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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear 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

The Translational Apparatus of Plastids and Its Role in Plant Development

(2014) Nadine Tiller et al.   Molecular Plant

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

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

tRNA anticodon shifts in eukaryotic genomes

(2014) H. H. Rogers et al.   RNA

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

Parasitic plants have increased rates of molecular evolution across all three genomes

(2013) Lindell Bromham et al.   BMC EVOLUTIONARY BIOLOGY

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

(2013) Sergey Nurk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

The Chloroplast Genome of a Symbiodinium sp. Clade C3 Isolate

(2013) Adrian C. Barbrook et al.   PROTIST

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

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer

(2012) Pierre Peterlongo et al.   BMC BIOINFORMATICS

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

(2012) Donata Cafasso et al.   GENOME

Versatile roles of Arabidopsis plastid ribosomal proteins in plant growth and development

(2012) Isidora Romani et al.   PLANT JOURNAL

Analysis of Complete Nucleotide Sequences of 12 Gossypium Chloroplast Genomes: Origin and Evolution of Allotetraploids

(2012) Qin Xu et al.   PLoS One

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

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

Correlation between Nuclear Plastid DNA Abundance and Plastid Number Supports the Limited Transfer Window Hypothesis

(2011) David Roy Smith 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

Nonessential Plastid-Encoded Ribosomal Proteins in Tobacco: A Developmental Role for Plastid Translation and Implications for Reductive Genome Evolution

(2011) Tobias T. Fleischmann et al.   PLANT CELL

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

Rate accelerations in nuclear 18S rDNA of mycoheterotrophic and parasitic angiosperms

(2010) Benny Lemaire et al.   JOURNAL OF PLANT RESEARCH

Phylogenetic relationships within Orchidaceae based on a low-copy nuclear coding gene, Xdh: Congruence with organellar and nuclear ribosomal DNA results

(2010) Marcin Górniak et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

Stable isotope signatures confirm carbon and nitrogen gain through ectomycorrhizas in the ghost orchid Epipogium aphyllum Swartz*

(2010) H. T. Liebel et al.   PLANT BIOLOGY

Identification of Nuclear Genes Encoding Chloroplast-Localized Proteins Required for Embryo Development in Arabidopsis

(2010) N. Bryant et al.   PLANT PHYSIOLOGY

The evolution of parasitism in plants

(2010) James H. Westwood et al.   TRENDS IN PLANT SCIENCE

Ectomycorrhizal Inocybe species associate with the mycoheterotrophic orchid Epipogium aphyllum but not its asexual propagules

(2009) Melanie Roy et al.   ANNALS OF BOTANY

The causes of mutation accumulation in mitochondrial genomes

(2009) M. Neiman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

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

(2008) D. R. Zerbino et al.   GENOME 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