Biology subjects

Torruella, G.

Publications and source records attributed to Torruella, G..

8 recordsLinked to original sources

bioRxiv2025

Protists Exhibit Stronger and More Recent Oceanic Genetic Structure than Archaeplastida and Metazoa

The global distribution of biodiversity is shaped by a complex interplay of evolutionary history and ecological processes. While biogeographic patterns are well defined for animals and plants, the global distributions of protists remain unclear. A key question is whether protists follow the same broad biogeographic principles as macroscopic life. To address this, we compiled 88 marine COI metabarcoding studies performing population-genetic analyses across ocean basins. Our results reveal that most protist phyla exhibit pronounced genetic structure among oceans, a pattern exceeding that reported for Archaeplastida and Metazoa. This likely reflects recent, and potentially human-mediated, introductions, influencing protist dispersal and contemporary community assembly. By demonstrating that protist distributions are not historically cosmopolitan, our study supports the existence of common eukaryotic biogeographic patterns that transcend organismal size.

microbiology↗

bioRxiv2024

Phylogenomics of neglected flagellated protists supports a revised eukaryotic tree of life

Eukaryotes evolved from prokaryotic predecessors in the early Proterozoic1,2 and radiated from their already complex last common ancestor3, diversifying into several supergroups with unresolved deep evolutionary connections4. They evolved extremely diverse lifestyles, playing crucial roles in the carbon cycle5,6. Heterotrophic flagellates are arguably the most diverse eukaryotes4,7-9 and often occupy basal positions in phylogenetic trees. However, many of them remain undersampled4,10 and/or incertae sedis4,11-18. Progressive improvement of phylogenomic methods and a wider protist sampling have reshaped and consolidated major clades in the eukaryotic tree13-19. This is illustrated by the Opimoda14, one of the largest eukaryotic supergroups (Amoebozoa, Ancyromonadida, Apusomonadida, Breviatea, CRuMs, Malawimonadida, and Opisthokonta -including animals and fungi-)4,14,19-22. However, their deepest evolutionary relationships still remain uncertain. Here, we sequenced transcriptomes of poorly studied flagellates23,24 (fourteen apusomonads25,26, seven ancyromonads27 and one cultured Mediterranean strain of Meteora sporadica17) and conducted comprehensive phylogenomics analyses with an expanded taxon sampling of early-branching protists. Our findings support the monophyly of Opimoda, with CRuMs being sister to the Amorphea (amoebozoans, breviates, apusomonads, and opisthokonts), and ancyromonads and malawimonads forming a moderately supported clade. By mapping key complex phenotypic traits onto this phylogenetic framework, we infer an opimodan biflagellate ancestor with an excavate-like feeding groove, which ancyromonads subsequently lost. While breviates and apusomonads retained the ancestral biflagellate state, some early-diverging Amorphea lost one or both flagella, facilitating the evolution of amoeboid morphologies, novel feeding modes, and palintomic cell division resulting in multinucleated cells. These innovations likely facilitated the subsequent evolution of fungal and metazoan multicellularity.

evolutionary biology↗

bioRxiv2023

Molecular and morphological characterisation of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida

Ancyromonads are small biflagellated protists with a bean-shaped morphology. They are cosmopolitan in marine, freshwater and soil environments, where they attach to surfaces while feeding on bacteria. These poorly known grazers stand out by their uncertain phylogenetic position in the tree of eukaryotes, forming a deep-branching orphan lineage that is considered key to better understanding the early evolution of eukaryotes. Despite their ecological and evolutionary interest, only limited knowledge exists about their true diversity. Here, we aimed to better characterise ancyromonads by integrating environmental surveys with behavioural observation and description of cell morphology, for which sample isolation and culturing is indispensable. We studied 18 ancyromonad strains, including 14 new isolates and 7 new species. Most of them belong to three new and genetically divergent genera: Caraotamonas, Nyramonas, and Olneymonas (encompassing 4 species). The remaining three new species belong to the already known genera Fabomonas and Ancyromonas. We also raised Striomonas, formerly a subgenus of Nutomonas, to full genus status, based on morphological and phylogenetic grounds. For all these new species, we studied their morphology under light and electron microscopy and carried out molecular phylogenetic analyses, including as well 18S rRNA gene sequences from several environmental surveys. Based on these analyses, we have updated the taxonomy of Ancyromonadida.

microbiology↗

bioRxiv2023

High quality genome and transcriptome data for two new species of Mantamonas, a deep-branching eukaryote clade

Mantamonads were long considered to represent an "orphan" lineage in the tree of eukaryotes, likely branching near the most frequently assumed position for the root of eukaryotes. Recent phylogenomic analyses have placed them as part of the "CRuMs" supergroup, along with collodictyonids and rigifilids. This supergroup appears to branch at the base of Amorphea, making it of special importance for understanding the deep evolutionary history of eukaryotes. However, the lack of representative species and complete genomic data associated with them has hampered the investigation of their biology and evolution. Here, we isolated and described two new species of mantamonads, Mantamonas vickermani sp. nov. and Mantamonas sphyraenae sp. nov., for each of which we generated transcriptomic sequence data, as well as a high-quality genome for the latter. The estimated size of the M. sphyraenae genome is 25 Mb; our de novo assembly appears to be highly contiguous and complete with 9,416 predicted protein-coding genes. This near-chromosome-scale genome assembly is the first described for the CRuMs supergroup.

genomics↗

bioRxiv2022

Expanding the molecular and morphological diversity of Apusomonadida, a deep-branching group of gliding bacterivorous protists

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 indicate that apusomonads are genetically diverse, few species have been described. Here, we morphologically characterize eleven new apusomonad strains. Based on molecular phylogenetic analyses of the rRNA gene operon, we describe four new strains of the known species Multimonas media, Podomonas capensis, Apusomonas proboscidea and Apusomonas australiensis, and rename Thecamonas oxoniensis as Mylnikovia oxoniensis n. gen., n. comb. Additionally, we describe four new genera and six new species: Catacumbia lutetiensis n. gen. n. sp., Cavaliersmithia chaoae n. gen. n. sp., Singekia montserratensis n. gen. n. sp., Singekia franciliensis n. gen. n. sp., Karpovia croatica n. gen. n. sp. and Chelonemonas dolani n. sp. Our comparative analysis suggests that apusomonad ancestor was a fusiform biflagellate with a dorsal pellicle, a plastic ventral surface and a sleeve covering the anterior flagellum, that thrived in marine, possibly oxygen-poor, environments. It likely had a complex cell cycle with dormant and multiple fission stages, and sex. Our results extend known apusomonad diversity, allow updating their taxonomy, and provide elements to understand early eukaryotic evolution.

microbiology↗

bioRxiv2021

Comparative proteogenomics deciphers the origin and evolution of eukaryotic chromatin

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 archaea. Proteomics uncovers the existence of histone post-translational modifications in Archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (e.g., methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.

evolutionary biology↗

bioRxiv2020

Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota

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 and Sanchytrium tribonematis, showed that they formed a monophyletic group without close affinity with known fungal clades. Here, we sequence single-cell genomes for both species to assess their phylogenetic position and evolution. Phylogenomic analyses using different protein datasets and a comprehensive taxon sampling result in an almost fully-resolved fungal tree, with Chytridiomycota as sister to all other fungi, and sanchytrids forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Comparative genomic analyses across fungi and their allies (Holomycota) reveal an atypically reduced metabolic repertoire for sanchytrids. We infer three main independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. Based on sanchytrids phylogenetic position and unique traits, we propose the designation of a novel phylum, Sanchytriomycota. In addition, our results indicate that most of the hyphal morphogenesis gene repertoire of multicellular fungi had already evolved in early holomycotan lineages.

evolutionary biology↗

bioRxiv2017

The transcriptome of Paraphelidium tribonemae illuminates the ancestry of Fungi and Opisthosporidia

Aphelids constitute a group of diverse, yet poorly known, parasites of algae [1, 2]. Their life cycle and morphology resemble those of zoosporic fungi (chytrids) and rozellids (Cryptomycota/Rozellosporidia), another specious group of parasites of fungi and oomycetes [3, 4]. Unlike fungi, which are osmotrophs, aphelids and rozellids are phagotrophs, feeding on the hosts cytoplasm. Combined RNA polymerase and rRNA gene trees [5] suggested that aphelids and rozellids relate to Microsporidia, extremely reduced parasites with remnant mitochondria [6]. Accordingly, aphelids, rozellids and Microsporidia were proposed to form a monophyletic clade, called Opisthosporidia, sister to Fungi [1]. Microsporidia would have subsequently lost the ancestral opisthosporidian phagotrophy. However, the limited phylogenetic signal of those genes combined with microsporidian fast-evolving sequences have resulted in incongruent tree topologies, showing either rozellids [5, 7] or aphelids [8] as the earliest-branching lineages of Opisthosporidia. We have generated the first transcriptome data for one aphelid species, Paraphelidium tribonemae [2]. In-depth multi-gene phylogenomic analyses using various protein datasets place aphelids in a deep, pivotal position as a sister group to Fungi, making Opisthosporidia paraphyletic. We infer a rich, free-living-like proteome for P. tribonemae, which includes cellulases likely involved in algal cell-wall penetration, enzymes involved in chitin biosynthesis and several metabolic pathways that were lost in the comparatively reduced Rozella allomycis genome [9]. Our results suggest that Fungi evolved from a complex phagotrophic opisthosporidian ancestor, likely a specialized endobiotic predator, which became osmotrophic at the fungal root and evolved towards phagotrophic parasitism in the rozellid/microsporidian line.

evolutionary biology↗