al.   PLANT CELL

Balanced Gene Losses, Duplications and Intensive Rearrangements Led to an Unusual Regularly Sized Genome in Arbutus unedo Chloroplasts

(2013) Fernando Martínez-Alberola et al.   PLoS One

Uncovering the Protein Translocon at the Chloroplast Inner Envelope Membrane

(2013) S. Kikuchi et al.   SCIENCE

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

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

(2012) M. Kearse et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Plastid genome evolution in mycoheterotrophic Ericaceae

(2012) Thomas Braukmann et al.   PLANT MOLECULAR 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

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

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

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

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

RecA maintains the integrity of chloroplast DNA molecules in Arabidopsis

(2010) Beth A. Rowan et al.   JOURNAL OF EXPERIMENTAL BOTANY

Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage

(2010) M. M. Guisinger et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

(2010) Isheng J Tsai et al.   GENOME BIOLOGY

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

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

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

(2008) G DROUIN et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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