1
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Yubuki N, Torruella G, Galindo LJ, Heiss AA, Ciobanu MC, Shiratori T, Ishida KI, Blaz J, Kim E, Moreira D, López-García P, Eme L. Molecular and morphological characterization of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida. J Eukaryot Microbiol 2023; 70:e12997. [PMID: 37606230 DOI: 10.1111/jeu.12997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 08/23/2023]
Abstract
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 a better understanding of the early evolution of eukaryotes. Despite their ecological and evolutionary interest, only limited knowledge exists about their true diversity. Here, we aimed to characterize ancyromonads better by integrating environmental surveys with behavioral observation and description of cell morphology, for which sample isolation and culturing are indispensable. We studied 18 ancyromonad strains, including 14 new isolates and seven new species. We described three new and genetically divergent genera: Caraotamonas, Nyramonas, and Olneymonas, together encompassing four 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, on morphological and phylogenetic grounds. We studied the morphology of diverse ancyromonads under light and electron microscopy and carried out molecular phylogenetic analyses, also including 18S rRNA gene sequences from several environmental surveys. Based on these analyses, we have updated the taxonomy of Ancyromonadida.
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Affiliation(s)
- Naoji Yubuki
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Guifré Torruella
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Luis Javier Galindo
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aaron A Heiss
- Department of Invertebrate Zoology, American Museum of Natural History, New York City, New York, USA
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | | | - Takashi Shiratori
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ken-Ichiro Ishida
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Jazmin Blaz
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Eunsoo Kim
- Department of Invertebrate Zoology, American Museum of Natural History, New York City, New York, USA
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Laura Eme
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
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2
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Milner DS, Galindo LJ, Irwin NAT, Richards TA. Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes. Annu Rev Microbiol 2023; 77:45-66. [PMID: 36944262 DOI: 10.1146/annurev-micro-032421-115538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, the ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire.
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Affiliation(s)
- David S Milner
- Department of Biology, University of Oxford, Oxford, United Kingdom;
| | | | - Nicholas A T Irwin
- Department of Biology, University of Oxford, Oxford, United Kingdom;
- Merton College, University of Oxford, Oxford, United Kingdom
| | - Thomas A Richards
- Department of Biology, University of Oxford, Oxford, United Kingdom;
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3
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Blaz J, Galindo LJ, Heiss AA, Kaur H, Torruella G, Yang A, Alexa Thompson L, Filbert A, Warring S, Narechania A, Shiratori T, Ishida KI, Dacks JB, López-García P, Moreira D, Kim E, Eme L. One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade. Sci Data 2023; 10:603. [PMID: 37689692 PMCID: PMC10492846 DOI: 10.1038/s41597-023-02488-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/18/2023] [Indexed: 09/11/2023] Open
Abstract
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.
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Affiliation(s)
- Jazmin Blaz
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Luis Javier Galindo
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Aaron A Heiss
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Department of Oceanography, Kyungpook National University, Daegu, South Korea
| | - Harpreet Kaur
- Division of Infectious Disease, Department of Medicine, University of Alberta and Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Guifré Torruella
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Ashley Yang
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - L Alexa Thompson
- Division of Infectious Disease, Department of Medicine, University of Alberta and Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Alexander Filbert
- Division of Infectious Disease, Department of Medicine, University of Alberta and Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Sally Warring
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Apurva Narechania
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Takashi Shiratori
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ken-Ichiro Ishida
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Joel B Dacks
- Department of Oceanography, Kyungpook National University, Daegu, South Korea
- Centre for Life's Origin and Evolution, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Purificación López-García
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Eunsoo Kim
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
- Division of EcoScience, Ewha Womans University, Seoul, South Korea.
| | - Laura Eme
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
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4
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Galindo LJ, Prokina K, Torruella G, Moreira D, López-García P. Maturases and Group II Introns in the Mitochondrial Genomes of the Deepest Jakobid Branch. Genome Biol Evol 2023; 15:7111303. [PMID: 37029959 PMCID: PMC10139444 DOI: 10.1093/gbe/evad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 04/09/2023] Open
Abstract
Ophirinina is a recently described suborder of jakobid protists (Excavata) with only one described species to date, Ophirina amphinema. Despite the acquisition and analysis of massive transcriptomic and mitogenomic sequence data from O. amphinema, its phylogenetic position among excavates remained inconclusive, branching either as sister group to all Jakobida or to all Discoba. From a morphological perspective, it has several typical jakobid features but also unusual traits for this group, including the morphology of mitochondrial cristae (sac-shaped to flattened-curved cristae) and the presence of two flagellar vanes. In this study, we have isolated, morphologically characterized, and sequenced genome and transcriptome data of two new Ophirinina species: Ophirina chinija sp. nov. and Agogonia voluta gen. et sp. nov. Ophirina chinija differs from O. amphinema in having rounded cell ends, subapically emerging flagella and a posterior cell protrusion. The much more distantly related A. voluta has several unique ultrastructural characteristics, including sac-shaped mitochondrial cristae and a complex 'B' fibre. Phylogenomic analyses with a large conserved-marker dataset supported the monophyly of Ophirina and Agogonia within the Ophirinina and, more importantly, resolved the conflicting position of ophirinids as the sister clade to all other jakobids. The characterization of the mitochondrial genomes showed that Agogonia differs from all known gene-rich jakobid mitogenomes by the presence of two group II introns and their corresponding maturase protein genes. A phylogenetic analysis of the diversity of known maturases confirmed that the Agogonia proteins are highly divergent from each other and define distant families among the prokaryotic and eukaryotic maturases. This opens the intriguing possibility that, compared to other jakobids, Ophirinina may have retained additional mitochondrial elements that may help to understand the early diversification of eukaryotes and the evolution of mitochondria.
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Affiliation(s)
- Luis Javier Galindo
- Unité d'Ecologie Systématique et Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, United Kingdom
| | - Kristina Prokina
- Unité d'Ecologie Systématique et Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
- Papanin Institute for Biology of Inland Waters RAS, Borok, Russia
| | - Guifré Torruella
- Unité d'Ecologie Systématique et Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
- Barcelona Supercomputing Center (BSC-CNS), Barcelona, Catalonia, Spain
- Institute for Research in Biomedicine (IRB), Barcelona, Catalonia, Spain
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Purificación López-García
- Unité d'Ecologie Systématique et Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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5
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Torruella G, Galindo LJ, Moreira D, Ciobanu M, Heiss AA, Yubuki N, Kim E, López-García P. Expanding the molecular and morphological diversity of Apusomonadida, a deep-branching group of gliding bacterivorous protists. J Eukaryot Microbiol 2023; 70:e12956. [PMID: 36453005 DOI: 10.1111/jeu.12956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 09/13/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022]
Abstract
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 11 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.
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Affiliation(s)
- Guifré Torruella
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France.,Barcelona Supercomputing Center (BSC-CNS), Barcelona, Spain.,Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Luis Javier Galindo
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France.,Department of Zoology, University of Oxford, Oxford, UK
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Maria Ciobanu
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Aaron A Heiss
- Department of Invertebrate Zoology, American Museum of Natural History, New York City, New York, USA.,Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Naoji Yubuki
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France.,Bioimaging Facility, University of British Columbia, Vancouver, BC, Canada
| | - Eunsoo Kim
- Department of Invertebrate Zoology, American Museum of Natural History, New York City, New York, USA.,Department of Life Science & Division of EcoScience, Ewha Womans University, Seoul, South Korea
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6
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Leonard G, Galindo LJ, Milner DS, Avelar GM, Gomes-Vieira AL, Gomes SL, Richards TA. A Genome Sequence Assembly of the Phototactic and Optogenetic Model Fungus Blastocladiella emersonii Reveals a Diversified Nucleotide-Cyclase Repertoire. Genome Biol Evol 2022; 14:6770634. [PMID: 36281075 PMCID: PMC9730499 DOI: 10.1093/gbe/evac157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2022] [Indexed: 01/04/2023] Open
Abstract
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 understanding the evolution of phototaxis and the molecular cell biology of the associated optogenetic circuits. Here, we report a highly contiguous genome assembly and gene annotation of the B. emersonii American Type Culture Collection 22665 strain. We integrate a PacBio long-read library with an Illumina paired-end genomic sequence survey leading to an assembly of 21 contigs totaling 34.27 Mb. Using these data, we assess the diversity of sensory system encoding genes. These analyses identify a rich complement of G-protein-coupled receptors, ion transporters, and nucleotide cyclases, all of which have been diversified by domain recombination and tandem duplication. In many cases, these domain combinations have led to the fusion of a protein domain to a transmembrane domain, tying a putative signaling function to the cell membrane. This pattern is consistent with the diversification of the B. emersonii sensory-signaling systems, which likely plays a varied role in the complex life cycle of this fungus.
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Affiliation(s)
- Guy Leonard
- Department of Biology, University of Oxford, United Kingdom
| | | | - David S Milner
- Department of Biology, University of Oxford, United Kingdom
| | - Gabriela Mol Avelar
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, United Kingdom
| | - André L Gomes-Vieira
- Departamento de Bioquímica, Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | - Suely L Gomes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
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7
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Galindo LJ, Torruella G, López-García P, Ciobanu M, Gutiérrez-Preciado A, Karpov SA, Moreira D. Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies. Syst Biol 2022:6651083. [PMID: 35900180 DOI: 10.1093/sysbio/syac054] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/12/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
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 relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the 'Opisthosporidia hypothesis'). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium, suggested that the aphelids are sister to fungi (the 'Aphelida+Fungi hypothesis'). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (A. insulamus and A. tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida+Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid-fungal split and the remaining 12 likely evolved de novo, constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favour of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia.
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Affiliation(s)
- Luis Javier Galindo
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Guifré Torruella
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-García
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Maria Ciobanu
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Ana Gutiérrez-Preciado
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Sergey A Karpov
- Zoological Institute RAS, Universitetskaya emb. 1, and St Petersburg State University, Universitetskaya emb. 7/9, St Petersburg 199034, Russia
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
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8
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Grau-Bové X, Navarrete C, Chiva C, Pribasnig T, Antó M, Torruella G, Galindo LJ, Lang BF, Moreira D, López-Garcia P, Ruiz-Trillo I, Schleper C, Sabidó E, Sebé-Pedrós A. A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. Nat Ecol Evol 2022; 6:1007-1023. [PMID: 35680998 PMCID: PMC7613034 DOI: 10.1038/s41559-022-01771-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/21/2022] [Indexed: 02/06/2023]
Abstract
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.
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Affiliation(s)
- Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Navarrete
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Thomas Pribasnig
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Meritxell Antó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Guifré Torruella
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Luis Javier Galindo
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Bernd Franz Lang
- Robert Cedergren Centre in Bioinformatics and Genomics, Department of Biochemistry, Université de Montréal, Montréal, Quebec, Canada
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-Garcia
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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9
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Javier Galindo L, López García P, Moreira D. First Molecular Characterization of the Elusive Marine Protist Meteora sporadica. Protist 2022; 173:125896. [DOI: 10.1016/j.protis.2022.125896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022]
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10
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Yubuki N, Galindo LJ, Reboul G, López-García P, Brown MW, Pollet N, Moreira D. Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina–Blastocystis Stramenopile Lineage. Mol Biol Evol 2019; 37:651-659. [DOI: 10.1093/molbev/msz250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
AbstractLateral gene transfer is a very common process in bacterial and archaeal evolution, playing an important role in the adaptation to new environments. In eukaryotes, its role and frequency remain highly debated, although recent research supports that gene transfer from bacteria to diverse eukaryotes may be much more common than previously appreciated. However, most of this research focused on animals and the true phylogenetic and functional impact of bacterial genes in less-studied microbial eukaryotic groups remains largely unknown. Here, we have analyzed transcriptome data from the deep-branching stramenopile Opalinidae, common members of frog gut microbiomes, and distantly related to the well-known genus Blastocystis. Phylogenetic analyses suggest the early acquisition of several bacterial genes in a common ancestor of both lineages. Those lateral gene transfers most likely facilitated the adaptation of the free-living ancestor of the Opalinidae–Blastocystis symbiotic group to new niches in the oxygen-depleted animal gut environment.
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Affiliation(s)
- Naoji Yubuki
- Unité d’Ecologie Systématique et Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Luis Javier Galindo
- Unité d’Ecologie Systématique et Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Guillaume Reboul
- Unité d’Ecologie Systématique et Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Purificación López-García
- Unité d’Ecologie Systématique et Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Nicolas Pollet
- Laboratoire Evolution Génomes Comportement et Ecologie, CNRS, IRD, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - David Moreira
- Unité d’Ecologie Systématique et Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
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Galindo LJ, Torruella G, Moreira D, Eglit Y, Simpson AGB, Völcker E, Clauß S, López-García P. Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190094. [PMID: 31587649 DOI: 10.1098/rstb.2019.0094] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
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 (SCG) and single-cell transcriptome amplification methods. The phylogeny of the complete 18S rRNA sequences of Pompholyxophrys and Lithocolla confirmed their suggested evolutionary relatedness to nucleariid amoebae, although with moderate support for internal splits. SCG amplification techniques also led to the identification of probable bacterial endosymbionts belonging to Chlamydiales and Rickettsiales in Pompholyxophrys. To improve the phylogenetic framework of nucleariids, we carried out phylogenomic analyses based on two datasets of, respectively, 264 conserved proteins and 74 single-copy protein domains. We obtained full support for the monophyly of the nucleariid amoebae, which comprise two major clades: (i) Parvularia-Fonticula and (ii) Nuclearia with the scaled genera Pompholyxophrys and Lithocolla. Based on these findings, the evolution of some traits of the earliest-diverging lineage of Holomycota can be inferred. Our results suggest that the last common ancestor of nucleariids was a freshwater, bacterivorous, non-flagellated filose and mucilaginous amoeba. From the ancestor, two groups evolved to reach smaller (Parvularia-Fonticula) and larger (Nuclearia and related scaled genera) cell sizes, leading to different ecological specialization. The Lithocolla + Pompholyxophrys clade developed exogenous or endogenous cell coverings from a Nuclearia-like ancestor. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- Luis Javier Galindo
- Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Guifré Torruella
- Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Yana Eglit
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alastair G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | | | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
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Galindo LJ, Torruella G, Moreira D, Timpano H, Paskerova G, Smirnov A, Nassonova E, López-García P. Evolutionary Genomics of Metchnikovella incurvata (Metchnikovellidae): An Early Branching Microsporidium. Genome Biol Evol 2018; 10:2736-2748. [PMID: 30239727 PMCID: PMC6190962 DOI: 10.1093/gbe/evy205] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2018] [Indexed: 01/30/2023] Open
Abstract
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 respect to most Microsporidia. Microsporidia are a highly diversified lineage of extremely reduced parasites related to Rozellida (Rozellosporidia = Rozellomycota = Cryptomycota) within the Holomycota clade of Opisthokonta. By sequencing DNA from a single-isolated infected gregarine cell we obtained an almost complete genome of a second metchnikovellid species, and the first one of a taxonomically described and well-documented species, Metchnikovella incurvata. Our phylogenomic analyses show that, despite being considerably divergent from each other, M. incurvata forms a monophyletic group with Amphiamplys sp., and confirm that metchnikovellids are one of the deep branches of Microsporidia. Comparative genomic analysis demonstrates that, like most Microsporidia, metchnikovellids lack mitochondrial genes involved in energy transduction and are thus incapable of synthesizing their own ATP via mitochondrial oxidative phosphorylation. They also lack the horizontally acquired ATP transporters widespread in most Microsporidia. We hypothesize that a family of mitochondrial carrier proteins evolved to transport ATP from the host into the metchnikovellid cell. We observe the progressive reduction of genes involved in DNA repair pathways along the evolutionary path of Microsporidia, which might explain, at least partly, the extremely high evolutionary rate of the most derived species. Our data also suggest that genome reduction and acquisition of novel genes co-occurred during the adaptation of Microsporidia to their hosts.
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Affiliation(s)
- Luis Javier Galindo
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Guifré Torruella
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Hélène Timpano
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Gita Paskerova
- Department of Invertebrate Zoology, Faculty of Biology, St Petersburg State University, Russia
| | - Alexey Smirnov
- Department of Invertebrate Zoology, Faculty of Biology, St Petersburg State University, Russia
| | - Elena Nassonova
- Department of Invertebrate Zoology, Faculty of Biology, St Petersburg State University, Russia.,Laboratory of Cytology of Unicellular Organisms, Institute of Cytology Russian Academy of Sciences, St. Petersburg, Russia
| | - Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
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Galindo LJ, Hernández-Beeftink T, Salas A, Jung Y, Reyes R, de Oca FM, Hernández M, Almeida TA. HMGA2 and MED12 alterations frequently co-occur in uterine leiomyomas. Gynecol Oncol 2018; 150:562-568. [PMID: 30017537 DOI: 10.1016/j.ygyno.2018.07.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/06/2018] [Accepted: 07/08/2018] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Around 70% of uterine leiomyomas show MED12 mutations while overexpression of HMGA2 mRNA is also highly frequent in fibroids. However, previous studies suggested that alterations in both genes are mutually exclusive. In the present study, we searched for mutation in MED12 and analyzed the expression of HMGA2 in 20 uterine leiomyomas and their matched myometrium. METHODS Normal and tumor tissue obtained from premenopausal women who underwent hysterectomy were collected after surgery and DNA, RNA and proteins were isolated and analyzed for MED12 mutations using Sanger sequencing, HMGA2 mRNA expression by quantitative PCR and HMGA2 protein detection by western blot and immunohistochemistry. RESULTS 75% of the tumors displayed MED12 mutation while 65% of them showed overexpression of HMGA2 mRNA in leiomyomata compared to myometrial tissues (p = 0,0008). Interestingly, 50% of the tumors showed mutations in MED12 and overexpression of HMGA2 mRNA simultaneously, suggesting that alterations in both genes are relatively frequent in uterine leiomyomas. CONCLUSIONS Contrary to the present findings, former studies showed that mutations in MED12 and overexpression of HMGA2 are mutually exclusive. Here, we observed that overexpression of HMGA2 mRNA in tumors measured by quantitative PCR and compared to myometrium is a common phenomenon in fibroids and is frequently associated with MED12 mutations. In addition, the common clonal origin of tumors overexpressing HMGA2 mRNA and its expression in few myometrial tissue points to HMGA2 up-regulation as an early event in leiomyoma tumorigenesis.
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Affiliation(s)
- Luis Javier Galindo
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de la Laguna, Avda. Astrofísico Fco. Sánchez s/n, 38207 La Laguna, Tenerife, Spain
| | - Tamara Hernández-Beeftink
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de la Laguna, Avda. Astrofísico Fco. Sánchez s/n, 38207 La Laguna, Tenerife, Spain
| | - Ana Salas
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de la Laguna, Avda. Astrofísico Fco. Sánchez s/n, 38207 La Laguna, Tenerife, Spain
| | - Yaiza Jung
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de la Laguna, Avda. Astrofísico Fco. Sánchez s/n, 38207 La Laguna, Tenerife, Spain
| | - Ricardo Reyes
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de la Laguna, Avda. Astrofísico Fco. Sánchez s/n, 38207 La Laguna, Tenerife, Spain
| | - Francisco Montes de Oca
- Hospital Quironsalud, Poeta Rodríguez Herrera 1, Santa Cruz de Tenerife 38006, Tenerife, Spain
| | - Mariano Hernández
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de la Laguna, Avda. Astrofísico Fco. Sánchez s/n, 38207 La Laguna, Tenerife, Spain; Instituto de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de la Laguna, Avda. Astrofísico Fco. Sánchez s/n, 38207 La Laguna, Tenerife, Spain
| | - Teresa A Almeida
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de la Laguna, Avda. Astrofísico Fco. Sánchez s/n, 38207 La Laguna, Tenerife, Spain; Instituto de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de la Laguna, Avda. Astrofísico Fco. Sánchez s/n, 38207 La Laguna, Tenerife, Spain.
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