Daniel Tamarit
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View article: WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing
WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing Open
Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylogenetic inference, particularly in deep…
View article: Guyparkeria halophila: Novel cell platform for the efficient valorization of carbon dioxide and thiosulfate into ectoine
Guyparkeria halophila: Novel cell platform for the efficient valorization of carbon dioxide and thiosulfate into ectoine Open
Utilizing carbon dioxide (CO2) for valuable chemical production is key to a circular economy. Current processes are costly due to limited microorganism use, low-value products, and the need for affordable energy. This study addresses these…
View article: Structure-based inference of eukaryotic complexity in Asgard archaea
Structure-based inference of eukaryotic complexity in Asgard archaea Open
Asgard archaea played a key role in the origin of the eukaryotic cell. While previous studies found that Asgard genomes encode diverse eukaryotic signature proteins (ESPs), representing homologs of proteins that play important roles in the…
View article: RNA-guided RNA silencing by an Asgard archaeal Argonaute
RNA-guided RNA silencing by an Asgard archaeal Argonaute Open
Argonaute proteins are the central effectors of RNA-guided RNA silencing pathways in eukaryotes, playing crucial roles in gene repression and defense against viruses and transposons. Eukaryotic Argonautes are subdivided into two clades: AG…
View article: Microbial Diversity and Open Questions about the Deep Tree of Life
Microbial Diversity and Open Questions about the Deep Tree of Life Open
In this perspective, we explore the transformative impact and inherent limitations of metagenomics and single-cell genomics on our understanding of microbial diversity and their integration into the Tree of Life. We delve into the key chal…
View article: RNA-guided RNA silencing by an Asgard archaeal Argonaute
RNA-guided RNA silencing by an Asgard archaeal Argonaute Open
Eukaryotic Argonaute proteins achieve gene repression and defense against viruses and transposons by RNA-guided RNA silencing. By contrast, known prokaryotic Argonautes adopt single-stranded DNA as guides and/or targets, leaving the evolut…
View article: Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switching
Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switching Open
Our knowledge of archaeal diversity and evolution has expanded rapidly in the past decade. However, hardly any genomes of the phylum Korarchaeota have been obtained due to the difficulty in accessing their natural habitats and – possibly –…
View article: Lifestyle transitions in endosymbiosis
Lifestyle transitions in endosymbiosis Open
A recommendation of: Diego Santos-Garcia, Olivier Morel, Hélène Henri, Adil El Filali, Marie Buysse, Valérie Noël, Karen D. McCoy, Yuval Gottlieb, Lisa Klasson, Lionel Zenner, Olivier Duron, Fabrice Vavre Genomic Changes During the Evoluti…
View article: Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes Open
In the ongoing debates about eukaryogenesis, the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors, members of the Asgard archaea play a key role as the closest archaeal relatives of e…
View article: Supplementary Data for <strong>Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes.</strong> Eme, Tamarit, Caceres,... and Ettema. <em>Nature </em>2023.<strong> </strong> https://www.nature.com/articles/s41586-023-06186-2
Supplementary Data for <strong>Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes.</strong> Eme, Tamarit, Caceres,... and Ettema. <em>Nature </em>2023.<strong> </strong> https://www.nature.com/articles/s41586-023-06186-2 Open
Supplementary Figures: High-resolution files. Proteomes: Asgard archaeal MAGs predicted proteomes. OrthoClusters: orthologous groups used for ALE inferences. Phylogenomics_datasets: Individual and concatenated alignments for the A64 and…
View article: Supplementary Data for Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
Supplementary Data for Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes Open
Supplementary Figures: High-resolution files Proteomes: Asgard archaeal MAGs predicted proteomes. OrthoClusters: orthologous groups used for ALE inferences Phylogenomics_datasets: Individual and concatenated alignments for the A64 and A…
View article: Phylogenomic datasets
Phylogenomic datasets Open
A64_individual_*: individual protein alignments and ML phylogenetic trees constructed with the A64 taxon sampling. A64_concatenation*: concatenated alignments, ML and bayesian phylogenetic trees constructed with the A64 taxon sampling. A17…
View article: Genome Evolution of a Symbiont Population for Pathogen Defense in Honeybees
Genome Evolution of a Symbiont Population for Pathogen Defense in Honeybees Open
The honeybee gut microbiome is thought to be important for bee health, but the role of the individual members is poorly understood. Here, we present closed genomes and associated mobilomes of 102 Apilactobacillus kunkeei isolates obtained …
View article: Prospective CO2 and CO bioconversion into ectoines using novel microbial platforms
Prospective CO2 and CO bioconversion into ectoines using novel microbial platforms Open
Microbial conversion of CO 2 and CO into chemicals is a promising route that can contribute to the cost-effective reduction of anthropogenic green house and waste gas emissions and create a more circular economy. However, the biotechnologi…
View article: A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses Open
Dataset including genome sequences (fasta nucleotide, fasta amino acid of predicted ORFs, and annotation files) and phylogenetic data (sequences, trimmed alignments, raw tree). For details, see Tamarit et al (2022) Nat Microbiol (In PressD…
View article: MAPR origins reveal a new class of prokaryotic cytochrome b<sub>5</sub> proteins and possible role in eukaryogenesis
MAPR origins reveal a new class of prokaryotic cytochrome b<sub>5</sub> proteins and possible role in eukaryogenesis Open
The multiple functions of PGRMC1, the archetypal heme-binding eukaryotic MAPR family member, include steroidogenic regulation, membrane trafficking, and steroid responsiveness. The interrelationships between these functions are currently p…
View article: A closed <i>Candidatus</i> Odinarchaeum genome exposes Asgard archaeal viruses
A closed <i>Candidatus</i> Odinarchaeum genome exposes Asgard archaeal viruses Open
Asgard archaea have recently been identified as the closest archaeal relatives of eukaryotes. Their ecology remains enigmatic, and their virome, completely unknown. Here, we describe the closed genome of Ca . Odinarchaeum yellowstonii LCB_…
View article: Characterisation of the Ubiquitin-ESCRT pathway in Asgard archaea sheds new light on origins of membrane trafficking in eukaryotes
Characterisation of the Ubiquitin-ESCRT pathway in Asgard archaea sheds new light on origins of membrane trafficking in eukaryotes Open
SUMMARY The ESCRT machinery performs a critical role in membrane remodelling events in all eukaryotic cells, including in membrane trafficking, membrane repair, cytokinetic abscission, in viral egress, and in the generation of extracellula…
View article: Chlamydial contribution to anaerobic metabolism during eukaryotic evolution
Chlamydial contribution to anaerobic metabolism during eukaryotic evolution Open
Genomic analysis of newly identified Chlamydiae reveals that their ancestors contributed to the evolution of anaerobic eukaryotes.
View article: Rethinking microbial symbioses
Rethinking microbial symbioses Open
When Anton de Bary famously coined the term symbiosis to allude to 'dissimilarly named organisms living together', he was convinced that the importance and ubiquity of symbioses had already been observed:Was ich vorbrachte,
View article: Marine sediments illuminate Chlamydiae diversity and evolution
Marine sediments illuminate Chlamydiae diversity and evolution Open
The bacterial phylum Chlamydiae, which is so far comprised of obligate symbionts of eukaryotic hosts, are well-known as human and animal pathogens 1-3 . However, the Chlamydiae also include so-called environmental lineages 4-6 that primari…
View article: Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium
Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium Open
Bacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their t…
View article: Origin and Evolution of the Bartonella Gene Transfer Agent
Origin and Evolution of the Bartonella Gene Transfer Agent Open
Gene transfer agents (GTAs) are domesticated bacteriophages that have evolved into molecular machines for the transfer of bacterial DNA. Despite their widespread nature and their biological implications, the mechanisms and selective forces…