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

Biogeographical diversification of mainland AsianDendrobium(Orchidaceae) and its implications for the historical dynamics of evergreen broad-leaved forests

(2016) Xiao-Guo Xiang et al.   JOURNAL OF BIOGEOGRAPHY

Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae

(2015) Michelle M. Barthet et al.   BMC EVOLUTIONARY BIOLOGY

An updated classification of Orchidaceae

(2015) Mark W. Chase et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

A phylogenetic analysis of molecular and morphological characters ofHerminium(Orchidaceae, Orchideae): evolutionary relationships, taxonomy, and patterns of character evolution

(2015) Bhakta Bahadur Raskoti et al.   CLADISTICS

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

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

Proposal of a Twin Aarginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes

(2015) Ryoma Kamikawa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Massive intracellular gene transfer during plastid genome reduction in nongreen Orobanchaceae

(2015) Natalie Cusimano et al.   NEW PHYTOLOGIST

Why chloroplasts and mitochondria retain their own genomes and genetic systems: Colocation for redox regulation of gene expression

(2015) John F. Allen   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family

(2015) Choun-Sea Lin et al.   Scientific Reports

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Photosynthesis in perennial mixotrophicEpipactisspp. (Orchidaceae) contributes more to shoot and fruit biomass than to hypogeous survival

(2014) Cédric Gonneau et al.   JOURNAL OF ECOLOGY

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

RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

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

Nutritional regulation in mixotrophic plants: new insights from Limodorum abortivum

(2014) Alessandro Bellino et al.   OECOLOGIA

Why do mixotrophic plants stay green? A comparison between green and achlorophyllous orchid individuals in situ

(2013) M. Roy et al.   ECOLOGICAL MONOGRAPHS

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

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

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

Multiple and different genomic rearrangements of the rbcL gene are present in the parasitic orchid Neottia nidus-avis

(2012) Donata Cafasso et al.   GENOME

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Large and linked in scientific publishing

(2012) Laurie Goodman et al.   GigaScience

Transcriptomes of the Parasitic Plant Family Orobanchaceae Reveal Surprising Conservation of Chlorophyll Synthesis

(2011) Norman J. Wickett et al.   CURRENT 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

Chloroplast genomes of photosynthetic eukaryotes

(2011) Beverley R. Green   PLANT JOURNAL

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

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Conservation of Plastid Sequences in the Plant Nuclear Genome for Millions of Years Facilitates Endosymbiotic Evolution

(2011) M. Rousseau-Gueutin et al.   PLANT PHYSIOLOGY

C and N stable isotope signatures reveal constraints to nutritional modes in orchids from the Mediterranean and Macaronesia

(2010) Heiko T. Liebel et al.   AMERICAN JOURNAL OF BOTANY

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae

(2010) Fu-Hui Wu et al.   BMC PLANT BIOLOGY

SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

(2010) Gaurav Vaidya et al.   CLADISTICS

The degree of mycoheterotrophic carbon gain in green, variegated and vegetative albino individuals of Cephalanthera damasonium is related to leaf chlorophyll concentrations

(2010) Marcus Stöckel et al.   NEW PHYTOLOGIST

Irradiance governs exploitation of fungi: fine-tuning of carbon gain by two partially myco-heterotrophic orchids

(2010) K. Preiss et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Two mycoheterotrophic orchids from Thailand tropical dipterocarpacean forests associate with a broad diversity of ectomycorrhizal fungi

(2009) Mélanie Roy et al.   BMC BIOLOGY

The chlorophyll-containing orchid Corallorhiza trifida derives little carbon through photosynthesis

(2009) Duncan D. Cameron et al.   NEW PHYTOLOGIST

Green plants that feed on fungi: facts and questions about mixotrophy

(2009) Marc-André Selosse et al.   TRENDS IN PLANT SCIENCE

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

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

Molecular evolution of rbcL in the mycoheterotrophic coralroot orchids (Corallorhiza Gagnebin, Orchidaceae)

(2008) Craig F. Barrett et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The ectomycorrhizal specialist orchid Corallorhiza trifida is a partial myco-heterotroph

(2008) Katja Zimmer et al.   NEW PHYTOLOGIST