Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans

ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria

(2021) Alexander Mühleip et al.   Nature Communications

Why the –omic future of Apicomplexa should include Gregarines

(2020) Julie Boisard et al.   BIOLOGY OF THE CELL

Genomics of New Ciliate Lineages Provides Insight into the Evolution of Obligate Anaerobiosis

(2020) Johana Rotterová et al.   CURRENT BIOLOGY

New methods to calculate concordance factors for phylogenomic datasets

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Horizontal Gene Transfer in Eukaryotes: Not if, but How Much?

(2020) Julia Van Etten et al.   TRENDS IN GENETICS

Releasing uncurated datasets is essential for reproducible phylogenomics

(2020) Eric D. Salomaki et al.   Nature Ecology & Evolution

Diversity of electron transport chains in anaerobic protists

(2020) Ryan M.R. Gawryluk et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

An investigation of irreproducibility in maximum likelihood phylogenetic inference

(2020) Xing-Xing Shen et al.   Nature Communications

Determinants, and implications, of the shape and size of thylakoids and cristae

(2020) John A Raven   JOURNAL OF PLANT PHYSIOLOGY

New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

(2019) Jürgen F H Strassert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recombinant RquA catalyzes the in vivo conversion of ubiquinone to rhodoquinone in Escherichia coli and Saccharomyces cerevisiae

(2019) Ann C. Bernert et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

The Relative Importance of Modeling Site Pattern Heterogeneity Versus Partition-Wise Heterotachy in Phylogenomic Inference

(2019) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments

(2019) Raja Hashim Ali et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Symbiotic Spectrum: Where Do the Gregarines Fit?

(2019) Sonja Rueckert et al.   TRENDS IN PARASITOLOGY

Rhodoquinone biosynthesis in C. elegans requires precursors generated by the kynurenine pathway

(2019) Samantha Del Borrello et al.   eLife

Multiple Independent Origins of Apicomplexan-Like Parasites

(2019) Varsha Mathur et al.   CURRENT BIOLOGY

Apicomplexan-like parasites are polyphyletic and widely but selectively dependent on cryptic plastid organelles

(2019) Jan Janouškovec et al.   eLife

There Is Treasure Everywhere: Reductive Plastid Evolution in Apicomplexa in Light of Their Close Relatives

(2019) Eric D. Salomaki et al.   Biomolecules

Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework

(2019) Javier del Campo et al.   Frontiers in Microbiology

PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences

(2018) Simon Whelan et al.   BIOINFORMATICS

Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group

(2018) Matthew W Brown et al.   Genome Biology and Evolution

Toxoplasma gondiiacetyl-CoA synthetase is involved in fatty acid elongation (of long fatty acid chains) during tachyzoite life stages

(2018) David Dubois et al.   JOURNAL OF LIPID RESEARCH

Highly diverged novel subunit composition of apicomplexan F-type ATP synthase identified from Toxoplasma gondii

(2018) Rahul Salunke et al.   PLOS BIOLOGY

Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis

(2018) Courtney W Stairs et al.   eLife

Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

(2018) Aaron A. Heiss et al.   Royal Society Open Science

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

(2018) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Elucidating the mitochondrial proteome of Toxoplasma gondii reveals the presence of a divergent cytochrome c oxidase

(2018) Azadeh Seidi et al.   eLife

A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida)

(2017) Timur G. Simdyanov et al.   PeerJ

Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes

(2017) Michelle M. Leger et al.   Nature Ecology & Evolution

Contentious relationships in phylogenomic studies can be driven by a handful of genes

(2017) Xing-Xing Shen et al.   Nature Ecology & Evolution

Motility in blastogregarines (Apicomplexa): Native and drug-induced organisation of Siedleckia nematoides cytoskeletal elements

(2017) Andrea Valigurová et al.   PLoS One

Evolution of mitosome metabolism and invasion-related proteins in Cryptosporidium

(2016) Shiyou Liu et al.   BMC GENOMICS

The Earliest Stages of Mitochondrial Adaptation to Low Oxygen Revealed in a Novel Rhizarian

(2016) Ryan M.R. Gawryluk et al.   CURRENT BIOLOGY

A Eukaryote without a Mitochondrial Organelle

(2016) Anna Karnkowska et al.   CURRENT BIOLOGY

A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts)

(2016) Romain Derelle et al.   MOLECULAR BIOLOGY AND EVOLUTION

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

(2016) Robert Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

EuPathDB: the eukaryotic pathogen genomics database resource

(2016) Cristina Aurrecoechea et al.   NUCLEIC ACIDS RESEARCH

Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista

(2016) Fabien Burki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Differential Gene Expression and Protein Localization ofCryptosporidium parvumFatty Acyl-CoA Synthetase Isoforms

(2015) Fengguang Guo et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Lateral Gene Transfer and Gene Duplication Played a Key Role in the Evolution of Mastigamoeba balamuthi Hydrogenosomes

(2015) Eva Nývltová et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diversity and origins of anaerobic metabolism in mitochondria and related organelles

(2015) Courtney W. Stairs et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mitochondrial ATP synthase is dispensable in blood-stagePlasmodium bergheirodent malaria but essential in the mosquito phase

(2015) Angelika Sturm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A SUF Fe-S Cluster Biogenesis System in the Mitochondrion-Related Organelles of the Anaerobic Protist Pygsuia

(2014) Courtney W. Stairs et al.   CURRENT BIOLOGY

Gregarine site-heterogeneous 18S rDNA trees, revision of gregarine higher classification, and the evolutionary diversification of Sporozoa

(2014) Thomas Cavalier-Smith   EUROPEAN JOURNAL OF PROTISTOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Comparative Ultrastructure and Molecular Phylogeny of Selenidium melongena n. sp. and S. terebellae Ray 1930 Demonstrate Niche Partitioning in Marine Gregarine Parasites (Apicomplexa)

(2014) Kevin C. Wakeman et al.   PROTIST

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

BCKDH: The Missing Link in Apicomplexan Mitochondrial Metabolism Is Required for Full Virulence of Toxoplasma gondii and Plasmodium berghei

(2014) Rebecca D. Oppenheim et al.   PLoS Pathogens

Highly divergent mitochondrion-related organelles in anaerobic parasitic protozoa

(2013) Takashi Makiuchi et al.   BIOCHIMIE

Mitochondrial metabolism of sexual and asexual blood stages of the malaria parasite Plasmodium falciparum

(2013) James I MacRae et al.   BMC BIOLOGY

Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis

(2013) Filip Husnik et al.   CELL

The metabolic roles of the endosymbiotic organelles of Toxoplasma and Plasmodium spp.

(2013) Lilach Sheiner et al.   CURRENT OPINION IN MICROBIOLOGY

Diversity of mitochondrial genome structure in the phylum Apicomplexa

(2013) Kenji Hikosaka et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

NIF-type iron-sulfur cluster assembly system is duplicated and distributed in the mitochondria and cytosol of Mastigamoeba balamuthi

(2013) E. Nyvltova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Hydrogenosomes in the diplomonad Spironucleus salmonicida

(2013) Jon Jerlström-Hultqvist et al.   Nature Communications

The submitochondrial distribution of ubiquinone affects respiration in long-livedMclk1+/−mice

(2012) Jérôme Lapointe et al.   JOURNAL OF CELL BIOLOGY

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

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

Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes

(2012) M. Muller et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Identification of a New Gene Required for the Biosynthesis of Rhodoquinone in Rhodospirillum rubrum

(2011) Z. T. Lonjers et al.   JOURNAL OF BACTERIOLOGY

Species Boundaries in Gregarine Apicomplexan Parasites: A Case Study-Comparison of Morphometric and Molecular Variability in Lecudina cf. tuzetae (Eugregarinorida, Lecudinidae)

(2011) SONJA RUECKERT et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Eukaryotic Pyruvate Formate Lyase and Its Activating Enzyme Were Acquired Laterally from a Firmicute

(2011) C. W. Stairs et al.   MOLECULAR BIOLOGY AND EVOLUTION

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Acetate formation in the energy metabolism of parasitic helminths and protists

(2010) Aloysius G.M. Tielens et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Diversity in mitochondrial metabolic pathways in parasitic protists Plasmodium and Cryptosporidium

(2010) Tatsushi Mogi et al.   PARASITOLOGY INTERNATIONAL

The evolution, metabolism and functions of the apicoplast

(2010) L. Lim et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mitochondrial Evolution and Functions in Malaria Parasites

(2009) Akhil B. Vaidya et al.   Annual Review of Microbiology

Genetic evidence for the requirement of the endocytic pathway in the uptake of coenzyme Q6 in Saccharomyces cerevisiae

(2009) Sergio Padilla-López et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Bacterial-type oxygen detoxification and iron-sulfur cluster assembly in amoebal relict mitochondria

(2009) Barbora Maralikova et al.   CELLULAR MICROBIOLOGY

Phylogenetic Diversity and Axial Distribution of Microbes in the Intestinal Tract of the Polychaete Neanthes glandicincta

(2009) Meng Li et al.   MICROBIAL ECOLOGY

A Genome-Sequence Survey for Ascogregarina taiwanensis Supports Evolutionary Affiliation but Metabolic Diversity between a Gregarine and Cryptosporidium

(2009) T. J. Templeton et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mitosomes in Entamoeba histolytica contain a sulfate activation pathway

(2009) F. Mi-ichi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organelles in Blastocystis that Blur the Distinction between Mitochondria and Hydrogenosomes

(2008) Alexandra Stechmann et al.   CURRENT BIOLOGY

Apicomplexan mitochondrial metabolism: a story of gains, losses and retentions

(2008) Frank Seeber et al.   TRENDS IN PARASITOLOGY