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View article: <i>De Novo</i> Genome Sequence Assembly of the RNAi-Tractable <i>Paramecium bursaria</i> 186b: An Endosymbiotic Model System
<i>De Novo</i> Genome Sequence Assembly of the RNAi-Tractable <i>Paramecium bursaria</i> 186b: An Endosymbiotic Model System Open
How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a useful approach to understand how endosymbiotic functions can arise. The ciliate protist Parameci…
View article: Evolutionary Insights into the Length Variation of DNA Damage Response Proteins Across Eukaryotes
Evolutionary Insights into the Length Variation of DNA Damage Response Proteins Across Eukaryotes Open
Across the tree of life, DNA damage response (DDR) proteins play a pivotal, yet dichotomous role in organismal development and evolution. Here, we present a comprehensive analysis of 432 DDR proteins encoded by 68 genomes, including that o…
View article: Reconstructing the last common ancestor of all eukaryotes
Reconstructing the last common ancestor of all eukaryotes Open
Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (…
View article: Immune-like glycan-sensing and horizontally-acquired glycan-processing orchestrate host control in a microbial endosymbiosis
Immune-like glycan-sensing and horizontally-acquired glycan-processing orchestrate host control in a microbial endosymbiosis Open
Endosymbiosis was a key factor in the evolution of eukaryotic cellular complexity. Yet the mechanisms that allow host regulation of intracellular symbionts, a pre-requisite for stable endosymbiosis and subsequent organelle evolution, are l…
View article: <i>De novo</i>genome sequence assembly of the RNAi-tractable endosymbiosis model system<i>Paramecium bursaria</i>186b reveals factors shaping intron repertoire
<i>De novo</i>genome sequence assembly of the RNAi-tractable endosymbiosis model system<i>Paramecium bursaria</i>186b reveals factors shaping intron repertoire Open
How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a useful approach to understand how endosymbiotic functions can arise. The ciliate protist Parameci…
View article: Duplication and neofunctionalization of a horizontally transferred xyloglucanase as a facet of the Red Queen coevolutionary dynamic
Duplication and neofunctionalization of a horizontally transferred xyloglucanase as a facet of the Red Queen coevolutionary dynamic Open
Oomycete protists share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a distant region of the tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-…
View article: Duplication and neofunctionalization of a horizontally-transferred xyloglucanase as a facet of the red queen co-evolutionary dynamic
Duplication and neofunctionalization of a horizontally-transferred xyloglucanase as a facet of the red queen co-evolutionary dynamic Open
Oomycetes are heterotrophic protists that share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a separate and distant region of the eukaryotic tree of life. It has been suggested that multi…
View article: A Genome Sequence Assembly of the Phototactic and Optogenetic Model Fungus <i>Blastocladiella emersonii</i> Reveals a Diversified Nucleotide-Cyclase Repertoire
A Genome Sequence Assembly of the Phototactic and Optogenetic Model Fungus <i>Blastocladiella emersonii</i> Reveals a Diversified Nucleotide-Cyclase Repertoire Open
The chytrid fungus Blastocladiella emersonii produces spores with swimming tails (zoospores); these cells can sense and swim toward light. Interest in this species stems from ongoing efforts to develop B. emersonii as a model for understan…
View article: A diversified and segregated mRNA spliced-leader system in the parasitic Perkinsozoa
A diversified and segregated mRNA spliced-leader system in the parasitic Perkinsozoa Open
Spliced-leader trans -splicing (SLTS) has been described in distantly related eukaryotes and acts to mark mRNAs with a short 5′ exon, giving different mRNAs identical 5′ sequence-signatures. The function of these systems is obscure. Perkin…
View article: The history and organization of the Workshop on Population and Speciation Genomics
The history and organization of the Workshop on Population and Speciation Genomics Open
With the advent of high-throughput genome sequencing, bioinformatics training has become essential for research in evolutionary biology and related fields. However, individual research groups are often not in the position to teach students…
View article: 18S Fungal Tree and Alignments
18S Fungal Tree and Alignments Open
18S fungal alignment and tree
View article: sGC cyclase alignment and tree
sGC cyclase alignment and tree Open
Alignment and tree
View article: Single-cell genomics uncovers the canonical mitochondrial genome of a deep-branching euglenozoan
Single-cell genomics uncovers the canonical mitochondrial genome of a deep-branching euglenozoan Open
Euglenozoan SAG assemblies.
View article: Emergent RNA–RNA interactions can promote stability in a facultative phototrophic endosymbiosis
Emergent RNA–RNA interactions can promote stability in a facultative phototrophic endosymbiosis Open
Significance Stable endosymbiosis between eukaryotic microbes has driven the evolution of further cellular complexity. Yet the mechanisms that can act to stabilize an emergent eukaryote–eukaryote endosymbiosis are unclear. Using the model …
View article: Emergent RNA-RNA interactions can promote stability in a nascent phototrophic endosymbiosis
Emergent RNA-RNA interactions can promote stability in a nascent phototrophic endosymbiosis Open
Eukaryote-eukaryote endosymbiosis was responsible for the spread of chloroplast (plastid) organelles. Stability is required for the metabolic and genetic integration that drives the establishment of new organelles, yet the mechanisms which…
View article: Characterization of the RNA-interference pathway as a tool for reverse genetic analysis in the nascent phototrophic endosymbiosis, <i>Paramecium bursaria</i>
Characterization of the RNA-interference pathway as a tool for reverse genetic analysis in the nascent phototrophic endosymbiosis, <i>Paramecium bursaria</i> Open
Endosymbiosis was fundamental for the evolution of eukaryotic complexity. Endosymbiotic interactions can be dissected through forward- and reverse-genetic experiments, such as RNA-interference (RNAi). However, distinguishing small (s)RNA p…
View article: Comparative genomics reveals new functional insights in uncultured MAST species
Comparative genomics reveals new functional insights in uncultured MAST species Open
Heterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences…
View article: Supplementary Tables from Characterization of the RNA-interference pathway as a tool for reverse genetic analysis in the nascent phototrophic endosymbiosis, <i>Paramecium bursaria</i>
Supplementary Tables from Characterization of the RNA-interference pathway as a tool for reverse genetic analysis in the nascent phototrophic endosymbiosis, <i>Paramecium bursaria</i> Open
Tables S1–5
View article: Additional file 1 of Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans
Additional file 1 of Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans Open
Additional file 1: Table S1. General statistics of assembled SAGs. Table S2. Proportion of mtDNA in SAGs. Table S3. List of proteins searched in EU17/18 reassembly. +, presence; +?, uncertain presence; -, absence.
View article: Characterisation of the RNA-interference pathway as a Tool for Genetics in the Nascent Phototrophic Endosymbiosis,<i>Paramecium bursaria</i>
Characterisation of the RNA-interference pathway as a Tool for Genetics in the Nascent Phototrophic Endosymbiosis,<i>Paramecium bursaria</i> Open
Endosymbiosis was fundamental for the evolution of eukaryotic complexity. Endosymbiotic interactions can be dissected through forward and reverse-genetic experiments, such as RNA-interference (RNAi). However, distinguishing small (s)RNA pa…
View article: Alignment files
Alignment files Open
- Alignment references in Fig.4,5,S6,S7
View article: Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink
Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink Open
Marine sediments are one of the largest carbon reservoir on Earth, yet the microbial communities, especially the eukaryotes, that drive these ecosystems are poorly characterised. Here, we report implementation of a sampling system that ena…
View article: A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure
A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure Open
Euglenozoa comprises euglenids, kinetoplastids, and diplonemids, with each group exhibiting different and highly unusual mitochondrial genome organizations. Although they are sister groups, kinetoplastids and diplonemids have very distinct…
View article: A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators
A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators Open
Giant viruses are remarkable for their large genomes, often rivaling those of small bacteria, and for having genes thought exclusive to cellular life. Most isolated to date infect nonmarine protists, leaving their strategies and prevalence…
View article: Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases
Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases Open
Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-ce…