Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S‐ITS‐23S rRNA operon

(2019) Joran Martijn et al.   ENVIRONMENTAL MICROBIOLOGY

Towards PacBio‐based pan‐eukaryote metabarcoding using full‐length ITS sequences

(2019) Leho Tedersoo et al.   Environmental Microbiology Reports

Enigmatic Diphyllatea eukaryotes: culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution

(2018) Russell J. S. Orr et al.   BMC EVOLUTIONARY BIOLOGY

High-throughput environmental sequencing reveals high diversity of litter and moss associated protist communities along a gradient of drainage and tree productivity

(2018) Thierry J. Heger et al.   ENVIRONMENTAL MICROBIOLOGY

Clarifying the Relationships between Microsporidia and Cryptomycota

(2018) David Bass et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

First Ultrastructural and Molecular Phylogenetic Evidence from the Blastogregarines, an Early Branching Lineage of Plesiomorphic Apicomplexa

(2018) Timur G. Simdyanov et al.   PROTIST

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

Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments

(2018) Felix Heeger et al.   Molecular Ecology Resources

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

(2018) Pierre Barbera et al.   SYSTEMATIC BIOLOGY

Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes

(2018) Gordon Lax et al.   NATURE

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Converting highly productive arable cropland in Europe to grassland: –a poor candidate for carbon sequestration

(2017) Paul Gosling et al.   Scientific Reports

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

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

(2017) Frédéric Mahé et al.   Nature Ecology & Evolution

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data

(2016) Melanie Schirmer et al.   BMC BIOINFORMATICS

Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification

(2016) Josef Wagner et al.   BMC MICROBIOLOGY

Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists

(2016) Stefan Geisen   ENVIRONMENTAL MICROBIOLOGY

Phylogeny-aware identification and correction of taxonomically mislabeled sequences

(2016) Alexey M. Kozlov et al.   NUCLEIC ACIDS RESEARCH

The Large Subunit rDNA Sequence of Plasmodiophora brassicae Does not Contain Intra-species Polymorphism

(2016) Arne Schwelm et al.   PROTIST

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

(2016) Patrick D. Schloss et al.   PeerJ

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

(2015) Ramon Massana et al.   ENVIRONMENTAL MICROBIOLOGY

Metatranscriptomic census of active protists in soils

(2015) Stefan Geisen et al.   ISME Journal

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems

(2014) Delphine Lallias et al.   ISME Journal

Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys

(2014) Frédéric Mahé et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Improved performance of the PacBio SMRT technology for 16S rDNA sequencing

(2014) Jennifer J. Mosher et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Placing Environmental Next-Generation Sequencing Amplicons from Microbial Eukaryotes into a Phylogenetic Context

(2014) Micah Dunthorn et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Global biogeography of highly diverse protistan communities in soil

(2012) Scott T Bates et al.   ISME Journal

Collodictyon--An Ancient Lineage in the Tree of Eukaryotes

(2012) S. Zhao et al.   MOLECULAR BIOLOGY AND EVOLUTION

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

(2012) Jan Pawlowski et al.   PLOS BIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Eukaryotic diversity and phylogeny using small- and large-subunit ribosomal RNA genes from environmental samples

(2009) William Marande et al.   ENVIRONMENTAL MICROBIOLOGY

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One

Helkesimastix marina n. sp. (Cercozoa: Sainouroidea superfam. n.) a Gliding Zooflagellate of Novel Ultrastructure and Unusual Ciliary Behaviour

(2009) Thomas Cavalier-Smith et al.   PROTIST