Guifré Torruella

Guifré Torruella
Barcelona Supercomputing Center · Department of Life Sciences

Biology

About

74
Publications
17,399
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2,088
Citations
Citations since 2016
55 Research Items
1860 Citations
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Introduction
As an evolutionary protistologist, my goal is to improve our knowledge on the origin & early eukaryote evolution, from its last common ancestor to our current biodiversity. My research involves sampling and culturing protists, sequencing and analysing their transcriptomes and genomes to tackle phylogenetic and comparative genomics questions.
Additional affiliations
March 2021 - present
Barcelona Supercomputing Center
Position
  • PostDoc Position
February 2015 - February 2021
Université Paris-Sud 11
Position
  • PostDoc Position
Description
  • http://www.ese.u-psud.fr/rubrique7.html?lang=fr
September 2009 - December 2014
Universitat de Barcelona
Position
  • PhD Student
Description
  • http://www.multicellgenome.com/
Education
October 2009 - December 2014
University of Barcelona
Field of study
  • Genètica
September 2004 - June 2009

Publications

Publications (74)
Article
Apusomonads are cosmopolitan bacterivorous biflagellate protists usually gliding on freshwater and marine sediment or wet soils. These nanoflagellates form a sister lineage to opisthokonts and may have retained ancestral features helpful to understanding the early evolution of this large supergroup. Although molecular environmental analyses indicat...
Preprint
Full-text available
Apusomonads are cosmopolitan bacterivorous biflagellate protists usually gliding on freshwater and marine sediment or wet soils. These nanoflagellates form a sister lineage to opisthokonts and may have retained ancestral features helpful to understanding the early evolution of this large supergroup. Although molecular environmental analyses indicat...
Poster
Early eukaryotic evolution is poorly understood. Lacking a fossil record, comparative genomics allows us to reconstruct the evolutionary history of species and their genes, infer the order of evolutionary changes and their functional implications. Thanks to sequencing transcriptomes and genomes of protists, it becomes possible to unveil the evoluti...
Article
The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relations...
Article
Full-text available
Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and ar...
Article
Full-text available
Nucleariids are a small group of free-living heterotrophic amoebae. Although these organisms present a variety of cell sizes and cell coverings, they are mostly spherical cells with radiating filopodia, sometimes with several nuclei. Nuclearia, the genus that gives the name to the group, contains species that are opportunistic consumers of detritus...
Preprint
Full-text available
Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically-comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and ar...
Article
Full-text available
Compared to multicellular fungi and unicellular yeasts, unicellular fungi with free-living flagellated stages (zoospores) remain poorly known and their phylogenetic position is often unresolved. Recently, rRNA gene phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and long kinetosomes, the sanchytrids Amoeboradix gromovi...
Preprint
Compared to well-known multicellular fungi and unicellular yeast, unicellular fungi with zoosporic, free-living flagellated stages remain poorly known and their phylogenetic position is often unresolved. Recently, 18S+28S rRNA gene molecular phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and record-long simplified kin...
Article
Full-text available
Nucleariid amoebae (Opisthokonta) have been known since the nineteenth century but their diversity and evolutionary history remain poorly understood. To overcome this limitation, we have obtained genomic and transcriptomic data from three Nuclearia , two Pompholyxophrys and one Lithocolla species using traditional culturing and single-cell genome (...
Poster
Full-text available
Aphelids are a poorly known group of parasitoids of algae that have raised considerable interest due to their pivotal phylogenetic position in the holomycotan branch of the opisthokonts. Based on 18S rRNA genes, they form a monophyletic group with Rozellosporidia (Cryptomycota) and the highly derived Microsporidia. This clade has been re-classified...
Article
Full-text available
Aphelids are little-known phagotrophic parasites of algae whose life cycle and morphology resemble those of the parasitic rozellids (Cryptomycota, Rozellomycota). In previous phylogenetic analyses of RNA polymerase and rRNA genes, aphelids, rozellids and Microsporidia (parasites of animals) formed a clade, named Opisthosporidia, which appeared as t...
Article
Full-text available
This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening...
Article
Full-text available
Metchnikovellids are highly specialized hyperparasites, which infect and reproduce inside gregarines (Apicomplexa) inhabiting marine invertebrates. Their phylogenetic affiliation was under constant discussion until recently, when analysis of the first near-complete metchnikovellid genome, that of Amphiamblys sp., placed it in a basal position with...
Preprint
Full-text available
Aphelids are poorly known phagotrophic parasites of algae whose life cycle and morphology resemble those of the widely diverse parasitic rozellids (Cryptomycota, Rozellomycota). In previous phylogenetic analyses of RNA polymerase and rRNA genes, aphelids and rozellids formed a monophyletic group together with the extremely reduced parasitic Microsp...
Presentation
Full-text available
Aphelids are a fairly unknown group of parasitoids of algae that have raised considerable interest due to their pivotal phylogenetic position in the holomycotan branch of the opisthokonts. Based on 18S rRNA genes, they form a monophyletic group with Rozellosporidia (Cryptomycota) and Microsporidia. This clade has been named as Opisthosporidia, whic...
Article
Full-text available
Some protists with microsporidian‐like cell biological characters, including Mitosporidium, Paramicrosporidium, and Nucleophaga, have SSU rRNA gene sequences that are much less divergent than canonical Microsporidia. We analysed the phylogenetic placement and environmental diversity of microsporidian‐like lineages that group near the base of the fu...
Presentation
Full-text available
Although molecular phylogenetic studies revealed that the fungi lineage do not have any specific synapomorphies (Richards, Leonard, and Wideman 2017), several characteristics have been traditionally used to define fungi: osmotrophy as feeding mode, chitin cell walls, polar growth, etc. To understand the origins of such characteristics in fungi, we...
Presentation
Full-text available
Aphelids are a poorly known group of parasitoids of algae that have raised considerable interest due to their pivotal phylogenetic position in the holomycotan branch of the opisthokonts. Based on 18S rRNA genes, they form a monophyletic group with Rozellosporidia (Cryptomycota) and the highly derived Microsporidia. This clade has been re-classified...
Article
Full-text available
The opisthokonts constitute a eukaryotic supergroup divided into two main clades: the holozoans, which include animals and their unicellular relatives, and the holomycotans, which include fungi, opisthosporidians and nucleariids. Nucleariids are phagotrophic filose amoebae that phenotypically resemble more their distant holozoan cousins than their...
Article
Full-text available
Which genomic innovations underpinned the origin of multicellular animals is still an open debate. Here, we investigate this question by reconstructing the genome architecture and gene family diversity of ancestral premetazoans, aiming to date the emergence of animal-like traits. Our comparative analysis involves genomes from animals and their clos...
Data
Table of genome structure statistics, from the data-set of eukaryotic genomes used in the study.Includes genome size and portion of the genome covered by genes, exons, introns and intergenic regions. Used in Figures 1, 3 and 4.DOI: http://dx.doi.org/10.7554/eLife.26036.004
Data
BVD57 phylogenomic dataset (see (Torruella et al., 2015)), including 87 unaligned protein domains (with PFAM accession number) per species.Used in Figure 2.DOI: http://dx.doi.org/10.7554/eLife.26036.009
Data
Reconstruction of intron site evolutionary histories, using a rates-across-sites Markov model for intron evolution, with branch-specific gain and loss rates (Csurös, 2008).Used in Figures 5 and 6.DOI: http://dx.doi.org/10.7554/eLife.26036.021
Data
Reconstruction of the evolutionary histories of protein domain pairs gains within orthogroups, using a phylogenetic birth-and-death probabilistic model that accounts for gains, losses and duplications (Csurös, 2010).Used in Figures 7, 8, 9 and 10.DOI: http://dx.doi.org/10.7554/eLife.26036.029
Data
Annotated repetitive sequences from 10 unicellular Holozoa genomes.Includes transposable elements, simple repeats, low complexity regions and small RNAs. Used in Figure 3.DOI: http://dx.doi.org/10.7554/eLife.26036.012
Data
Reconstruction of the evolution of the NMD machinery (He and Jacobson, 2015) and key SR splicing factors (Plass et al., 2008).Used in Figure 5.DOI: http://dx.doi.org/10.7554/eLife.26036.022
Data
List of genome and transcriptome assemblies and annotations, including abbreviations, taxonomic classification and data sources.DOI: http://dx.doi.org/10.7554/eLife.26036.008
Data
List of annotated transposable element families in 10 unicellular Holozoa genomes, with copy counts.Used in Figure 3.DOI: http://dx.doi.org/10.7554/eLife.26036.013
Data
Reconstruction of the evolutionary histories of individual protein domains, using Dollo parsimony and accounting for gains and losses (Csurös, 2010).Used in Figures 7, 8, 9 and 10.DOI: http://dx.doi.org/10.7554/eLife.26036.030
Data
Rates of gain and loss of orthogroups for extant and ancestral eukaryotes, using a phylogenetic birth-and-death probabilistic model that accounts for gains, losses and duplications.Used in Figure 1.DOI: http://dx.doi.org/10.7554/eLife.26036.005
Data
List of annotated transposable element families shared between the genomes of 10 unicellular holozoans and 11 animals, including the number of species where the TE family is present.Three lists are included: all TE families present in any holozoan, a list restricted to the most abundant TE families accounting for 75% of all copies in each holozoan...
Data
Rates of gain and loss of intron sites for extant and ancestral eukaryotes, calculated for a rates-across-sites Markov model for intron evolution with branch-specific gain and loss rates (Csurös, 2008).Used in Figure 5.DOI: http://dx.doi.org/10.7554/eLife.26036.020
Data
Rates of gain and loss of protein domain pairs within a given orthogroup for extant and ancestral eukaryotes, calculated for a phylogenetic birth-and-death probabilistic model that accounts for gains, losses and duplications (Csurös, 2010).Used in Figures 7, 8 and 9.DOI: http://dx.doi.org/10.7554/eLife.26036.028
Data
Probability of emergence of protein domain combinations present in the LCA of Metazoa in previous ancestral nodes (from LCA of Metazoa to LCA of Unikonta/Amorphea).Only protein domain combinations with >90% presence probability in the LCA of Metazoa were included. Protein domain combinations that are not gained with >90% probability in any of the s...
Article
Aphelids remain poorly known parasitoids of algae and have recently raised considerable interest due to their phylogenetic position at the base of Holomycota. Together with Cryptomycota (Rozellosporidia) and Microsporidia, they have been recently re-classified as the Opisthosporidia, which constitutes the sister group to the fungi within the Holomy...
Article
Full-text available
Apusomonads are a mysterious group of heterotrophic gliding biflagellates branching deeply in the eukaryotic tree of life as sister group to opisthokonts (including animals, fungi and a variety of unicellular protists). Despite their evolutionary interest, their diversity and ecology remain largely unknown, with very few described species and envir...
Article
Aphelids are a poorly known group of parasitoids of algae that have raised considerable interest due to their pivotal phylogenetic position. Together with Cryptomycota and the highly derived Microsporidia, they have been recently re-classified as the Opisthosporidia, which constitute the sister group to the fungi within the Holomycota. Despite thei...
Presentation
Full-text available
Opisthokonts, one of the largest eukaryotic supergroups, is divided into two major clades: the Holozoa, encompassing animals and their unicellular relatives, and the Holomycota, including fungi and their unicellular relatives. The earliest-branching lineage in Holomycota, which has received many names (e.g. Nucleariidae, Cristidiscoidia, Discicrist...
Article
Full-text available
Graphical Abstract Highlights d Taxon-rich phylogenomics provides an evolutionary framework for the opisthokonts d Specialized osmotrophy evolved independently in fungi and animal relatives d Opisthokonts underwent independent secondary losses of the flagellum d The last opisthokont common ancestor had a complex repertoire of chitin synthases Corre...
Poster
Full-text available
Apusomonadida is a eukaryotic group of gliding biflagellates that prey on bacteria. Their diversity and biology remains fairly unknown, with only 10 species morphologically and molecularly described and few environmental sequences available on public databases. The clearly monophyletic clade of apusomonads comprises 5 known lineages, although the r...
Presentation
Full-text available
The differentiation between prokaryotes and eukaryotes is probably the most important structural separation in the history of life. Among the eukaryotes we find a broad biological diversity that encompasses unicellular and multicellular, autotrophic and heterotrophic lineages. In fact, a large part of the eukaryotic biological diversity, especially...
Article
Full-text available
Significance The root of eukaryote phylogeny formally represents the last eukaryotic common ancestor (LECA), but its position has remained controversial. Using new genome sequences, we revised and expanded two datasets of eukaryotic proteins of bacterial origin, which previously yielded conflicting views on the eukaryotic root. Analyses using state...
Article
Full-text available
Phosphotyrosine (pTyr) signaling is involved in development and maintenance of metazoans' multicellular body through cell-to-cell communication. Tyrosine kinases (TKs), tyrosine phosphatases, and other proteins relaying the signal compose the cascade. Domain architectures of the pTyr signaling proteins are diverse in metazoans, reflecting their com...
Article
Full-text available
Significance Independent transitions to multicellularity in eukaryotes involved the evolution of complex transcriptional regulation toolkits to control cell differentiation. By using comparative genomics, we show that plants and animals required richer transcriptional machineries compared with other eukaryotic multicellular lineages. We suggest thi...
Article
Full-text available
Significance The T-box transcription factors are key players in animal development and they were considered strictly animal-specific. We show that T-box genes have instead an important premetazoan evolutionary history, being present in several nonmetazoan unicellular taxa. Notably, we find that Capsaspora owczarzaki , a unicellular relative of anim...
Article
Full-text available
To reconstruct the evolutionary origin of multicellular animals from their unicellular ancestors, the genome sequences of diverse unicellular relatives are essential. However, only the genome of the choanoflagellate Monosiga brevicollis has been reported to date. Here we completely sequence the genome of the filasterean Capsaspora owczarzaki, the c...
Data
Full-text available
Supplementary Figures S1-S36, Supplementary Tables S1-S9, Supplementary Notes 1-5 and Supplementary References
Presentation
Full-text available
The MultiCellGenome Lab1 aims to elucidate the evolutionary transition between unicellular and multicellular organisms in the animal lineage. Using extant unicellular species phylogenetically related to metazoa, we look for genes related with multicellular functions such as cell adhesion, cell communication, growth control, etc. To do so, we need a...
Presentation
Full-text available
The MultiCellGenome Lab1 aims to elucidate the evolutionary transition between unicellular and multicellular organisms in the animal lineage. Using extant unicellular species phylogenetically related to metazoa, we look for genes related with multicellular functions such as cell adhesion, cell communication, growth control, etc. To do so, we need a...
Article
Full-text available
Many of the eukaryotic phylogenomic analyses published to date were based on alignments of hundreds to thousands of genes. Frequently, in such analyses, the most realistic evolutionary models currently available are often used to minimize the impact of systematic error. However, controversy remains over whether or not idiosyncratic gene family dyna...
Poster
Full-text available
It was known that lysine is synthesized in 2 pathways, the diaminopimelate (DAP) in eubacteria, plants and algae, and the α-aminoadipate (AAA) almost exclusive to fungi (figure 1). Sumathi et al. 2006 found in Corallochytrium limacisporum a key gene of the AAA pathway, the α-aminoadipate reductase gene (AAR), and they proposed that was a molecular...
Article
Full-text available
Lysine biosynthesis occurs in two ways: the diaminopimelate (DAP) pathway and the alpha-aminoadipate (AAA) pathway. The former is present in eubacteria, plants, and algae, whereas the latter was understood to be almost exclusive to fungi. The recent finding of the alpha-aminoadipate reductase (AAR) gene, one of the core genes of the AAA pathway, in...

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Projects

Projects (3)
Project
To obtain and analyse high-quality genome data for biflagellated bacterivorous protists to study from the early eukaryote diversification to the origin of opisthokonts. In particular, we'll focus on Apusomonadida, a poorly studied lineage of gliding protists thriving in most water bodies around the world, marine, freshwater and soil. Their pivotal phylogenetic position as the sister lineage to Opisthokonta, as well as their affinities with other eukaryote protist groups closer to the root of the tree, makes them fundamental to include in such evolutionary studies.