Mitochondrial genomic data are effective at placing mycoheterotrophic lineages in plant phylogeny

Long Branch Attraction Biases in Phylogenetics

(2021) Edward Susko et al.   SYSTEMATIC BIOLOGY

Discordant Phylogenomic Placement of Hydnoraceae and Lactoridaceae Within Piperales Using Data From All Three Genomes

(2021) Matthias Jost et al.   Frontiers in Plant Science

Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants

(2021) William J. Baker et al.   AMERICAN JOURNAL OF BOTANY

Defining coalescent genes: Theory meets practice in organelle phylogenomics

(2021) Jeff J Doyle   SYSTEMATIC BIOLOGY

The Genomic Impact of Mycoheterotrophy in Orchids

(2021) Marcin Jąkalski et al.   Frontiers in Plant Science

Cheating in arbuscular mycorrhizal mutualism: a network and phylogenetic analysis of mycoheterotrophy

(2020) Benoît Perez‐Lamarque et al.   NEW PHYTOLOGIST

Phylogenetics of the mycoheterotrophic genus Thismia (Thismiaceae: Dioscoreales) with a focus on the Old World taxa: delineation of novel natural groups and insights into the evolution of morphological traits

(2020) Ekaterina A Shepeleva et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

A bi‐organellar phylogenomic study of Pandanales: inference of higher‐order relationships and unusual rate‐variation patterns

(2020) Marybel Soto Gomez et al.   CLADISTICS

Unprecedented parallel photosynthetic losses in a heterotrophic orchid genus

(2019) Craig F Barrett et al.   MOLECULAR BIOLOGY AND EVOLUTION

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Mycoheterotrophic Epirixanthes (Polygalaceae) has a typical angiosperm mitogenome but unorthodox plastid genomes

(2019) G Petersen et al.   ANNALS OF BOTANY

Thirteen New Plastid Genomes from Mixotrophic and Autotrophic Species Provide Insights into Heterotrophy Evolution in Neottieae Orchids

(2019) Félix Lallemand et al.   Genome Biology and Evolution

Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes

(2019) Yun-Xia Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

One thousand plant transcriptomes and the phylogenomics of green plants

(2019)   NATURE

Organellomic data sets confirm a cryptic consensus on (unrooted) land‐plant relationships and provide new insights into bryophyte molecular evolution

(2019) David Bell et al.   AMERICAN JOURNAL OF BOTANY

Plant organellar RNA editing: what 30 years of research has revealed

(2019) Ian D. Small et al.   PLANT JOURNAL

Phylogenomic inference in extremis : A case study with mycoheterotroph plastomes

(2018) Vivienne K. Y. Lam et al.   AMERICAN JOURNAL OF BOTANY

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots

(2018) Thomas J. Givnish et al.   AMERICAN JOURNAL OF BOTANY

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering

(2018) Matthew G Johnson et al.   SYSTEMATIC BIOLOGY

The biogeographical history of the interaction between mycoheterotrophic Thismia (Thismiaceae) plants and mycorrhizal Rhizophagus (Glomeraceae) fungi

(2017) Vincent S. F. T. Merckx et al.   JOURNAL OF BIOGEOGRAPHY

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

More on the Best Evolutionary Rate for Phylogenetic Analysis

(2017) Seraina Klopfstein et al.   SYSTEMATIC BIOLOGY

Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes

(2017) Gitte Petersen et al.   PLoS One

A few-gene plastid phylogenetic framework for mycoheterotrophic monocots

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

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

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV

(2016)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Phylogenomics and historical biogeography of the monocot order Liliales: out of Australia and through Antarctica

(2016) Thomas J. Givnish et al.   CLADISTICS

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

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

The elusive predisposition to mycoheterotrophy in Ericaceae

(2016) Félix Lallemand et al.   NEW PHYTOLOGIST

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

(2016) John V. Freudenstein et al.   TAXON

Monocot fossils suitable for molecular dating analyses

(2015) William J. D. Iles et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

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

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

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

Are there geographic mosaics of mycorrhizal specificity and partial mycoheterotrophy? A case study inMoneses uniflora(Ericaceae)

(2015) Nicole A. Hynson et al.   NEW PHYTOLOGIST

Miniaturized mitogenome of the parasitic plantViscum scurruloideumis extremely divergent and dynamic and has lost allnadgenes

(2015) Elizabeth Skippington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Massive gene loss in mistletoe (Viscum, Viscaceae) mitochondria

(2015) G. Petersen et al.   Scientific Reports

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

Thismia americana, the 101st Anniversary of a Botanical Mystery

(2014) Vincent S. F. T. Merckx et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

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

As old as the mountains: the radiations of the Ericaceae

(2014) Orlando Schwery et al.   NEW PHYTOLOGIST

The plant mitochondrial genome: Dynamics and maintenance

(2013) José M. Gualberto et al.   BIOCHIMIE

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

(2013) Lindell Bromham et al.   BMC EVOLUTIONARY BIOLOGY

Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae

(2012) P. Roxanne Steele et al.   AMERICAN JOURNAL OF BOTANY

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Plastid genome evolution in mycoheterotrophic Ericaceae

(2012) Thomas Braukmann et al.   PLANT MOLECULAR BIOLOGY

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

raxmlGUI: a graphical front-end for RAxML

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

Phylogeny of Pyroleae (Ericaceae): implications for character evolution

(2010) Zhen-wen Liu et al.   JOURNAL OF PLANT RESEARCH

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

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

Evolution of mycoheterotrophy in plants: a phylogenetic perspective

(2010) Vincent Merckx et al.   NEW PHYTOLOGIST

Angiosperm phylogeny inferred from sequences of four mitochondrial genes

(2010) Yin-Long QIU et al.   Journal of Systematics and Evolution

Myco-heterotrophy: when fungi host plants

(2009) Vincent Merckx et al.   ANNALS OF BOTANY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

The Complete Mitochondrial Genome Sequence of the Hornwort Megaceros aenigmaticus Shows a Mixed Mode of Conservative Yet Dynamic Evolution in Early Land Plant Mitochondrial Genomes

(2009) Libo Li et al.   JOURNAL OF MOLECULAR EVOLUTION

Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?

(2009) ARON J. FAZEKAS et al.   Molecular Ecology Resources

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

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

Diversification of myco-heterotrophic angiosperms: evidence from Burmanniaceae

(2008) Vincent Merckx et al.   BMC EVOLUTIONARY BIOLOGY