4.7 Article

Marine gregarine genomes reveal the breadth of apicomplexan diversity with a partially conserved glideosome machinery

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

SMART: recent updates, new developments and status in 2020

Ivica Letunic et al.

Summary: SMART is a web resource for protein domain identification and annotation, with over 1300 manually curated models and 68 new models added for various recombinase families. Updates also include synchronization with UniProt, Ensembl, and STRING databases, as well as enhancements to the protein display engine and domain architecture analysis components.

NUCLEIC ACIDS RESEARCH (2021)

Article Evolutionary Biology

Phylogenomics Identifies a NewMajor Subgroup of Apicomplexans, Marosporida class nov., with Extreme Apicoplast Genome Reduction

Varsha Mathur et al.

Summary: The study sequenced the transcriptomes and apicoplast genomes of three deep-branching apicomplexans, revealing a new lineage that retains plastid genomes and the canonical apicomplexan plastid metabolism. This new lineage, proposed as Marosporida class nov., occupies an intermediate position in apicomplexan phylogeny and adds complexity to the stepwise reductive evolution models in these parasites.

GENOME BIOLOGY AND EVOLUTION (2021)

Article Biochemistry & Molecular Biology

Inhibition of protein N-myristoylation blocks Plasmodium falciparum intraerythrocytic development, egress and invasion

Anja C. Schlott et al.

Summary: Inhibition of protein myristoylation in the human malaria parasite affects parasite development and growth, with impacts on parasite egress, rhoptry protein mislocalization, and erythrocyte invasion. The inhibition of N-myristoyl transferase disrupts multiple processes in the parasite lifecycle, making it a potential drug target for combating malaria.

PLOS BIOLOGY (2021)

Article Biology

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

Eric D. Salomaki et al.

Summary: Apicomplexan lineages exhibit diverse functional restructuring of mitochondrial metabolism, likely driven by adaptations to parasitism and anaerobiosis. Our findings suggest that apicomplexans have evolved convergent adaptations, sharing characteristics such as morphology, energy metabolism, and intracellular lifestyle.

BMC BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Parallel functional reduction in the mitochondria of apicomplexan parasites

Varsha Mathur et al.

Summary: Gregarines are an early-diverging lineage of apicomplexan parasites that provide insights into the origin and evolution of the group. They exhibit significantly reduced energy metabolism in their mitochondria, but retain distinctive tubular cristae. This parallel reduction in gregarine mitochondria expands the diversity of organisms containing MROs and highlights the role of parallel transitions in apicomplexan evolution.

CURRENT BIOLOGY (2021)

Article Microbiology

Blocking Palmitoylation of Toxoplasma gondii Myosin Light Chain 1 Disrupts Glideosome Composition but Has Little Impact on Parasite Motility

Pramod K. Rompikuntal et al.

Summary: The key binding element between TgMLC1 and TgGAP45 in the force transduction machinery of T. gondii was found to be the palmitoylation of C8 and C11 residues on TgMLC1, contradicting the current model. Surprisingly, mutations disrupting this binding had little impact on parasite motility, challenging the widely held linear motor model and emphasizing the need for further research on how apicomplexan parasites generate necessary forces for movement.

MSPHERE (2021)

Article Biochemistry & Molecular Biology

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships

Alexander K. Tice et al.

Summary: PhyloFisher is an easy-to-use software package that includes a manually curated database of eukaryotic taxa and a variety of tools and utilities for state-of-the-art phylogenomic investigations.

PLOS BIOLOGY (2021)

Article Biochemical Research Methods

KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold

Takuya Aramaki et al.

BIOINFORMATICS (2020)

Article Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Review Cell Biology

Why the -omic future of Apicomplexa should include gregarines

Julie Boisard et al.

BIOLOGY OF THE CELL (2020)

Article Immunology

Toxoplasma gondii Mechanisms of Entry Into Host Cells

Juliana Portes et al.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2020)

Review Cell & Tissue Engineering

Calcium-dependent Protein Kinases in Malaria Parasite Development and Infection

George Ghartey-Kwansah et al.

CELL TRANSPLANTATION (2020)

Article Microbiology

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Sina M. Adl et al.

JOURNAL OF EUKARYOTIC MICROBIOLOGY (2019)

Article Microbiology

Validation of a universal set of primers to study animal-associated microeukaryotic communities

Javier del Campo et al.

ENVIRONMENTAL MICROBIOLOGY (2019)

Article Biochemistry & Molecular Biology

Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments

Raja Hashim Ali et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Review Parasitology

The Symbiotic Spectrum: Where Do the Gregarines Fit?

Sonja Rueckert et al.

TRENDS IN PARASITOLOGY (2019)

Article Biochemistry & Molecular Biology

Multiple Independent Origins of Apicomplexan-Like Parasites

Varsha Mathur et al.

CURRENT BIOLOGY (2019)

Article Multidisciplinary Sciences

Alveolar proteins stabilize cortical microtubules in Toxoplasma gondii

Clare R. Harding et al.

NATURE COMMUNICATIONS (2019)

Article Biochemical Research Methods

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

Simon Whelan et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

Structural Basis of Phosphatidic Acid Sensing by APH in Apicomplexan Parasites

Nick Darvill et al.

STRUCTURE (2018)

Article Biochemistry & Molecular Biology

EuPathDB: the eukaryotic pathogen genomics database resource

Cristina Aurrecoechea et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Microbiology

Structures related to attachment and motility in the marine eugregarine Cephaloidophora cf. communis (Apicomplexa)

Magdalena Kovacikova et al.

EUROPEAN JOURNAL OF PROTISTOLOGY (2017)

Article Biochemistry & Molecular Biology

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Review Microbiology

Gliding motility powers invasion and egress in Apicomplexa

Karine Frenal et al.

NATURE REVIEWS MICROBIOLOGY (2017)

Review Biochemistry & Molecular Biology

Genomics of apicomplexan parasites

Lakshmipuram Seshadri Swapna et al.

CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (2017)

Article Cell Biology

AMA1 and MAEBL are important for Plasmodium falciparum sporozoite infection of the liver

Annie S. P. Yang et al.

CELLULAR MICROBIOLOGY (2017)

Article Biochemical Research Methods

SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification

Joao Victor de Araujo Oliveira et al.

BMC BIOINFORMATICS (2016)

Article Microbiology

Phosphatidic Acid-Mediated Signaling Regulates Microneme Secretion in Toxoplasma

Hayley E. Bullen et al.

CELL HOST & MICROBE (2016)

Review Cell Biology

Reassessing the mechanics of parasite motility and host-cell invasion

Isabelle Tardieux et al.

JOURNAL OF CELL BIOLOGY (2016)

Article Multidisciplinary Sciences

Highly rearranged mitochondrial genome in Nycteria parasites (Haemosporidia) from bats

Gregory Karadjian et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Review Parasitology

Apicomplexan Energy Metabolism: Carbon Source Promiscuity and the Quiescence Hyperbole

Damien Jacot et al.

TRENDS IN PARASITOLOGY (2016)

Review Biochemistry & Molecular Biology

The apicomplexan glideosome and adhesins - Structures and function

Lauren E. Boucher et al.

JOURNAL OF STRUCTURAL BIOLOGY (2015)

Article Biotechnology & Applied Microbiology

Identification of invasion proteins of Cryptosporidium parvum

Preeti Singh et al.

WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY (2015)

Article Microbiology

Toxoplasma Actin Is Required for Efficient Host Cell Invasion

Lisa L. Drewry et al.

Article Biochemical Research Methods

InterProScan 5: genome-scale protein function classification

Philip Jones et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

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

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biochemical Research Methods

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

Infernal 1.1: 100-fold faster RNA homology searches

Eric P. Nawrocki et al.

BIOINFORMATICS (2013)

Article Zoology

The enigma of eugregarine epicytic folds: where gliding motility originates?

Andrea Valigurova et al.

FRONTIERS IN ZOOLOGY (2013)

Article Biochemistry & Molecular Biology

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

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

Rfam 11.0: 10 years of RNA families

Sarah W. Burge et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Genetics & Heredity

Age of the last common ancestor of extant Plasmodium parasite lineages

Toshiyuki Hayakawa et al.

Article Biochemical Research Methods

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

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti†

Emmanuel Cornillot et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Cell Biology

Actin depolymerizing factor controls actin turnover and gliding motility in Toxoplasma gondii

Simren Mehta et al.

MOLECULAR BIOLOGY OF THE CELL (2011)

Article Biotechnology & Applied Microbiology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Review Immunology

The cell biology of cryptosporidium infection

Steven P. O'Hara et al.

MICROBES AND INFECTION (2011)

Article Multidisciplinary Sciences

How and Why DNA Barcodes Underestimate the Diversity of Microbial Eukaryotes

Gwenael Piganeau et al.

PLOS ONE (2011)

Article Multidisciplinary Sciences

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

Vincent Ranwez et al.

PLOS ONE (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Microbiology

Functional Dissection of the Apicomplexan Glideosome Molecular Architecture

Karine Frenal et al.

CELL HOST & MICROBE (2010)

Article Multidisciplinary Sciences

A Molecular Clock for Malaria Parasites

Robert E. Ricklefs et al.

SCIENCE (2010)

Article Biochemical Research Methods

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

Salvador Capella-Gutierrez et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

A Novel Family of Apicomplexan Glideosome-associated Proteins with an Inner Membrane-anchoring Role

Hayley E. Bullen et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2009)

Article Biochemistry & Molecular Biology

Vital role for the Plasmodium actin capping protein (CP) beta-subunit in motility of malaria sporozoites

Markus Ganter et al.

MOLECULAR MICROBIOLOGY (2009)

Review Parasitology

No TRAP, no invasion

Belinda J. Morahan et al.

TRENDS IN PARASITOLOGY (2009)

Article Parasitology

GpMyoF, a WD40 repeat-containing myosin associated with the myonemes of Gregarina polymorpha

Matthew B. Heintzelman et al.

JOURNAL OF PARASITOLOGY (2008)

Article Biochemistry & Molecular Biology

The thrombospondin-related protein CpMIC1 (CpTSP8) belongs to the repertoire of micronemal proteins of Cryptosporidium parvum

Lorenza Putignani et al.

MOLECULAR AND BIOCHEMICAL PARASITOLOGY (2008)

Article Parasitology

TRAP-like protein of Plasmodium sporozoites: linking gliding motility to host-cell traversal

Celine Lacroix et al.

TRENDS IN PARASITOLOGY (2008)

Article Biochemistry & Molecular Biology

PAML 4: Phylogenetic analysis by maximum likelihood

Ziheng Yang

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biochemistry & Molecular Biology

Characterization of the Babesia gibsoni P18 as a homologue of thrombospondin related adhesive protein

Jinlin Zhou et al.

MOLECULAR AND BIOCHEMICAL PARASITOLOGY (2006)

Review Microbiology

Regulation of apicomplexan actin-based motility

Jake Baum et al.

NATURE REVIEWS MICROBIOLOGY (2006)

Article Microbiology

Toxoplasma MIC2 is a major determinant of invasion and virulence

My-Hang Huynh et al.

PLOS PATHOGENS (2006)

Article Biochemistry & Molecular Biology

AUGUSTUS:: ab initio prediction of alternative transcripts

Mario Stanke et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes

DE Neafsey et al.

MOLECULAR BIOLOGY AND EVOLUTION (2005)

Article Biochemical Research Methods

GMAP: a genomic mapping and alignment program for mRNA and EST sequences

TD Wu et al.

BIOINFORMATICS (2005)

Article Cell Biology

Actin and myosin in Gregarina polymorpha

MB Heintzelman

CELL MOTILITY AND THE CYTOSKELETON (2004)

Article Biochemical Research Methods

Gene finding in novel genomes

I Korf

BMC BIOINFORMATICS (2004)

Article Cell Biology

Identification of the membrane receptor of a class XIV myosin in Toxoplasma gondii

E Gaskins et al.

JOURNAL OF CELL BIOLOGY (2004)

Article Biochemistry & Molecular Biology

GeneWise and genomewise

E Birney et al.

GENOME RESEARCH (2004)

Article Biotechnology & Applied Microbiology

Versatile and open software for comparing large genomes

S Kurtz et al.

GENOME BIOLOGY (2004)

Article Biochemistry & Molecular Biology

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

BJ Haas et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

OrthoMCL: Identification of ortholog groups for eukaryotic genomes

L Li et al.

GENOME RESEARCH (2003)

Article Biochemical Research Methods

MrBayes 3: Bayesian phylogenetic inference under mixed models

F Ronquist et al.

BIOINFORMATICS (2003)

Article Immunology

Cryptosporidium parvum genes containing thrombospondin type 1 domains

MQ Deng et al.

INFECTION AND IMMUNITY (2002)

Review Biochemistry & Molecular Biology

'The glideosome':: a dynamic complex powering gliding motion and host cell invasion by Toxoplasma gondii

C Opitz et al.

MOLECULAR MICROBIOLOGY (2002)

Article Biochemistry & Molecular Biology

Molecular characterization of a thrombospondin-related anonymous protein homologue in Neospora caninum

JL Lovett et al.

MOLECULAR AND BIOCHEMICAL PARASITOLOGY (2000)

Article Biochemistry & Molecular Biology

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

J Castresana

MOLECULAR BIOLOGY AND EVOLUTION (2000)

Article Biochemistry & Molecular Biology

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models

ZH Yang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2000)