Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae

Phylogenomic Insights into the Origin of Primary Plastids

(2021) Iker Irisarri et al.   SYSTEMATIC BIOLOGY

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

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

Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis

(2020) Chihiro Sarai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic insights into plastid evolution

(2020) Shannon J Sibbald et al.   Genome Biology and Evolution

The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants

(2020) Linzhou Li et al.   Nature Ecology & Evolution

Five Non-motile Dinotom Dinoflagellates of the Genus Dinothrix

(2020) Norico Yamada et al.   Frontiers in Plant Science

Principles of plastid reductive evolution illuminated by nonphotosynthetic chrysophytes

(2019) Richard G. Dorrell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Diatom genes originating from red and green algae: Implications for the secondary endosymbiosis models

(2019) A.A. Morozov et al.   Marine Genomics

Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments

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

Non-photosynthetic predators are sister to red algae

(2019) Ryan M. R. Gawryluk et al.   NATURE

Multiple Independent Origins of Apicomplexan-Like Parasites

(2019) Varsha Mathur et al.   CURRENT BIOLOGY

Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases

(2019) Anurag Priyam et al.   MOLECULAR BIOLOGY AND EVOLUTION

A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators

(2019) David M. Needham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis

(2019) Elisabeth Hehenberger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2019) Jan Janouškovec et al.   eLife

PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics

(2019) Max E Schön et al.   BIOINFORMATICS

Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists

(2019) Jeremy G. Wideman et al.   Nature Microbiology

The New Tree of Eukaryotes

(2019) Fabien Burki et al.   TRENDS IN ECOLOGY & EVOLUTION

My Secret Life

(2018) Mary-Dell Chilton   Annual Review of Plant Biology

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

(2018) Gordon Lax et al.   NATURE

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

(2017) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads

(2017) Daniel H. Huson et al.   Microbiome

Functional Relationship between a Dinoflagellate Host and Its Diatom Endosymbiont

(2016) Elisabeth Hehenberger et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Genomic perspectives on the birth and spread of plastids: Fig. 1.

(2015) John M. Archibald   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate

(2015) Sebastian G. Gornik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

The rise and fall of Picobiliphytes: How assumed autotrophs turned out to be heterotrophs

(2014) David Moreira et al.   BIOESSAYS

Toward an empirical framework for interpreting plastid evolution

(2014) John W. Stiller   JOURNAL OF PHYCOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista

(2014) Akinori Yabuki et al.   Scientific Reports

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Endosymbiotic Gene Transfer in Tertiary Plastid-Containing Dinoflagellates

(2013) Fabien Burki et al.   EUKARYOTIC CELL

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

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

Picomonas judraskeda Gen. Et Sp. Nov.: The First Identified Member of the Picozoa Phylum Nov., a Widespread Group of Picoeukaryotes, Formerly Known as ‘Picobiliphytes’

(2013) Ramkumar Seenivasan et al.   PLoS One

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

(2013) P. M. Shih 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

Re-evaluating the Green versus Red Signal in Eukaryotes with Secondary Plastid of Red Algal Origin

(2012) Fabien Burki et al.   Genome Biology and Evolution

Reevaluating the Green Contribution to Diatom Genomes

(2012) Philippe Deschamps et al.   Genome Biology and Evolution

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

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

Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade

(2011) J. Viklund et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists

(2011) H. S. Yoon et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

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

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

Plastid Evolution

(2008) Sven B. Gould et al.   Annual Review of Plant Biology

Widespread distribution of a unique marine protistan lineage

(2008) Marie L. Cuvelier et al.   ENVIRONMENTAL MICROBIOLOGY

The origin of plastids

(2008) C.J Howe et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

EEF2 Analysis Challenges the Monophyly of Archaeplastida and Chromalveolata

(2008) Eunsoo Kim et al.   PLoS One