Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex

On the brink: the highly reduced plastomes of nonphotosynthetic Ericaceae

(2017) Thomas W. A. Braukmann et al.   NEW PHYTOLOGIST

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

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

Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids

(2017) Choun-Sea Lin et al.   PLANT JOURNAL

A Reanalysis of Relationships Among Calypsoinae (Orchidaceae: Epidendroideae): Floral and Vegetative Evolution and the Placement of Yoania

(2017) John V. Freudenstein et al.   SYSTEMATIC BOTANY

Independent degradation in genes of the plastid ndh gene family in species of the orchid genus Cymbidium (Orchidaceae; Epidendroideae)

(2017) Hyoung Tae Kim et al.   PLoS One

Drastic reduction of plastome size in the mycoheterotrophic Thismia tentaculata relative to that of its autotrophic relative Tacca chantrieri

(2016) Gwynne S. Lim et al.   AMERICAN JOURNAL OF BOTANY

Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasiteCytinus hypocistis(Cytinaceae)

(2016) Cristina Roquet et al.   ANNALS 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

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

Partial mycoheterotrophy is more widespread among orchids than previously assumed

(2016) Gerhard Gebauer et al.   NEW PHYTOLOGIST

Complete Plastid Genome of the Recent Holoparasite Lathraea squamaria Reveals Earliest Stages of Plastome Reduction in Orobanchaceae

(2016) Tahir H. Samigullin et al.   PLoS One

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

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

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

Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage

(2016) Chodon Sass et al.   PeerJ

An updated classification of Orchidaceae

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

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

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

Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing

(2015) Eric Samorodnitsky et al.   HUMAN MUTATION

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

Orchid phylogenomics and multiple drivers of their extraordinary diversification

(2015) Thomas J. Givnish et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries

(2015) Hyoung Tae Kim et al.   PLoS One

Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: The tortoise and the hare IV

(2014) Joey Shaw et al.   AMERICAN JOURNAL OF BOTANY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

Do chlorophyllous orchids heterotrophically use mycorrhizal fungal carbon?

(2014) Marc-André Selosse et al.   TRENDS IN PLANT SCIENCE

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

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

(2013) Lindell Bromham et al.   BMC EVOLUTIONARY BIOLOGY

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

(2013) M. Roy et al.   ECOLOGICAL MONOGRAPHS

Unlocking the vault: next-generation museum population genomics

(2013) Ke Bi et al.   MOLECULAR ECOLOGY

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

(2013) S. Wicke et al.   PLANT CELL

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

A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid Genomes

(2013) Gregory W. Stull et al.   Applications in Plant Sciences

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

ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R

(2012) Andrei-Alin Popescu et al.   BIOINFORMATICS

Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture

(2012) Lecong Zhou et al.   BMC GENOMICS

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

(2012) V. Nolte et al.   GENOME RESEARCH

Testing hypotheses for genealogical discordance in a rainforest lizard

(2012) Sonal Singhal et al.   MOLECULAR ECOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

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

An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid

(2011) CRAIG F. BARRETT et al.   MOLECULAR ECOLOGY

The role of plastids in plant speciation

(2011) STEPHAN GREINER et al.   MOLECULAR ECOLOGY

Performance comparison of exome DNA sequencing technologies

(2011) Michael J Clark et al.   NATURE BIOTECHNOLOGY

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

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Comprehensive comparison of three commercial human whole-exome capture platforms

(2011) Asan et al.   GENOME BIOLOGY

A Phylogenetic Model for Investigating Correlated Evolution of Substitution Rates and Continuous Phenotypic Characters

(2010) N. Lartillot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeography of Douglas-fir based on mitochondrial and chloroplast DNA sequences: testing hypotheses from the fossil record

(2010) PAUL F. GUGGER et al.   MOLECULAR ECOLOGY

Evolution of mycoheterotrophy in plants: a phylogenetic perspective

(2010) Vincent Merckx et al.   NEW PHYTOLOGIST

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Earliest orchid macrofossils: Early Miocene Dendrobium and Earina (Orchidaceae: Epidendroideae) from New Zealand

(2009) John G. Conran et al.   AMERICAN JOURNAL OF BOTANY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing

(2009) Emily Hodges et al.   Nature Protocols

Patterns of Morphological and Plastid DNA Variation in the Corallorhiza striata Species Complex (Orchidaceae)

(2009) Craig F. Barrett et al.   SYSTEMATIC BOTANY

Relationships and evolution of matK in a group of leafless orchids (Corallorhiza and Corallorhizinae; Orchidaceae: Epidendroideae)

(2008) John V. Freudenstein et al.   AMERICAN JOURNAL OF BOTANY

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

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

Distribution and Evolution of Pseudogenes, Gene Losses, and a Gene Rearrangement in the Plastid Genome of the Nonphotosynthetic Liverwort, Aneura mirabilis (Metzgeriales, Jungermanniopsida)

(2008) Norman J. Wickett et al.   JOURNAL OF MOLECULAR EVOLUTION

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

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH