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Yu D, DU S, Wei X, Zhu J, Ding Y, Hu F, Liu M, Zhang F. Whole-genome-based phylogenetic analyses provide new insights into the evolution of springtails (Hexapoda: Collembola). Mol Phylogenet Evol 2024; 200:108169. [PMID: 39121953 DOI: 10.1016/j.ympev.2024.108169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Springtails (Collembola) stand as one of the most abundant, widespread, and ancient terrestrial arthropods on earth. However, their evolutionary history and deep phylogenetic relationships remain elusive. In this study, we employed phylogenomic approaches to elucidate the basal relationships among Collembola. We sampled whole-genome data representing all major collembolan lineages in proportion to their known diversity. To account for potential phylogenomic biases, we implemented various data extraction, locus sampling, and signal filtering strategies to generate matrices. Subsequently, we applied a diverse array of tree-searching and rate-modelling methods to reconstruct the phylogeny. Our analyses, utilizing different matrices and methods, converged on the same unrooted relationships among collembolan ingroups, supporting the current ordinal classification and challenging the monophyly of Arthropleona and Symphypleona s.l. However, discrepancies across analyses existed in the root of Collembola. Among various root positions, those based on more informative matrices and biologically realistic models, favoring a basal topology of Entomobryomorpha + (Symphypleona s.s. + (Neelipleona + Poduromorpha)), were supported by subsequent methodological assessment, topology tests, and rooting analyses. This optimal topology suggests multiple independent reduction of the pronotum in non-poduromorph orders and aligns with the plesiomorphic status of neuroendocrine organs and epicuticular structure of Entomobryomorpha. Fossil-calibrated dating analyses based on the optimal topology indicated late-Paleozoic to mid-Mesozoic origins of the crown Collembola and four orders. In addition, our results questioned the monophyly of Isotomidae and Neanuridae, underscoring the need for further attention to the systematics of these families. Overall, this study provides novel insights into the phylogenetic backbone of Collembola, which will inform future studies on the systematics, ecology, and evolution of this significant arthropod lineage.
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Affiliation(s)
- Daoyuan Yu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shiyu DU
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiping Wei
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jie Zhu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yinhuan Ding
- Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Nanjing 212400, China.
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Manqiang Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Feng Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
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2
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Banos H, Wong TKF, Daneau J, Susko E, Minh BQ, Lanfear R, Brown MW, Eme L, Roger AJ. GTRpmix: A Linked General Time-Reversible Model for Profile Mixture Models. Mol Biol Evol 2024; 41:msae174. [PMID: 39158305 PMCID: PMC11371462 DOI: 10.1093/molbev/msae174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/25/2024] [Accepted: 08/12/2024] [Indexed: 08/20/2024] Open
Abstract
Profile mixture models capture distinct biochemical constraints on the amino acid substitution process at different sites in proteins. These models feature a mixture of time-reversible models with a common matrix of exchangeabilities and distinct sets of equilibrium amino acid frequencies known as profiles. Combining the exchangeability matrix with each profile generates the matrix of instantaneous rates of amino acid exchange for that profile. Currently, empirically estimated exchangeability matrices (e.g. the LG matrix) are widely used for phylogenetic inference under profile mixture models. However, these were estimated using a single profile and are unlikely optimal for profile mixture models. Here, we describe the GTRpmix model that allows maximum likelihood estimation of a common exchangeability matrix under any profile mixture model. We show that exchangeability matrices estimated under profile mixture models differ from the LG matrix, dramatically improving model fit and topological estimation accuracy for empirical test cases. Because the GTRpmix model is computationally expensive, we provide two exchangeability matrices estimated from large concatenated phylogenomic-supermatrices to be used for phylogenetic analyses. One, called Eukaryotic Linked Mixture (ELM), is designed for phylogenetic analysis of proteins encoded by nuclear genomes of eukaryotes, and the other, Eukaryotic and Archaeal Linked mixture (EAL), for reconstructing relationships between eukaryotes and Archaea. These matrices, combined with profile mixture models, fit data better and have improved topology estimation relative to the LG matrix combined with the same mixture models. Starting with version 2.3.1, IQ-TREE2 allows users to estimate linked exchangeabilities (i.e. amino acid exchange rates) under profile mixture models.
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Affiliation(s)
- Hector Banos
- Department of Mathematics, California State University San Bernardino, San Bernardino, CA, USA
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Thomas K F Wong
- School of Computing, College of Engineering and Computing and Cybernetics, Australian National University, Canberra, ACT 2600, Australia
- Ecology and Evolution, Research School of Biology, College of Science, Australian National University, Canberra, ACT 2600, Australia
| | - Justin Daneau
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Edward Susko
- Department of Mathematics and Statistics, Faculty of Science, Dalhousie University, Halifax, NS, Canada
| | - Bui Quang Minh
- School of Computing, College of Engineering and Computing and Cybernetics, Australian National University, Canberra, ACT 2600, Australia
| | - Robert Lanfear
- Ecology and Evolution, Research School of Biology, College of Science, Australian National University, Canberra, ACT 2600, Australia
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Laura Eme
- Laboratoire d’Ecologie, systématique et Evolution, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
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3
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Klirs Y, Novosolov M, Gissi C, Garić R, Pupko T, Stach T, Huchon D. Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss. Genome Biol Evol 2024; 16:evae181. [PMID: 39162337 DOI: 10.1093/gbe/evae181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 07/19/2024] [Accepted: 08/13/2024] [Indexed: 08/21/2024] Open
Abstract
Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation of the majority of the mitochondrial genome of O. dioica by means of combining several DNA and amplicon reads obtained by Illumina and MinIon Oxford Nanopore Technologies with public RNA sequences. We document extensive RNA editing, since all homopolymer stretches present in the mitochondrial DNA correspond to 6U-regions in the mitochondrial RNA. Out of the 13 canonical protein-coding genes, we were able to detect eight, plus an unassigned open reading frame that lacked sequence similarity to canonical mitochondrial protein-coding genes. We show that the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal. In addition to two very short rRNAs, we could only identify a single tRNA (tRNA-Met), suggesting multiple losses of tRNA genes, supported by a corresponding loss of mitochondrial aminoacyl-tRNA synthetases in the nuclear genome. Based on the eight canonical protein-coding genes identified, we reconstructed maximum likelihood and Bayesian phylogenetic trees and inferred an extreme evolutionary rate of this mitochondrial genome. The phylogenetic position of appendicularians among tunicates, however, could not be accurately determined.
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Affiliation(s)
- Yael Klirs
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Maria Novosolov
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
- Faculty of Health and Medical Sciences, GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Carmela Gissi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari 70126, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
- CoNISMa, Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma 00196, Italy
| | - Rade Garić
- Institute for Marine and Coastal Research, University of Dubrovnik, Dubrovnik 20000, Croatia
| | - Tal Pupko
- George S. Wise Faculty of Life Sciences, The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Thomas Stach
- Department of Molecular Parasitology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dorothée Huchon
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, Tel Aviv 6997801, Israel
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4
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Taylor DJ, Barnhart MH. Genomic transfers help to decipher the ancient evolution of filoviruses and interactions with vertebrate hosts. PLoS Pathog 2024; 20:e1011864. [PMID: 39226335 DOI: 10.1371/journal.ppat.1011864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 08/21/2024] [Indexed: 09/05/2024] Open
Abstract
Although several filoviruses are dangerous human pathogens, there is conflicting evidence regarding their origins and interactions with animal hosts. Here we attempt to improve this understanding using the paleoviral record over a geological time scale, protein structure predictions, tests for evolutionary maintenance, and phylogenetic methods that alleviate sources of bias and error. We found evidence for long branch attraction bias in the L gene tree for filoviruses, and that using codon-specific models and protein structural comparisons of paleoviruses ameliorated conflict and bias. We found evidence for four ancient filoviral groups, each with extant viruses and paleoviruses with open reading frames. Furthermore, we found evidence of repeated transfers of filovirus-like elements to mouse-like rodents. A filovirus-like nucleoprotein ortholog with an open reading frame was detected in three subfamilies of spalacid rodents (present since the Miocene). We provide evidence that purifying selection is acting to maintain amino acids, protein structure and open reading frames in these elements. Our finding of extant viruses nested within phylogenetic clades of paleoviruses informs virus discovery methods and reveals the existence of Lazarus taxa among RNA viruses. Our results resolve a deep conflict in the evolutionary framework for filoviruses and reveal that genomic transfers to vertebrate hosts with potentially functional co-options have been more widespread than previously appreciated.
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Affiliation(s)
- Derek J Taylor
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Max H Barnhart
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
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5
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Cho A, Lax G, Keeling PJ. Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages. Mol Phylogenet Evol 2024; 198:108120. [PMID: 38852907 DOI: 10.1016/j.ympev.2024.108120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/13/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and a single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signal or low phylogenetic noise. For some previously contentious relationships, we find a variety of analyses and gene filtering criteria consistently unite previously unstable groupings with strong statistical support. For example, we recovered a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister-lineage to Pinguiophyceae. Selecting genes with high phylogenetic signal or data quality recovered more stable topologies. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving phylogenetic relationships, and discrete gene properties affect lineages of stramenopiles differently. This is something which may be explored to further our understanding of the molecular evolution of stramenopiles.
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Affiliation(s)
- Anna Cho
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
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6
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Shomar H, Georjon H, Feng Y, Olympio B, Guillaume M, Tesson F, Cury J, Wu F, Bernheim A. Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold. Nat Ecol Evol 2024; 8:1667-1679. [PMID: 38965412 DOI: 10.1038/s41559-024-02463-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024]
Abstract
Evolutionary arms races between cells and viruses drive the rapid diversification of antiviral genes in diverse life forms. Recent discoveries have revealed the existence of immune genes that are shared between prokaryotes and eukaryotes and show molecular and mechanistic similarities in their response to viruses. However, the evolutionary dynamics underlying the conservation and adaptation of these antiviral genes remain mostly unexplored. Here, we show that viperins constitute a highly conserved family of immune genes across diverse prokaryotes and eukaryotes and identify mechanisms by which they diversified in eukaryotes. Our findings indicate that viperins are enriched in Asgard archaea and widely distributed in all major eukaryotic clades, suggesting their presence in the last eukaryotic common ancestor and their acquisition in eukaryotes from an archaeal lineage. We show that viperins maintain their immune function by producing antiviral nucleotide analogues and demonstrate that eukaryotic viperins diversified through serial innovations on the viperin gene, such as the emergence and selection of substrate specificity towards pyrimidine nucleotides, and through partnerships with genes maintained through genetic linkage, notably with nucleotide kinases. These findings unveil biochemical and genomic transitions underlying the adaptation of immune genes shared by prokaryotes and eukaryotes. Our study paves the way for further understanding of the conservation of immunity across domains of life.
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Affiliation(s)
- Helena Shomar
- Institut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes Lab, Paris, France
| | - Héloïse Georjon
- Institut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes Lab, Paris, France
- Generare Bioscience, Paris, France
| | - Yanlei Feng
- School of Life Sciences, College of Science, Eastern Institute of Technology, Ningbo, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Bismarck Olympio
- Institut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes Lab, Paris, France
| | - Marie Guillaume
- Institut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes Lab, Paris, France
| | - Florian Tesson
- Institut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes Lab, Paris, France
| | - Jean Cury
- Institut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes Lab, Paris, France
| | - Fabai Wu
- School of Life Sciences, College of Science, Eastern Institute of Technology, Ningbo, China.
| | - Aude Bernheim
- Institut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes Lab, Paris, France.
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7
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Li Y, Moritz C, Brennan IG, Zwick A, Nicholls J, Grealy A, Slipinski A. Evolution across the adaptive landscape in a hyperdiverse beetle radiation. Curr Biol 2024; 34:3685-3697.e6. [PMID: 39067451 DOI: 10.1016/j.cub.2024.06.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024]
Abstract
The extraordinary diversification of beetles on Earth is a textbook example of adaptive evolution. Yet, the tempo and drivers of this super-radiation remain largely unclear. Here, we address this problem by investigating macroevolutionary dynamics in darkling beetles (Coleoptera: Tenebrionidae), one of the most ecomorphologically diverse beetle families (with over 30,000 species). Using multiple genomic datasets and analytical approaches, we resolve the long-standing inconsistency over deep relationships in the family. In conjunction with a landmark-based dataset of body shape morphology, we show that the evolutionary history of darkling beetles is marked by ancient rapid radiations, frequent ecological transitions, and rapid bursts of morphological diversification. On a global scale, our analyses uncovered a significant pulse of phenotypic diversification proximal to the Cretaceous-Palaeogene (K/Pg) mass extinction and convergence of body shape associated with recurrent ecological specializations. On a regional scale, two major Australasian radiations, the Adeliini and the Heleine clade, exhibited contrasting patterns of ecomorphological diversification, representing phylogenetic niche conservatism versus adaptive radiation. Our findings align with the Simpsonian model of adaptive evolution across the macroevolutionary landscape and highlight a significant role of ecological opportunity in driving the immense ecomorphological diversity in a hyperdiverse beetle group.
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Affiliation(s)
- Yun Li
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia.
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
| | - James Nicholls
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
| | - Alicia Grealy
- Australian National Herbarium, CSIRO, Canberra, ACT 2601, Australia
| | - Adam Slipinski
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
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8
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Backenstose NJC, MacGuigan DJ, Osborne CA, Bernal MA, Thomas EK, Normandeau E, Yule DL, Stott W, Ackiss AS, Albert VA, Bernatchez L, Krabbenhoft TJ. Origin of the Laurentian Great Lakes fish fauna through upward adaptive radiation cascade prior to the Last Glacial Maximum. Commun Biol 2024; 7:978. [PMID: 39134631 PMCID: PMC11319351 DOI: 10.1038/s42003-024-06503-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 06/25/2024] [Indexed: 08/15/2024] Open
Abstract
The evolutionary histories of adaptive radiations can be marked by dramatic demographic fluctuations. However, the demographic histories of ecologically-linked co-diversifying lineages remain understudied. The Laurentian Great Lakes provide a unique system of two such radiations that are dispersed across depth gradients with a predator-prey relationship. We show that the North American Coregonus species complex ("ciscoes") radiated rapidly prior to the Last Glacial Maximum (80-90 kya), a globally warm period, followed by rapid expansion in population size. Similar patterns of demographic expansion were observed in the predator species, Lake Charr (Salvelinus namaycush), following a brief time lag, which we hypothesize was driven by predator-prey dynamics. Diversification of prey into deep water created ecological opportunities for the predators, facilitating their demographic expansion, which is consistent with an upward adaptive radiation cascade. This study provides a new timeline and environmental context for the origin of the Laurentian Great Lakes fish fauna, and firmly establishes this system as drivers of ecological diversification and rapid speciation through cyclical glaciation.
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Affiliation(s)
| | - Daniel J MacGuigan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | | | - Moisés A Bernal
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | | | - Eric Normandeau
- Plateforme de bio-informatique de l'IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, G1V 0A6, Canada
| | - Daniel L Yule
- US Geological Survey, Lake Superior Biological Station, Great Lakes Science Center, Ashland, WI, USA
| | - Wendylee Stott
- Freshwater Institute, Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, MB, R3T 2N6, Canada
| | - Amanda S Ackiss
- US Geological Survey, Great Lakes Science Center, Ann Arbor, MI, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Trevor J Krabbenhoft
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
- RENEW Institute, University at Buffalo, Buffalo, NY, USA.
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9
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Williams SK, Jerlström Hultqvist J, Eglit Y, Salas-Leiva DE, Curtis B, Orr RJS, Stairs CW, Atalay TN, MacMillan N, Simpson AGB, Roger AJ. Extreme mitochondrial reduction in a novel group of free-living metamonads. Nat Commun 2024; 15:6805. [PMID: 39122691 PMCID: PMC11316075 DOI: 10.1038/s41467-024-50991-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 07/15/2024] [Indexed: 08/12/2024] Open
Abstract
Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway by lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.
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Affiliation(s)
- Shelby K Williams
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Jon Jerlström Hultqvist
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Yana Eglit
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biology, Dalhousie University, Halifax, Canada
| | - Dayana E Salas-Leiva
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Bruce Curtis
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Russell J S Orr
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Tuğba N Atalay
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Naomi MacMillan
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Alastair G B Simpson
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biology, Dalhousie University, Halifax, Canada
| | - Andrew J Roger
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada.
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.
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10
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Thomé PC, Wolinska J, Van Den Wyngaert S, Reñé A, Ilicic D, Agha R, Grossart HP, Garcés E, Monaghan MT, Strassert JFH. Phylogenomics including new sequence data of phytoplankton-infecting chytrids reveals multiple independent lifestyle transitions across the phylum. Mol Phylogenet Evol 2024; 197:108103. [PMID: 38754710 DOI: 10.1016/j.ympev.2024.108103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/01/2023] [Accepted: 05/11/2024] [Indexed: 05/18/2024]
Abstract
Parasitism is the most common lifestyle on Earth and has emerged many times independently across the eukaryotic tree of life. It is frequently found among chytrids (Chytridiomycota), which are early-branching unicellular fungi that feed osmotrophically via rhizoids as saprotrophs or parasites. Chytrids are abundant in most aquatic and terrestrial environments and fulfil important ecosystem functions. As parasites, they can have significant impacts on host populations. They cause global amphibian declines and influence the Earth's carbon cycle by terminating algal blooms. To date, the evolution of parasitism within the chytrid phylum remains unclear due to the low phylogenetic resolution of rRNA genes for the early diversification of fungi, and because few parasitic lineages have been cultured and genomic data for parasites is scarce. Here, we combine transcriptomics, culture-independent single-cell genomics and a phylogenomic approach to overcome these limitations. We newly sequenced 29 parasitic taxa and combined these with existing data to provide a robust backbone topology for the diversification of Chytridiomycota. Our analyses reveal multiple independent lifestyle transitions between parasitism and saprotrophy among chytrids and multiple host shifts by parasites. Based on these results and the parasitic lifestyle of other early-branching holomycotan lineages, we hypothesise that the chytrid last common ancestor was a parasite of phytoplankton.
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Affiliation(s)
- Pauline C Thomé
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Silke Van Den Wyngaert
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany; Department of Biology, University of Turku, Turku, Finland
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Barcelona, Spain
| | - Doris Ilicic
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Ramsy Agha
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany; Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Barcelona, Spain
| | - Michael T Monaghan
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Jürgen F H Strassert
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.
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11
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Porfirio-Sousa AL, Tice AK, Morais L, Ribeiro GM, Blandenier Q, Dumack K, Eglit Y, Fry NW, Gomes E Souza MB, Henderson TC, Kleitz-Singleton F, Singer D, Brown MW, Lahr DJG. Amoebozoan testate amoebae illuminate the diversity of heterotrophs and the complexity of ecosystems throughout geological time. Proc Natl Acad Sci U S A 2024; 121:e2319628121. [PMID: 39012821 PMCID: PMC11287125 DOI: 10.1073/pnas.2319628121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 06/01/2024] [Indexed: 07/18/2024] Open
Abstract
Heterotrophic protists are vital in Earth's ecosystems, influencing carbon and nutrient cycles and occupying key positions in food webs as microbial predators. Fossils and molecular data suggest the emergence of predatory microeukaryotes and the transition to a eukaryote-rich marine environment by 800 million years ago (Ma). Neoproterozoic vase-shaped microfossils (VSMs) linked to Arcellinida testate amoebae represent the oldest evidence of heterotrophic microeukaryotes. This study explores the phylogenetic relationship and divergence times of modern Arcellinida and related taxa using a relaxed molecular clock approach. We estimate the origin of nodes leading to extant members of the Arcellinida Order to have happened during the latest Mesoproterozoic and Neoproterozoic (1054 to 661 Ma), while the divergence of extant infraorders postdates the Silurian. Our results demonstrate that at least one major heterotrophic eukaryote lineage originated during the Neoproterozoic. A putative radiation of eukaryotic groups (e.g., Arcellinida) during the early-Neoproterozoic sustained by favorable ecological and environmental conditions may have contributed to eukaryotic life endurance during the Cryogenian severe ice ages. Moreover, we infer that Arcellinida most likely already inhabited terrestrial habitats during the Neoproterozoic, coexisting with terrestrial Fungi and green algae, before land plant radiation. The most recent extant Arcellinida groups diverged during the Silurian Period, alongside other taxa within Fungi and flowering plants. These findings shed light on heterotrophic microeukaryotes' evolutionary history and ecological significance in Earth's ecosystems, using testate amoebae as a proxy.
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Affiliation(s)
- Alfredo L. Porfirio-Sousa
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo05508-090, Brazil
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS39762
| | - Alexander K. Tice
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS39762
- Department of Biological Sciences, Texas Tech University, Lubbock, TX79409
| | - Luana Morais
- Department of Geophysics, Institute of Astronomy, Geophysics and Atmospheric Sciences, University of São Paulo, São Paulo05508-090, Brazil
- Department of Applied Geology, Institute of Geosciences and Exact Sciences, São Paulo State University, Rio Claro13506-900, Brazil
| | - Giulia M. Ribeiro
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo05508-090, Brazil
| | - Quentin Blandenier
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS39762
| | - Kenneth Dumack
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne50674, Germany
| | - Yana Eglit
- Department of Biology, Dalhousie University, Halifax, NSB3H 4R2, Canada
- Department of Biology, Institute for Comparative Genomics, Dalhousie University, Halifax, NSV8P 3E6, Canada
- Department of Biology, University of Victoria, Victoria, BCV8P 3E6, Canada
| | - Nicholas W. Fry
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS39762
| | | | - Tristan C. Henderson
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS39762
| | | | - David Singer
- Soil Science and Environment Group, Changins, Haute école spécialisée de Suisse occidentale University of Applied Sciences and Arts Western Switzerland, Nyon1148, Switzerland
| | - Matthew W. Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS39762
- Department of Biological Sciences, Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS39762
| | - Daniel J. G. Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo05508-090, Brazil
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12
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Cooney EC, Jacobson DM, Wolfe GV, Bright KJ, Saldarriaga JF, Keeling PJ, Leander BS, Strom SL. Morphology, behavior, and phylogenomics of Oxytoxum lohmannii, Dinoflagellata. J Eukaryot Microbiol 2024:e13050. [PMID: 39019843 DOI: 10.1111/jeu.13050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/19/2024]
Abstract
Dinoflagellates are an abundant and diverse group of protists representing a wealth of unique biology and ecology. While many dinoflagellates are photosynthetic or mixotrophic, many taxa are heterotrophs, often with complex feeding strategies. Compared to their photosynthetic counterparts, heterotrophic dinoflagellates remain understudied, as they are difficult to culture. One exception, a long-cultured isolate originally classified as Amphidinium but recently reclassified as Oxytoxum, has been the subject of a number of feeding, growth, and chemosensory studies. This lineage was recently determined to be closely related to Prorocentrum using phylogenetics of ribosomal RNA gene sequences, but the exact nature of this relationship remains unresolved. Using transcriptomes sequenced from culture and three single cells from the environment, we produce a robust phylogeny of 242 genes, revealing Oxytoxum is likely sister to the Prorocentrum clade, rather than nested within it. Molecular investigations uncover evidence of a reduced, nonphotosynthetic plastid and proteorhodopsin, a photoactive proton pump acquired horizontally from bacteria. We describe the ultrastructure of O. lohmannii, including densely packed trichocysts, and a new type of mucocyst. We observe that O. lohmannii feeds preferentially on cryptophytes using myzocytosis, but can also feed on various phytoflagellates using conventional phagocytosis. O. lohmannii is amenable to culture, providing an opportunity to better study heterotrophic dinoflagellate biology and feeding ecology.
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Affiliation(s)
- Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Gordon V Wolfe
- Department of Biological Sciences, California State University, Chico, Chico, California, USA
| | - Kelley J Bright
- Shannon Point Marine Center, Western Washington University, Anacortes, USA
| | - Juan F Saldarriaga
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Brian S Leander
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Suzanne L Strom
- Shannon Point Marine Center, Western Washington University, Anacortes, USA
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13
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Cooney EC, Holt CC, Hehenberger E, Adams JA, Leander BS, Keeling PJ. Investigation of heterotrophs reveals new insights in dinoflagellate evolution. Mol Phylogenet Evol 2024; 196:108086. [PMID: 38677354 DOI: 10.1016/j.ympev.2024.108086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These features include, but are not limited to, massive genomes organized using bacterially-derived histone-like proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than histones, and a complex history of photobiology with many independent losses of photosynthesis, numerous cases of serial secondary and tertiary plastid gains, and the presence of horizontally acquired bacterial rhodopsins and type II RuBisCo. Elucidating how this all evolved depends on knowing the phylogenetic relationships between dinoflagellate lineages. Half of these species are heterotrophic, but existing molecular data is strongly biased toward the photosynthetic dinoflagellates due to their amenability to cultivation and prevalence in culture collections. These biases make it impossible to interpret the evolution of photosynthesis, but may also affect phylogenetic inferences that impact our understanding of character evolution. Here, we address this problem by isolating individual cells from the Salish Sea and using single cell, culture-free transcriptomics to expand molecular data for dinoflagellates to include 27 more heterotrophic taxa, resulting in a roughly balanced representation. Using these data, we performed a comprehensive search for proteins involved in chromatin packaging, plastid function, and photoactivity across all dinoflagellates. These searches reveal that 1) photosynthesis was lost at least 21 times, 2) two known types of HLP were horizontally acquired around the same time rather than sequentially as previously thought; 3) multiple rhodopsins are present across the dinoflagellates, acquired multiple times from different donors; 4) kleptoplastic species have nucleus-encoded genes for proteins targeted to their temporary plastids and they are derived from multiple lineages, and 5) warnowiids are the only heterotrophs that retain a whole photosystem, although some photosynthesis-related electron transport genes are widely retained in heterotrophs, likely as part of the iron-sulfur cluster pathway that persists in non-photosynthetic plastids.
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Affiliation(s)
- Elizabeth C Cooney
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Hakai Institute, 1747 Hyacinthe Bay Rd., Heriot Bay, BC V0P 1H0, Canada.
| | - Corey C Holt
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Hakai Institute, 1747 Hyacinthe Bay Rd., Heriot Bay, BC V0P 1H0, Canada.
| | - Elisabeth Hehenberger
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Jayd A Adams
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
| | - Brian S Leander
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Department of Zoology, University of British Columbia, 4200 - 6270, University Blvd., Vancouver, BC V6T 1Z4, Canada.
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
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14
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Aishan Z, Mu ZL, Li ZC, Luo XY, Huangfu N. The First Three Mitochondrial Genomes for the Characterization of the Genus Egeirotrioza (Hemiptera: Triozidae) and Phylogenetic Implications. Genes (Basel) 2024; 15:842. [PMID: 39062621 PMCID: PMC11275608 DOI: 10.3390/genes15070842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
(1) Background: Mitochondrial genomes are important markers for the study of phylogenetics and systematics. Triozidae includes some primary pests of Populus euphratica. The phylogenetic relationships of this group remain controversial due to the lack of molecular data. (2) Methods: Mitochondria of Egeirotrioza Boselli were sequenced and assembled. We analyzed the sequence length, nucleotide composition, and evolutionary rate of Triozidae, combined with the 13 published mitochondrial genomes. (3) Results: The evolutionary rate of protein-coding genes was as follows: ATP8 > ND6 > ND5 > ND2 > ND4 > ND4L > ND1 > ND3 > APT6 > CYTB > COX3 > COX2 > COX1. We reconstructed the phylogenetic relationships of Triozidae based on 16 triozid mitochondrial genomes (thirteen ingroups and three outgroups) using the maximum likelihood (ML) and Bayesian inference (BI) approaches. The phylogenetic analysis of the 16 Triozidae mitochondrial genomes showed that Egeirotrioza was closely related to Leptynoptera. (4) Conclusions: We have identified 13 PCGs, 22 tRNAs, 2 rRNAs, and 1 control region (CR) of all newly sequenced mitochondrial genomes, which were the mitochondrial gene type in animals. The results of this study provide valuable genomic information for the study of psyllid species.
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Affiliation(s)
- Zhulidezi Aishan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (Z.A.); (Z.-L.M.); (Z.-C.L.)
| | - Ze-Lu Mu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (Z.A.); (Z.-L.M.); (Z.-C.L.)
| | - Zi-Cong Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (Z.A.); (Z.-L.M.); (Z.-C.L.)
| | - Xin-Yu Luo
- Department of Entomology, China Agricultural University, Beijing 100193, China;
| | - Ning Huangfu
- National Natural History Museum of China, Beijing 100050, China
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15
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Dziuba MK, McIntire KM, Seto K, Davenport ES, Rogalski MA, Gowler CD, Baird E, Vaandrager M, Huerta C, Jaye R, Corcoran FE, Withrow A, Ahrendt S, Salamov A, Nolan M, Tejomurthula S, Barry K, Grigoriev IV, James TY, Duffy MA. Phylogeny, morphology, virulence, ecology, and host range of Ordospora pajunii (Ordosporidae), a microsporidian symbiont of Daphnia spp. mBio 2024; 15:e0058224. [PMID: 38651867 PMCID: PMC11237803 DOI: 10.1128/mbio.00582-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
The impacts of microsporidia on host individuals are frequently subtle and can be context dependent. A key example of the latter comes from a recently discovered microsporidian symbiont of Daphnia, the net impact of which was found to shift from negative to positive based on environmental context. Given this, we hypothesized low baseline virulence of the microsporidian; here, we investigated the impact of infection on hosts in controlled conditions and the absence of other stressors. We also investigated its phylogenetic position, ecology, and host range. The genetic data indicate that the symbiont is Ordospora pajunii, a newly described microsporidian parasite of Daphnia. We show that O. pajunii infection damages the gut, causing infected epithelial cells to lose microvilli and then rupture. The prevalence of this microsporidian could be high (up to 100% in the lab and 77% of adults in the field). Its overall virulence was low in most cases, but some genotypes suffered reduced survival and/or reproduction. Susceptibility and virulence were strongly host-genotype dependent. We found that North American O. pajunii were able to infect multiple Daphnia species, including the European species Daphnia longispina, as well as Ceriodaphnia spp. Given the low, often undetectable virulence of this microsporidian and potentially far-reaching consequences of infections for the host when interacting with other pathogens or food, this Daphnia-O. pajunii symbiosis emerges as a valuable system for studying the mechanisms of context-dependent shifts between mutualism and parasitism, as well as for understanding how symbionts might alter host interactions with resources. IMPORTANCE The net outcome of symbiosis depends on the costs and benefits to each partner. Those can be context dependent, driving the potential for an interaction to change between parasitism and mutualism. Understanding the baseline fitness impact in an interaction can help us understand those shifts; for an organism that is generally parasitic, it should be easier for it to become a mutualist if its baseline virulence is relatively low. Recently, a microsporidian was found to become beneficial to its Daphnia hosts in certain ecological contexts, but little was known about the symbiont (including its species identity). Here, we identify it as the microsporidium Ordospora pajunii. Despite the parasitic nature of microsporidia, we found O. pajunii to be, at most, mildly virulent; this helps explain why it can shift toward mutualism in certain ecological contexts and helps establish O. pajunii is a valuable model for investigating shifts along the mutualism-parasitism continuum.
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Affiliation(s)
- Marcin K. Dziuba
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kristina M. McIntire
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kensuke Seto
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Elizabeth S. Davenport
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Mary A. Rogalski
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Biology Department, Bowdoin College, Brunswick, Maine, USA
| | - Camden D. Gowler
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Emma Baird
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Megan Vaandrager
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Cristian Huerta
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Riley Jaye
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Fiona E. Corcoran
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alicia Withrow
- Center for Advanced Microscopy, Michigan State University, East Lansing, Michigan, USA
| | - Steven Ahrendt
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Asaf Salamov
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matt Nolan
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sravanthi Tejomurthula
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Igor V. Grigoriev
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Timothy Y. James
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Meghan A. Duffy
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
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16
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Nakayama T, Nomura M, Yabuki A, Shiba K, Inaba K, Inagaki Y. Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates. Sci Rep 2024; 14:12774. [PMID: 38834652 DOI: 10.1038/s41598-024-63502-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/29/2024] [Indexed: 06/06/2024] Open
Abstract
The diversity of marine cyanobacteria has been extensively studied due to their vital roles in ocean primary production. However, little is understood about the diversity of cyanobacterial species involved in symbiotic relationships. In this study, we successfully sequenced the complete genome of a cyanobacterium in symbiosis with Citharistes regius, a dinoflagellate species thriving in the open ocean. A phylogenomic analysis revealed that the cyanobacterium (CregCyn) belongs to the marine picocyanobacterial lineage, akin to another cyanobacterial symbiont (OmCyn) of a different dinoflagellate closely related to Citharistes. Nevertheless, these two symbionts are representing distinct lineages, suggesting independent origins of their symbiotic lifestyles. Despite the distinct origins, the genome analyses of CregCyn revealed shared characteristics with OmCyn, including an obligate symbiotic relationship with the host dinoflagellates and a degree of genome reduction. In contrast, a detailed analysis of genome subregions unveiled that the CregCyn genome carries genomic islands that are not found in the OmCyn genome. The presence of the genomic islands implies that exogenous genes have been integrated into the CregCyn genome at some point in its evolution. This study contributes to our understanding of the complex history of the symbiosis between dinoflagellates and cyanobacteria, as well as the genomic diversity of marine picocyanobacteria.
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Affiliation(s)
- Takuro Nakayama
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
| | - Mami Nomura
- Faculty of Science, Yamagata University, Yamagata, Yamagata, Japan
| | - Akinori Yabuki
- Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Kogiku Shiba
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Yuji Inagaki
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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17
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Na I, Campos C, Lax G, Kwong WK, Keeling PJ. Phylogenomics reveals Adeleorina are an ancient and distinct subgroup of Apicomplexa. Mol Phylogenet Evol 2024; 195:108060. [PMID: 38485105 DOI: 10.1016/j.ympev.2024.108060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/21/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
Apicomplexans are a diverse phylum of unicellular eukaryotes that share obligate relationships with terrestrial and aquatic animal hosts. Many well-studied apicomplexans are responsible for several deadly zoonotic and human diseases, most notably malaria caused by Plasmodium. Interest in the evolutionary origin of apicomplexans has also spurred recent work on other more deeply-branching lineages, especially gregarines and sister groups like squirmids and chrompodellids. But a full picture of apicomplexan evolution is still lacking several lineages, and one major, diverse lineage that is notably absent is the adeleorinids. Adeleorina apicomplexans comprises hundreds of described species that infect invertebrate and vertebrate hosts across the globe. Although historically considered coccidians, phylogenetic trees based on limited data have shown conflicting branch positions for this subgroup, leaving this question unresolved. Phylogenomic trees and large-scale analyses comparing cellular functions and metabolism between major subgroups of apicomplexans have not incorporated Adeleorina because only a handful of molecular markers and a couple organellar genomes are available, ultimately excluding this group from contributing to our understanding of apicomplexan evolution and biology. To address this gap, we have generated complete genomes from mitochondria and plastids, as well as multiple deep-coverage single-cell transcriptomes of nuclear genes from two Adeleorina species, Klossia helicina and Legerella nova, and inferred a 206-protein phylogenomic tree of Apicomplexa. We observed distinct structures reported in species descriptions as remnant host structures surrounding adeleorinid oocysts. Klossia helicina and L. nova branched, as expected, with monoxenous adeleorinids within the Adeleorina and their mitochondrial and plastid genomes exhibited similarity to published organellar adeleorinid genomes. We show with a phylogeneomic tree and subsequent phylogenomic analyses that Adeleorina are not closely related to any of the currently sampled apicomplexan subgroups, and instead fall as a sister to a large clade encompassing Coccidia, Protococcidia, Hematozoa, and Nephromycida, collectively. This resolves Adeleorina as a key independently-branching group, separate from coccidians, on the tree of Apicomplexa, which now has all known major lineages sampled.
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Affiliation(s)
- Ina Na
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
| | - Claudia Campos
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Waldan K Kwong
- Department of Botany, University of British Columbia, Vancouver, BC, Canada; Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
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18
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Liu G, Pan Q, Dai Y, Wang X, Li M, Zhu P, Zhou X. Phylogenomics of Afrotherian mammals and improved resolution of extant Paenungulata. Mol Phylogenet Evol 2024; 195:108047. [PMID: 38460890 DOI: 10.1016/j.ympev.2024.108047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/19/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Molecular investigations have gathered a diverse set of mammals-predominantly African natives like elephants, hyraxes, and aardvarks-into a clade known as Afrotheria. Nevertheless, the precise phylogenetic relationships among these species remain contentious. Here, we sourced orthologous markers and ultraconserved elements to discern the interordinal connections among Afrotherian mammals. Our phylogenetic analyses bolster the common origin of Afroinsectiphilia and Paenungulata, and propose Afrosoricida as the closer relative to Macroscelidea rather than Tubulidentata, while also challenging the notion of Sirenia and Hyracoidea as sister taxa. The approximately unbiased test and the gene concordance factor uniformly recognized the alliance of Proboscidea with Hyracoidea as the dominant topology within Paenungulata. Investigation into sites with extremly high phylogenetic signal unveiled their potential to intensify conflicts in the Paenungulata topology. Subsequent exploration suggested that incomplete lineage sorting was predominantly responsible for the observed contentious relationships, whereas introgression exerted a subsidiary influence. The divergence times estimated in our study hint at the Cretaceous-Paleogene (K-Pg) extinction event as a catalyst for Afrotherian diversification. Overall, our findings deliver a tentative but insightful overview of Afrotheria phylogeny and divergence, elucidating these relationships through the lens of phylogenomics.
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Affiliation(s)
- Gaoming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichen Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingfen Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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19
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Baños H, Susko E, Roger AJ. Is Over-parameterization a Problem for Profile Mixture Models? Syst Biol 2024; 73:53-75. [PMID: 37843172 PMCID: PMC11129589 DOI: 10.1093/sysbio/syad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 09/12/2023] [Accepted: 10/13/2023] [Indexed: 10/17/2023] Open
Abstract
Biochemical constraints on the admissible amino acids at specific sites in proteins lead to heterogeneity of the amino acid substitution process over sites in alignments. It is well known that phylogenetic models of protein sequence evolution that do not account for site heterogeneity are prone to long-branch attraction (LBA) artifacts. Profile mixture models were developed to model heterogeneity of preferred amino acids at sites via a finite distribution of site classes each with a distinct set of equilibrium amino acid frequencies. However, it is unknown whether the large number of parameters in such models associated with the many amino acid frequency vectors can adversely affect tree topology estimates because of over-parameterization. Here, we demonstrate theoretically that for long sequences, over-parameterization does not create problems for estimation with profile mixture models. Under mild conditions, tree, amino acid frequencies, and other model parameters converge to true values as sequence length increases, even when there are large numbers of components in the frequency profile distributions. Because large sample theory does not necessarily imply good behavior for shorter alignments we explore the performance of these models with short alignments simulated with tree topologies that are prone to LBA artifacts. We find that over-parameterization is not a problem for complex profile mixture models even when there are many amino acid frequency vectors. In fact, simple models with few site classes behave poorly. Interestingly, we also found that misspecification of the amino acid frequency vectors does not lead to increased LBA artifacts as long as the estimated cumulative distribution function of the amino acid frequencies at sites adequately approximates the true one. In contrast, misspecification of the amino acid exchangeability rates can severely negatively affect parameter estimation. Finally, we explore the effects of including in the profile mixture model an additional "F-class" representing the overall frequencies of amino acids in the data set. Surprisingly, the F-class does not help parameter estimation significantly and can decrease the probability of correct tree estimation, depending on the scenario, even though it tends to improve likelihood scores.
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Affiliation(s)
- Hector Baños
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Institute for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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20
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Hiltunen Thorén M, Onuț-Brännström I, Alfjorden A, Pecková H, Swords F, Hooper C, Holzer AS, Bass D, Burki F. Comparative genomics of Ascetosporea gives new insight into the evolutionary basis for animal parasitism in Rhizaria. BMC Biol 2024; 22:103. [PMID: 38702750 PMCID: PMC11069148 DOI: 10.1186/s12915-024-01898-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/22/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Ascetosporea (Endomyxa, Rhizaria) is a group of unicellular parasites infecting aquatic invertebrates. They are increasingly being recognized as widespread and important in marine environments, causing large annual losses in invertebrate aquaculture. Despite their importance, little molecular data of Ascetosporea exist, with only two genome assemblies published to date. Accordingly, the evolutionary origin of these parasites is unclear, including their phylogenetic position and the genomic adaptations that accompanied the transition from a free-living lifestyle to parasitism. Here, we sequenced and assembled three new ascetosporean genomes, as well as the genome of a closely related amphizoic species, to investigate the phylogeny, origin, and genomic adaptations to parasitism in Ascetosporea. RESULTS Using a phylogenomic approach, we confirm the monophyly of Ascetosporea and show that Paramyxida group with Mikrocytida, with Haplosporida being sister to both groups. We report that the genomes of these parasites are relatively small (12-36 Mb) and gene-sparse (~ 2300-5200 genes), while containing surprisingly high amounts of non-coding sequence (~ 70-90% of the genomes). Performing gene-tree aware ancestral reconstruction of gene families, we demonstrate extensive gene losses at the origin of parasitism in Ascetosporea, primarily of metabolic functions, and little gene gain except on terminal branches. Finally, we highlight some functional gene classes that have undergone expansions during evolution of the group. CONCLUSIONS We present important new genomic information from a lineage of enigmatic but important parasites of invertebrates and illuminate some of the genomic innovations accompanying the evolutionary transition to parasitism in this lineage. Our results and data provide a genetic basis for the development of control measures against these parasites.
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Affiliation(s)
- Markus Hiltunen Thorén
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, Uppsala, SE-752 36, Sweden.
- Present Address: Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius V. 20 A, Stockholm, SE-114 18, Sweden.
- Present Address: The Royal Swedish Academy of Sciences, Stockholm, SE-114 18, Sweden.
| | - Ioana Onuț-Brännström
- Present Address: Department of Ecology and Genetics, Uppsala University, Norbyv. 18D, Uppsala, SE-752 36, Sweden
- Present Address: Natural History Museum, Oslo University, Oslo, 0562, Norway
| | - Anders Alfjorden
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, Uppsala, SE-752 36, Sweden
| | - Hana Pecková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, 370 05, Czech Republic
| | - Fiona Swords
- Marine Institute, Rinville, Oranmore, H91R673, Ireland
| | - Chantelle Hooper
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset, DT4 8UB, UK
- Sustainable Aquaculture Futures, Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Astrid S Holzer
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, 370 05, Czech Republic
- Division of Fish Health, University of Veterinary Medicine, Veterinärplatz 1, Vienna, 1210, Austria
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset, DT4 8UB, UK
- Sustainable Aquaculture Futures, Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Natural History Museum (NHM), Science, London, SW7 5BD, UK
| | - Fabien Burki
- Department of Organismal Biology, Uppsala University, Norbyv. 18D, Uppsala, SE-752 36, Sweden.
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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21
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Yap-Chiongco MK, Bergmeier FS, Roberts NG, Jörger KM, Kocot KM. Phylogenomic reconstruction of Solenogastres (Mollusca, Aplacophora) informs hypotheses on body size evolution. Mol Phylogenet Evol 2024; 194:108029. [PMID: 38341006 DOI: 10.1016/j.ympev.2024.108029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/24/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Body size is a fundamental characteristic of animals that impacts every aspect of their biology from anatomical complexity to ecology. In Mollusca, Solenogastres has been considered important to understanding the group's early evolution as most morphology-based phylogenetic reconstructions placed it as an early branching molluscan lineage. Under this scenario, molluscs were thought to have evolved from a small, turbellarian-like ancestor and small (i.e., macrofaunal) body size was inferred to be plesiomorphic for Solenogastres. More recently, phylogenomic studies have shown that aplacophorans (Solenogastres + Caudofoveata) form a clade with chitons (Polyplacophora), which is sister to all other molluscs, suggesting a relatively large-bodied (i.e., megafaunal) ancestor for Mollusca. Meanwhile, recent investigations into aplacophoran phylogeny have called the assumption that the last common ancestor of Solenogastres was small-bodied into question, but sampling of meiofaunal species was limited, biasing these studies towards large-bodied taxa and leaving fundamental questions about solenogaster body size evolution unanswered. Here, we supplemented available data with transcriptomes from eight diverse meiofaunal species of Solenogastres and conducted phylogenomic analyses on datasets of up to 949 genes. Maximum likelihood analyses support the meiofaunal family Meiomeniidae as the sister group to all other solenogasters, congruent with earlier ideas of a small-bodied ancestor of Solenogastres. In contrast, Bayesian Inference analyses support the large-bodied family Amphimeniidae as the sister group to all other solenogasters. Investigation of phylogenetic signal by comparing site-wise likelihood scores for the two competing hypotheses support the Meiomeniidae-first topology. In light of these results, we performed ancestral character state reconstruction to explore the implications of both hypotheses on understanding of Solenogaster evolution and review previous hypotheses about body size evolution and its potential consequences for solenogaster biology. Both hypotheses imply that body size evolution has been highly dynamic over the course of solenogaster evolution and that their relatively static body plan has successfully allowed for evolutionary transitions between meio-, macro- and megafaunal size ranges.
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Affiliation(s)
| | | | - Nickellaus G Roberts
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
| | - Katharina M Jörger
- SNSB-Bavarian State Collection for Zoology, Section Mollusca, Munich, Germany
| | - Kevin M Kocot
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA; Alabama Museum of Natural History, The University of Alabama, Tuscaloosa, AL, USA.
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22
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Balart-García P, Bradford TM, Beasley-Hall PG, Polak S, Cooper SJB, Fernández R. Highly dynamic evolution of the chemosensory system driven by gene gain and loss across subterranean beetles. Mol Phylogenet Evol 2024; 194:108027. [PMID: 38365165 DOI: 10.1016/j.ympev.2024.108027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/22/2024] [Accepted: 02/04/2024] [Indexed: 02/18/2024]
Abstract
Chemical cues in subterranean habitats differ highly from those on the surface due to the contrasting environmental conditions, such as absolute darkness, high humidity or food scarcity. Subterranean animals underwent changes to their sensory systems to facilitate the perception of essential stimuli for underground lifestyles. Despite representing unique systems to understand biological adaptation, the genomic basis of chemosensation across cave-dwelling species remains unexplored from a macroevolutionary perspective. Here, we explore the evolution of chemoreception in three beetle tribes that underwent at least six independent transitions to the underground, through a phylogenomics spyglass. Our findings suggest that the chemosensory gene repertoire varies dramatically between species. Overall, no parallel changes in the net rate of evolution of chemosensory gene families were detected prior, during, or after the habitat shift among subterranean lineages. Contrarily, we found evidence of lineage-specific changes within surface and subterranean lineages. However, our results reveal key duplications and losses shared between some of the lineages transitioning to the underground, including the loss of sugar receptors and gene duplications of the highly conserved ionotropic receptors IR25a and IR8a, involved in thermal and humidity sensing among other olfactory roles in insects. These duplications were detected both in independent subterranean lineages and their surface relatives, suggesting parallel evolution of these genes across lineages giving rise to cave-dwelling species. Overall, our results shed light on the genomic basis of chemoreception in subterranean beetles and contribute to our understanding of the genomic underpinnings of adaptation to the subterranean lifestyle at a macroevolutionary scale.
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Affiliation(s)
- Pau Balart-García
- Metazoa Phylogenomics Lab, Biodiversity Program, Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain.
| | - Tessa M Bradford
- Environment Institute, Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; South Australian Museum, Adelaide, South Australia 5000, Australia
| | - Perry G Beasley-Hall
- Environment Institute, Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; South Australian Museum, Adelaide, South Australia 5000, Australia
| | - Slavko Polak
- Notranjska Museum Postojna, Kolodvorska c. 3, 6230 Postojna, Slovenia
| | - Steven J B Cooper
- Environment Institute, Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; South Australian Museum, Adelaide, South Australia 5000, Australia
| | - Rosa Fernández
- Metazoa Phylogenomics Lab, Biodiversity Program, Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain.
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23
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Arthofer P, Panhölzl F, Delafont V, Hay A, Reipert S, Cyran N, Wienkoop S, Willemsen A, Sifaoui I, Arberas-Jiménez I, Schulz F, Lorenzo-Morales J, Horn M. A giant virus infecting the amoeboflagellate Naegleria. Nat Commun 2024; 15:3307. [PMID: 38658525 PMCID: PMC11043551 DOI: 10.1038/s41467-024-47308-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Giant viruses (Nucleocytoviricota) are significant lethality agents of various eukaryotic hosts. Although metagenomics indicates their ubiquitous distribution, available giant virus isolates are restricted to a very small number of protist and algal hosts. Here we report on the first viral isolate that replicates in the amoeboflagellate Naegleria. This genus comprises the notorious human pathogen Naegleria fowleri, the causative agent of the rare but fatal primary amoebic meningoencephalitis. We have elucidated the structure and infection cycle of this giant virus, Catovirus naegleriensis (a.k.a. Naegleriavirus, NiV), and show its unique adaptations to its Naegleria host using fluorescence in situ hybridization, electron microscopy, genomics, and proteomics. Naegleriavirus is only the fourth isolate of the highly diverse subfamily Klosneuvirinae, and like its relatives the NiV genome contains a large number of translation genes, but lacks transfer RNAs (tRNAs). NiV has acquired genes from its Naegleria host, which code for heat shock proteins and apoptosis inhibiting factors, presumably for host interactions. Notably, NiV infection was lethal to all Naegleria species tested, including the human pathogen N. fowleri. This study expands our experimental framework for investigating giant viruses and may help to better understand the basic biology of the human pathogen N. fowleri.
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Affiliation(s)
- Patrick Arthofer
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Florian Panhölzl
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Vincent Delafont
- Ecologie et Biologie des Interactions Laboratory (EBI), Microorganisms, hosts & environments team, Université de Poitiers, UMR CNRS, Poitiers, France
| | - Alban Hay
- Ecologie et Biologie des Interactions Laboratory (EBI), Microorganisms, hosts & environments team, Université de Poitiers, UMR CNRS, Poitiers, France
| | - Siegfried Reipert
- University of Vienna, Research Support Facilities UBB, Vienna, Austria
| | - Norbert Cyran
- University of Vienna, Research Support Facilities UBB, Vienna, Austria
| | - Stefanie Wienkoop
- University of Vienna, Department of Functional and Evolutionary Ecology, Division of Molecular Systems Biology, Vienna, Austria
| | - Anouk Willemsen
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Ines Sifaoui
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, and Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Tenerife, Islas Canarias, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Iñigo Arberas-Jiménez
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, and Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Tenerife, Islas Canarias, Spain
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Jacob Lorenzo-Morales
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, and Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Tenerife, Islas Canarias, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Matthias Horn
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria.
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24
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Odelgard A, Hägglund E, Guy L, Andersson SGE. Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota. Genome Biol Evol 2024; 16:evae068. [PMID: 38547507 PMCID: PMC11032199 DOI: 10.1093/gbe/evae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2024] [Indexed: 04/22/2024] Open
Abstract
The recently isolated bacterium "Candidatus Uabimicrobium amorphum" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that "Ca. Uabimicrobium amorphum" represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in "Ca. Uabimicrobium amorphum", of which 66 families contained eukaryotic-like Serine/Threonine kinases with Pkinase domains. In total, we predicted 525 functional Serine/Threonine kinases in "Ca. Uabimicrobium amorphum", which represent 8% of the proteome and is the highest fraction of Serine/Threonine kinases in a bacterial proteome. The majority of Serine/Threonine kinases in this species are membrane proteins and 30% contain long, tandem arrays of WD40 or TPR domains. The pKinase domain was predicted to be located in the cytoplasm, while the WD40 and TPR domains were predicted to be located in the periplasm. Such domain combinations were also identified in the Serine/Threonine kinases of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the Serine/Threonine kinases in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the Serine/Threonine kinases in "Ca. Uabimicrobium amorphum". The results imply that expansions of eukaryotic-like signal transduction systems are not restricted to multicellular organisms, but have occurred in parallel in prokaryotes with predatory lifestyles and phagocytotic-like behaviors.
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Affiliation(s)
- Anna Odelgard
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Emil Hägglund
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala University, Uppsala, Sweden
| | - Siv G E Andersson
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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25
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Novák Vanclová AM, Nef C, Füssy Z, Vancl A, Liu F, Bowler C, Dorrell RG. New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates. EMBO Rep 2024; 25:1859-1885. [PMID: 38499810 PMCID: PMC11014865 DOI: 10.1038/s44319-024-00103-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 03/20/2024] Open
Abstract
Dinoflagellates are a diverse group of ecologically significant micro-eukaryotes that can serve as a model system for plastid symbiogenesis due to their susceptibility to plastid loss and replacement via serial endosymbiosis. Kareniaceae harbor fucoxanthin-pigmented plastids instead of the ancestral peridinin-pigmented ones and support them with a diverse range of nucleus-encoded plastid-targeted proteins originating from the haptophyte endosymbiont, dinoflagellate host, and/or lateral gene transfers (LGT). Here, we present predicted plastid proteomes from seven distantly related kareniaceans in three genera (Karenia, Karlodinium, and Takayama) and analyze their evolutionary patterns using automated tree building and sorting. We project a relatively limited ( ~ 10%) haptophyte signal pointing towards a shared origin in the family Chrysochromulinaceae. Our data establish significant variations in the functional distributions of these signals, emphasizing the importance of micro-evolutionary processes in shaping the chimeric proteomes. Analysis of plastid genome sequences recontextualizes these results by a striking finding the extant kareniacean plastids are in fact not all of the same origin, as two of the studied species (Karlodinium armiger, Takayama helix) possess plastids from different haptophyte orders than the rest.
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Affiliation(s)
- Anna Mg Novák Vanclová
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.
- Institute Jacques Monod, Paris, France.
| | - Charlotte Nef
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Zoltán Füssy
- Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Adél Vancl
- Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| | - Fuhai Liu
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Centre de Recherches Interdisciplinaires, Paris, France
- Tsinghua-UC Berkeley Shenzhen Institute, Shenzhen, China
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Richard G Dorrell
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, Sorbonne Université, Paris, France.
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26
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Zhang Q, Lu YW, Liu XY, Li Y, Gao WN, Sun JT, Hong XY, Shao R, Xue XF. Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea). BMC Biol 2024; 22:70. [PMID: 38519936 PMCID: PMC10960459 DOI: 10.1186/s12915-024-01870-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Eriophyoid mites (Eriophyoidea) are among the largest groups in the Acariformes; they are strictly phytophagous. The higher-level phylogeny of eriophyoid mites, however, remains unresolved due to the limited number of available morphological characters-some of them are homoplastic. Nevertheless, the eriophyoid mites sequenced to date showed highly variable mitochondrial (mt) gene orders, which could potentially be useful for resolving the higher-level phylogenetic relationships. RESULTS Here, we sequenced and compared the complete mt genomes of 153 eriophyoid mite species, which showed 54 patterns of rearranged mt gene orders relative to that of the hypothetical ancestor of arthropods. The shared derived mt gene clusters support the monophyly of eriophyoid mites (Eriophyoidea) as a whole and the monophylies of six clades within Eriophyoidea. These monophyletic groups and their relationships were largely supported in the phylogenetic trees inferred from mt genome sequences as well. Our molecular dating results showed that Eriophyoidea originated in the Triassic and diversified in the Cretaceous, coinciding with the diversification of angiosperms. CONCLUSIONS This study reveals multiple molecular synapomorphies (i.e. shared derived mt gene clusters) at different levels (i.e. family, subfamily or tribe level) from the complete mt genomes of 153 eriophyoid mite species. We demonstrated the use of derived mt gene clusters in unveiling the higher-level phylogeny of eriophyoid mites, and underlines the origin of these mites and their co-diversification with angiosperms.
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Affiliation(s)
- Qi Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yi-Wen Lu
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xin-Yu Liu
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ye Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Wei-Nan Gao
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Renfu Shao
- Centre for Bioinnovation, School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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27
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Schwaha T, Decker SH, Baranyi C, Saadi AJ. Rediscovering the unusual, solitary bryozoan Monobryozoon ambulans Remane, 1936: first molecular and new morphological data clarify its phylogenetic position. Front Zool 2024; 21:5. [PMID: 38443908 PMCID: PMC10913646 DOI: 10.1186/s12983-024-00527-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND One of the most peculiar groups of the mostly colonial phylum Bryozoa is the taxon Monobryozoon, whose name already implies non-colonial members of the phylum. Its peculiarity and highly unusual lifestyle as a meiobenthic clade living on sand grains has fascinated many biologists. In particular its systematic relationship to other bryozoans remains a mystery. Despite numerous searches for M. ambulans in its type locality Helgoland, a locality with a long-lasting marine station and tradition of numerous courses and workshops, it has never been reencountered until today. Here we report the first observations of this almost mythical species, Monobryozoon ambulans. RESULTS For the first time since 1938, we present new modern, morphological analyses of this species as well as the first ever molecular data. Our detailed morphological analysis confirms most previous descriptions, but also ascertains the presence of special ambulatory polymorphic zooids. We consider these as bud anlagen that ultimately consecutively separate from the animal rendering it pseudo-colonial. The remaining morphological data show strong ties to alcyonidioidean ctenostome bryozoans. Our morphological data is in accordance with the phylogenomic analysis, which clusters it with species of Alcyonidium as a sister group to multiporate ctenostomes. Divergence time estimation and ancestral state reconstruction recover the solitary state of M. ambulans as a derived character that probably evolved in the Late Cretaceous. In this study, we also provide the entire mitogenome of M. ambulans, which-despite the momentary lack of comparable data-provides important data of a unique and rare species for comparative aspects in the future. CONCLUSIONS We were able to provide first sequence data and modern morphological data for the unique bryozoan, M. ambulans, which are both supporting an alcyonidioidean relationship within ctenostome bryozoans.
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Affiliation(s)
- Thomas Schwaha
- Department of Evolutionary Biology, University of Vienna, Schlachthausgasse 43, 1030, Vienna, Austria.
| | - Sebastian H Decker
- Department of Evolutionary Biology, University of Vienna, Schlachthausgasse 43, 1030, Vienna, Austria
| | - Christian Baranyi
- Department of Evolutionary Biology, University of Vienna, Schlachthausgasse 43, 1030, Vienna, Austria
| | - Ahmed J Saadi
- Department of Evolutionary Biology, University of Vienna, Schlachthausgasse 43, 1030, Vienna, Austria
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Chmelová Ľ, Záhonová K, Albanaz ATS, Hrebenyk L, Horváth A, Yurchenko V, Škodová-Sveráková I. Distribution and Functional Analysis of Isocitrate Dehydrogenases across Kinetoplastids. Genome Biol Evol 2024; 16:evae042. [PMID: 38447055 PMCID: PMC10946238 DOI: 10.1093/gbe/evae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/09/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024] Open
Abstract
Isocitrate dehydrogenase is an enzyme converting isocitrate to α-ketoglutarate in the canonical tricarboxylic acid (TCA) cycle. There are three different types of isocitrate dehydrogenase documented in eukaryotes. Our study points out the complex evolutionary history of isocitrate dehydrogenases across kinetoplastids, where the common ancestor of Trypanosomatidae and Bodonidae was equipped with two isoforms of the isocitrate dehydrogenase enzyme: the NADP+-dependent isocitrate dehydrogenase 1 with possibly dual localization in the cytosol and mitochondrion and NADP+-dependent mitochondrial isocitrate dehydrogenase 2. In the extant trypanosomatids, isocitrate dehydrogenase 1 is present only in a few species suggesting that it was lost upon separation of Trypanosoma spp. and replaced by the mainly NADP+-dependent cytosolic isocitrate dehydrogenase 3 of bacterial origin in all the derived lineages. In this study, we experimentally demonstrate that the omnipresent isocitrate dehydrogenase 2 has a dual localization in both mitochondrion and cytosol in at least four species that possess only this isoform. The apparent lack of the NAD+-dependent isocitrate dehydrogenase activity in trypanosomatid mitochondrion provides further support to the existence of the noncanonical TCA cycle across trypanosomatids and the bidirectional activity of isocitrate dehydrogenase 3 when operating with NADP+ cofactor instead of NAD+. This observation can be extended to all 17 species analyzed in this study, except for Leishmania mexicana, which showed only low isocitrate dehydrogenase activity in the cytosol. The variability in isocitrate oxidation capacity among species may reflect the distinct metabolic strategies and needs for reduced cofactors in particular environments.
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Affiliation(s)
- Ľubomíra Chmelová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Amanda T S Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Liudmyla Hrebenyk
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Anton Horváth
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Ingrid Škodová-Sveráková
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
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Tang W, Li X, Ye B, Shi B, Zhang H, Dang Z, Sun Y, Danqu L, Xia C, Quzhen D, Zhao X, Chui W, Huang F. Characterization of the complete mitochondrial genome and phylogenetic analyses of Haemaphysalis tibetensis Hoogstraal, 1965 (Acari: Ixodidae). Ticks Tick Borne Dis 2024; 15:102311. [PMID: 38262211 DOI: 10.1016/j.ttbdis.2024.102311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/25/2024]
Abstract
Ticks are specialized ectoparasites that feed on blood, causing physical harm to the host and facilitating pathogen transmission. The genus Haemaphysalis contains vectors for numerous infectious agents. These agents cause various diseases in humans and animals. Mitochondrial genome sequences serve as reliable molecular markers, forming a crucial basis for evolutionary analyses, studying species origins, and exploring molecular phylogeny. We extracted mitochondrial genome from the enriched mitochondria of Haemaphysalis tibetensis and obtained a 14,714-bp sequence. The mitochondrial genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNAs (tRNAs), and two control regions. The nucleotide composition of H. tibetensis mitochondrial genome was 38.38 % for A, 9.61 % for G, 39.32 % for T, and 12.69 % for C. The A + T content of H. tibetensis mitochondrial genome was 77.7 %, significantly higher than the G + C content. The repeat units of H. tibetensis exhibited two identical repeat units of 33 bp in length, positioned downstream of nad1 and rrnL genes. Furthermore, phylogenetic analyses based on the 13 PCGs indicated that Haemaphysalis tibetensis (subgenus Allophysalis) formed a monophyletic clade with Haemaphysalis nepalensis (subgenus Herpetobia) and Haemaphysalis danieli (subgenus Allophysalis). Although the species Haemaphysalis inermis, Haemaphysalis kitaokai, Haemaphysalis kolonini, and Haemaphysalis colasbelcouri belong to the subgenus Alloceraea, which were morphologically primitive hemaphysalines just like H. tibetensis, these four tick species cannot form a single clade with H. tibetensis. In this study, the whole mitochondrial genome sequence of H. tibetensis from Tibet was obtained, which enriched the mitochondrial genome data of ticks and provided genetic markers to study the population heredity and molecular evolution of the genus Haemaphysalis.
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Affiliation(s)
- Wenqiang Tang
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Xin Li
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Bijin Ye
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Bin Shi
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Haoji Zhang
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Zhisheng Dang
- National Institute of Parasitic Diseases at China CDC/Chinese Center for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, NHC Key Laboratory for Parasite and Vector Biology, Shanghai 200025, China
| | - Yuexiang Sun
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Lamu Danqu
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Chenyang Xia
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Danzeng Quzhen
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Xialing Zhao
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China
| | - Wenting Chui
- Animal Disease Prevention and Control Center of Qinghai Province, China
| | - Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China.
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Bierenbroodspot MJ, Darienko T, de Vries S, Fürst-Jansen JMR, Buschmann H, Pröschold T, Irisarri I, de Vries J. Phylogenomic insights into the first multicellular streptophyte. Curr Biol 2024; 34:670-681.e7. [PMID: 38244543 PMCID: PMC10849092 DOI: 10.1016/j.cub.2023.12.070] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024]
Abstract
Streptophytes are best known as the clade containing the teeming diversity of embryophytes (land plants).1,2,3,4 Next to embryophytes are however a range of freshwater and terrestrial algae that bear important information on the emergence of key traits of land plants. Among these, the Klebsormidiophyceae stand out. Thriving in diverse environments-from mundane (ubiquitous occurrence on tree barks and rocks) to extreme (from the Atacama Desert to the Antarctic)-Klebsormidiophyceae can exhibit filamentous body plans and display remarkable resilience as colonizers of terrestrial habitats.5,6 Currently, the lack of a robust phylogenetic framework for the Klebsormidiophyceae hampers our understanding of the evolutionary history of these key traits. Here, we conducted a phylogenomic analysis utilizing advanced models that can counteract systematic biases. We sequenced 24 new transcriptomes of Klebsormidiophyceae and combined them with 14 previously published genomic and transcriptomic datasets. Using an analysis built on 845 loci and sophisticated mixture models, we establish a phylogenomic framework, dividing the six distinct genera of Klebsormidiophyceae in a novel three-order system, with a deep divergence more than 830 million years ago. Our reconstructions of ancestral states suggest (1) an evolutionary history of multiple transitions between terrestrial-aquatic habitats, with stem Klebsormidiales having conquered land earlier than embryophytes, and (2) that the body plan of the last common ancestor of Klebsormidiophyceae was multicellular, with a high probability that it was filamentous whereas the sarcinoids and unicells in Klebsormidiophyceae are likely derived states. We provide evidence that the first multicellular streptophytes likely lived about a billion years ago.
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Affiliation(s)
- Maaike J Bierenbroodspot
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Sophie de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Janine M R Fürst-Jansen
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Technikumplatz 17, 09648 Mittweida, Germany
| | - Thomas Pröschold
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Innsbruck, Research Department for Limnology, 5310 Mondsee, Austria
| | - Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany; Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Martin-Luther-King Platz 3, 20146 Hamburg, Germany.
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany.
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31
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Harada R, Hirakawa Y, Yabuki A, Kim E, Yazaki E, Kamikawa R, Nakano K, Eliáš M, Inagaki Y. Encyclopedia of Family A DNA Polymerases Localized in Organelles: Evolutionary Contribution of Bacteria Including the Proto-Mitochondrion. Mol Biol Evol 2024; 41:msae014. [PMID: 38271287 PMCID: PMC10877234 DOI: 10.1093/molbev/msae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
DNA polymerases synthesize DNA from deoxyribonucleotides in a semiconservative manner and serve as the core of DNA replication and repair machinery. In eukaryotic cells, there are 2 genome-containing organelles, mitochondria, and plastids, which were derived from an alphaproteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNA polymerases that localize and work in them to maintain their genomes. The evolution of organellar DNA polymerases has yet to be fully understood because of 2 unsettled issues. First, the diversity of organellar DNA polymerases has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNA polymerases that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNA polymerases known to date show no phylogenetic affinity to those of the extant alphaproteobacteria or cyanobacteria. In this study, we identified from diverse eukaryotes 134 family A DNA polymerase sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNA polymerases were further examined experimentally. The results presented here suggest that the diversity of organellar DNA polymerases has been shaped by multiple transfers of the PolI gene from phylogenetically broad bacteria, and their occurrence in eukaryotes was additionally impacted by secondary plastid endosymbioses. Finally, we propose that the last eukaryotic common ancestor may have possessed 2 mitochondrial DNA polymerases, POP, and a candidate of the direct descendant of the proto-mitochondrial DNA polymerase I, rdxPolA, identified in this study.
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Affiliation(s)
- Ryo Harada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yoshihisa Hirakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Akinori Yabuki
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Eunsoo Kim
- Division of EcoScience, Ewha Womans University, Seoul, South Korea
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Euki Yazaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Japan
- Interdisciplinary Theoretical and Mathematical Sciences program (iTHEMS), RIKEN, Wako, Saitama, Japan
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kentaro Nakano
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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Eglit Y, Shiratori T, Jerlström-Hultqvist J, Williamson K, Roger AJ, Ishida KI, Simpson AGB. Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora. Curr Biol 2024; 34:451-459.e6. [PMID: 38262350 DOI: 10.1016/j.cub.2023.12.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 01/25/2024]
Abstract
"Kingdom-level" branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down.1,2,3,4 Some are completely new discoveries, whereas others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19th century but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted.2Meteora sporadica5 is a protist with a unique morphology; cells glide over substrates along a long axis of anterior and posterior projections while a pair of lateral "arms" swing back and forth, a motility system without any obvious parallels. Originally, Meteora was described by light microscopy only, from a short-term enrichment of deep-sea sediment. A small subunit ribosomal RNA (SSU rRNA) sequence was reported recently, but the phylogenetic placement of Meteora remained unresolved.6 Here, we investigated two cultivated Meteora sporadica isolates in detail. Transmission electron microscopy showed that both the anterior-posterior projections and the arms are supported by microtubules originating from a cluster of subnuclear microtubule organizing centers (MTOCs). Neither have a flagellar axoneme-like structure. Sequencing the mitochondrial genome showed this to be among the most gene-rich known, outside jakobids. Remarkably, phylogenomic analyses of 254 nuclear protein-coding genes robustly support a close relationship with Hemimastigophora. Our study suggests that Meteora and Hemimastigophora together represent a morphologically diverse "supergroup" and thus are important for resolving the tree of eukaryote life and early eukaryote evolution.
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Affiliation(s)
- Yana Eglit
- Institute for Comparative Genomics, Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Takashi Shiratori
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Jon Jerlström-Hultqvist
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Kelsey Williamson
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Andrew J Roger
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Ken-Ichiro Ishida
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
| | - Alastair G B Simpson
- Institute for Comparative Genomics, Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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Cai C. Ant backbone phylogeny resolved by modelling compositional heterogeneity among sites in genomic data. Commun Biol 2024; 7:106. [PMID: 38233456 PMCID: PMC10794244 DOI: 10.1038/s42003-024-05793-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/08/2024] [Indexed: 01/19/2024] Open
Abstract
Ants are the most ubiquitous and ecologically dominant arthropods on Earth, and understanding their phylogeny is crucial for deciphering their character evolution, species diversification, and biogeography. Although recent genomic data have shown promise in clarifying intrafamilial relationships across the tree of ants, inconsistencies between molecular datasets have also emerged. Here I re-examine the most comprehensive published Sanger-sequencing and genome-scale datasets of ants using model comparison methods that model among-site compositional heterogeneity to understand the sources of conflict in phylogenetic studies. My results under the best-fitting model, selected on the basis of Bayesian cross-validation and posterior predictive model checking, identify contentious nodes in ant phylogeny whose resolution is modelling-dependent. I show that the Bayesian infinite mixture CAT model outperforms empirical finite mixture models (C20, C40 and C60) and that, under the best-fitting CAT-GTR + G4 model, the enigmatic Martialis heureka is sister to all ants except Leptanillinae, rejecting the more popular hypothesis supported under worse-fitting models, that place it as sister to Leptanillinae. These analyses resolve a lasting controversy in ant phylogeny and highlight the significance of model comparison and adequate modelling of among-site compositional heterogeneity in reconstructing the deep phylogeny of insects.
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Affiliation(s)
- Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China.
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Maire J, Collingro A, Tandon K, Jameson VJ, Judd LM, Horn M, Blackall LL, van Oppen MJH. Chlamydiae as symbionts of photosynthetic dinoflagellates. THE ISME JOURNAL 2024; 18:wrae139. [PMID: 39046276 PMCID: PMC11317633 DOI: 10.1093/ismejo/wrae139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/13/2024] [Accepted: 07/23/2024] [Indexed: 07/25/2024]
Abstract
Chlamydiae are ubiquitous intracellular bacteria and infect a wide diversity of eukaryotes, including mammals. However, chlamydiae have never been reported to infect photosynthetic organisms. Here, we describe a novel chlamydial genus and species, Candidatus Algichlamydia australiensis, capable of infecting the photosynthetic dinoflagellate Cladocopium sp. (originally isolated from a scleractinian coral). Algichlamydia australiensis was confirmed to be intracellular by fluorescence in situ hybridization and confocal laser scanning microscopy and temporally stable at the population level by monitoring its relative abundance across four weeks of host growth. Using a combination of short- and long-read sequencing, we recovered a high-quality (completeness 91.73% and contamination 0.27%) metagenome-assembled genome of A. australiensis. Phylogenetic analyses show that this chlamydial taxon represents a new genus and species within the Simkaniaceae family. Algichlamydia australiensis possesses all the hallmark genes for chlamydiae-host interactions, including a complete type III secretion system. In addition, a type IV secretion system is encoded on a plasmid and has previously been observed for only three other chlamydial species. Twenty orthologous groups of genes are unique to A. australiensis, one of which is structurally similar to a protein known from Cyanobacteria and Archaeplastida involved in thylakoid biogenesis and maintenance, hinting at potential chlamydiae interactions with the chloroplasts of Cladocopium cells. Our study shows that chlamydiae infect dinoflagellate symbionts of cnidarians, the first photosynthetic organism reported to harbor chlamydiae, thereby expanding the breadth of chlamydial hosts and providing a new contribution to the discussion around the role of chlamydiae in the establishment of the primary plastid.
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Affiliation(s)
- Justin Maire
- School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Kshitij Tandon
- School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Vanta J Jameson
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute of Infection and Immunity, Parkville, VIC 3010, Australia
- Melbourne Cytometry Platform, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Louise M Judd
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Linda L Blackall
- School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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35
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Cho A, Tikhonenkov DV, Lax G, Prokina KI, Keeling PJ. Phylogenomic position of genetically diverse phagotrophic stramenopile flagellates in the sediment-associated MAST-6 lineage and a potentially halotolerant placididean. Mol Phylogenet Evol 2024; 190:107964. [PMID: 37951557 DOI: 10.1016/j.ympev.2023.107964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 11/02/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
Unlike morphologically conspicuous ochrophytes, many flagellates belonging to basally branching stramenopiles are small and often overlooked. As a result, many of these lineages are known only through molecular surveys and identified as MArine STramenopiles (MAST), and remain largely uncharacterized at the cellular or genomic level. These likely phagotrophic flagellates are not only phylogenetically diverse, but also extremely abundant in some environments, making their characterization all the more important. MAST-6 is one example of a phylogenetically distinct group that has been known to be associated with sediments, but little else is known about it. Indeed, until the present study, only a single species from this group, Pseudophyllomitus vesiculosus (Pseudophyllomitidae), has been both formally described and associated with genomic information. Here, we describe four new species including two new genera of sediment-dwelling MAST-6, Vomastramonas tehuelche gen. et sp. nov., Mastreximonas tlaamin gen. et sp. nov., one undescribed Pseudophyllomitus sp., BSC2, and a new species belonging to Placididea, the potentially halotolerant Haloplacidia sinai sp. nov. We also provide two additional bikosian transcriptomes from a public culture collection, to allow for better phylogenetic reconstructions of deep-branching stramenopiles. With the SSU rRNA sequences of the new MAST-6 species, we investigate the phylogenetic diversity of the MAST-6 group and show a high relative abundance of MAST-6 related to M. tlaamin in samples across various depths and geographical locations. Using the new MAST-6 species, we also update the phylogenomic tree of stramenopiles, particularly focusing on the paraphyly of Bigyra.
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Affiliation(s)
- Anna Cho
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
| | - Denis V Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Science, Borok 152742, Russia
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
| | - Kristina I Prokina
- Papanin Institute for Biology of Inland Waters, Russian Academy of Science, Borok 152742, Russia; Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
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36
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Jones RE, Tice AK, Eliáš M, Eme L, Kolísko M, Nenarokov S, Pánek T, Rokas A, Salomaki E, Strassert JFH, Shen XX, Žihala D, Brown MW. Create, Analyze, and Visualize Phylogenomic Datasets Using PhyloFisher. Curr Protoc 2024; 4:e969. [PMID: 38265166 DOI: 10.1002/cpz1.969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
PhyloFisher is a software package written primarily in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of protein sequences from eukaryotic organisms. Unlike many existing phylogenomic pipelines, PhyloFisher comes with a manually curated database of 240 protein-coding genes, a subset of a previous phylogenetic dataset sampled from 304 eukaryotic taxa. The software package can also utilize a user-created database of eukaryotic proteins, which may be more appropriate for shallow evolutionary questions. PhyloFisher is also equipped with a set of utilities to aid in running routine analyses, such as the prediction of alternative genetic codes, removal of genes and/or taxa based on occupancy/completeness of the dataset, testing for amino acid compositional heterogeneity among sequences, removal of heterotachious and/or fast-evolving sites, removal of fast-evolving taxa, supermatrix creation from randomly resampled genes, and supermatrix creation from nucleotide sequences. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Constructing a phylogenomic dataset Basic Protocol 2: Performing phylogenomic analyses Support Protocol 1: Installing PhyloFisher Support Protocol 2: Creating a custom phylogenomic database.
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Affiliation(s)
- Robert E Jones
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, Mississippi, USA
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, Mississippi, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Laura Eme
- Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Saclay France, Orsay, France
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice Czech Republic, USA
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Serafim Nenarokov
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice Czech Republic, USA
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Eric Salomaki
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice Czech Republic, USA
- Center for Computational Biology of Human Disease and Center for Computation and Visualization, Brown University, Providence, Rhode Island, USA
| | - Jürgen F H Strassert
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Xing-Xing Shen
- Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - David Žihala
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, Mississippi, USA
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37
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Nishihara H, Toda Y, Kuramoto T, Kamohara K, Goto A, Hoshino K, Okada S, Kuraku S, Okabe M, Ishimaru Y. A vertebrate-wide catalogue of T1R receptors reveals diversity in taste perception. Nat Ecol Evol 2024; 8:111-120. [PMID: 38093021 PMCID: PMC10781636 DOI: 10.1038/s41559-023-02258-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/25/2023] [Indexed: 01/12/2024]
Abstract
Taste is a vital chemical sense for feeding behaviour. In mammals, the umami and sweet taste receptors comprise three members of the taste receptor type 1 (T1R/TAS1R) family: T1R1, T1R2 and T1R3. Because their functional homologues exist in teleosts, only three TAS1R genes generated by gene duplication are believed to have been inherited from the common ancestor of bony vertebrates. Here, we report five previously uncharacterized TAS1R members in vertebrates, TAS1R4, TAS1R5, TAS1R6, TAS1R7 and TAS1R8, based on genome-wide survey of diverse taxa. We show that mammalian and teleost fish TAS1R2 and TAS1R3 genes are paralogues. Our phylogenetic analysis suggests that the bony vertebrate ancestor had nine TAS1Rs resulting from multiple gene duplications. Some TAS1Rs were lost independently in descendent lineages resulting in retention of only three TAS1Rs in mammals and teleosts. Combining functional assays and expression analysis of non-teleost fishes we show that the novel T1Rs form heterodimers in taste-receptor cells and recognize a broad range of ligands such as essential amino acids, including branched-chain amino acids, which have not been previously considered as T1R ligands. This study reveals diversity of taste sensations in both modern vertebrates and their ancestors, which might have enabled vertebrates to adapt to diverse habitats on Earth.
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Affiliation(s)
- Hidenori Nishihara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan.
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
| | - Yasuka Toda
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Tae Kuramoto
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Kota Kamohara
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Azusa Goto
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Kyoko Hoshino
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Shinji Okada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Japan
- Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan
| | - Masataka Okabe
- Department of Anatomy, The Jikei University School of Medicine, Tokyo, Japan
| | - Yoshiro Ishimaru
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan.
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38
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Morreale DP, St Geme III JW, Planet PJ. Phylogenomic analysis of the understudied Neisseriaceae species reveals a poly- and paraphyletic Kingella genus. Microbiol Spectr 2023; 11:e0312323. [PMID: 37882538 PMCID: PMC10715097 DOI: 10.1128/spectrum.03123-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/15/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Understanding the evolutionary relationships between the species in the Neisseriaceae family has been a persistent challenge in bacterial systematics due to high recombination rates in these species. Previous studies of this family have focused on Neisseria meningitidis and N. gonorrhoeae. However, previously understudied Neisseriaceae species are gaining new attention, with Kingella kingae now recognized as a common human pathogen and with Alysiella and Simonsiella being unique in the bacterial world as multicellular organisms. A better understanding of the genomic evolution of the Neisseriaceae can lead to the identification of specific genes and traits that underlie the remarkable diversity of this family.
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Affiliation(s)
- Daniel P. Morreale
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joseph W. St Geme III
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Paul J. Planet
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Comparative Genomics, American Museum of Natural History, New York, New York, USA
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39
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Huang F, Li X, Ye B, Zhou Y, Dang Z, Tang W, Wang L, Zhang H, Chui W, Kui J. Characterization of the Complete Mitochondrial Genome and Phylogenetic Analyses of Eurytrema coelomaticum (Trematoda: Dicrocoeliidae). Genes (Basel) 2023; 14:2199. [PMID: 38137020 PMCID: PMC10743053 DOI: 10.3390/genes14122199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Eurytrema coelomaticum, a pancreatic fluke, is recognized as a causative agent of substantial economic losses in ruminants. This infection, commonly referred to as eurytrematosis, is a significant concern due to its detrimental impact on livestock production. However, there is a paucity of knowledge regarding the mitochondrial genome of E. coelomaticum. In this study, we performed the initial sequencing of the complete mitochondrial genome of E. coelomaticum. Our findings unveiled that the mitochondrial genome of E. coelomaticum spans a length of 15,831 bp and consists of 12 protein-coding genes, 22 tRNA genes, two rRNA genes, and two noncoding regions. The A+T content constituted 62.49% of the genome. Moreover, all 12 protein-coding genes of E. coelomaticum exhibit the same arrangement as those of E. pancreaticum and other published species belonging to the family Dicrocoeliidae. The presence of a short string of additional amino acids (approximately 20~23 aa) at the N-terminal of the cox1 protein in both E. coelomaticum and E. pancreaticum mitochondrial genomes has contributed to the elongation of the cox1 gene in genus Eurytrema, surpassing that of all previously sequenced Dicrocoeliidae. The phylogenetic analysis displayed a close relationship between E. coelomaticum and E. pancreaticum, along with a genus-level association between Eurytrema and Lyperosomum. These findings underscore the importance of mitochondrial genomic data for comparative studies of Dicrocoeliidae and even Digenea, offering valuable DNA markers for future investigations in the systematic, epidemiological, and population genetic studies of this parasite and other digenean trematodes.
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Affiliation(s)
- Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Xin Li
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Bijin Ye
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Yule Zhou
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Zhisheng Dang
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People’s Republic of China (NHC), World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Wenqiang Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
- Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850009, China
| | - Long Wang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Haoji Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Wenting Chui
- Animal Disease Prevention and Control Center of Qinghai Province, Xining 810003, China
| | - Jun Kui
- Huangzhong District Animal Husbandry and Veterinary Station, Xining 811600, China
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40
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Bowman J, Enard D, Lynch VJ. Phylogenomics reveals an almost perfect polytomy among the almost ungulates ( Paenungulata). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570590. [PMID: 38106080 PMCID: PMC10723481 DOI: 10.1101/2023.12.07.570590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Phylogenetic studies have resolved most relationships among Eutherian Orders. However, the branching order of elephants (Proboscidea), hyraxes (Hyracoidea), and sea cows (Sirenia) (i.e., the Paenungulata) has remained uncertain since at least 1758, when Linnaeus grouped elephants and manatees into a single Order (Bruta) to the exclusion of hyraxes. Subsequent morphological, molecular, and large-scale phylogenomic datasets have reached conflicting conclusions on the branching order within Paenungulates. We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261 Eutherian mammals to infer phylogenetic relationships within Paenungulates. We find that gene trees almost equally support the three alternative resolutions of Paenungulate relationships and that despite strong support for a Proboscidea+Hyracoidea split in the multispecies coalescent (MSC) tree, there is significant evidence for gene tree uncertainty, incomplete lineage sorting, and introgression among Proboscidea, Hyracoidea, and Sirenia. Indeed, only 8-10% of genes have statistically significant phylogenetic signal to reject the hypothesis of a Paenungulate polytomy. These data indicate little support for any resolution for the branching order Proboscidea, Hyracoidea, and Sirenia within Paenungulata and suggest that Paenungulata may be as close to a real, or at least unresolvable, polytomy as possible.
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Affiliation(s)
- Jacob Bowman
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
| | - David Enard
- Department of Ecology and Evolutionary Biology. University of Arizona, Tucson, AZ, USA
| | - Vincent J. Lynch
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
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41
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Harada R, Inagaki Y. Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data. Protist 2023; 174:125997. [PMID: 38039844 DOI: 10.1016/j.protis.2023.125997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
Multiple genes encoding family A DNA polymerases (famA DNAPs), which are evolutionary relatives of DNA polymerase I (PolI) in bacteria and phages, have been found in eukaryotic genomes, and many of these proteins are used mainly in organelles. Among members of the phylum Euglenozoa, distinct types of famA DNAP, PolIA, PolIBCD+, POP, and eugPolA, have been found. It is intriguing how the suite of famA DNAPs had been established during the evolution of Euglenozoa, but the DNAP data have not been sampled from the taxa that sufficiently represent the diversity of this phylum. In particular, little sequence data were available for basal branching species in Euglenozoa until recently. Thanks to the single-cell transcriptome data from symbiontids and phagotrophic euglenids, we have an opportunity to cover the "hole" in the repertory of famA DNAPs in the deep branches in Euglenozoa. The current study identified 16 new famA DNAP sequences in the transcriptome data from 33 phagotrophic euglenids and two symbiontids, respectively. Based on the new famA DNAP sequences, the updated diversity and evolution of famA DNAPs in Euglenozoa are discussed.
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Affiliation(s)
- Ryo Harada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan; Center for Computational Sciences, University of Tsukuba, Japan.
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42
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Thomé PC, Irisarri I, Wolinska J, Monaghan MT, Strassert JFH. Single-cell genomics reveals new rozellid lineages and supports their sister relationship to Microsporidia. Biol Lett 2023; 19:20230398. [PMID: 38087939 PMCID: PMC10716661 DOI: 10.1098/rsbl.2023.0398] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The phylum Rozellomycota has been proposed for a group of early-branching holomycotan lineages representing obligate parasites and hyperparasites of zoosporic fungi, oomycotes or phytoplankton. Given their predominantly intracellular lifestyle, rozellids are typically known from environmental ribosomal DNA data, except for the well-studied Rozella species. To date, the phylogenetic relationship between rozellids and microsporidians (Microsporidia) is not fully understood and most reliable hypotheses are based on phylogenomic analyses that incorporate the only publicly available rozellid genome of Rozella allomycis. Here, we provide genomic data of three new rozellid lineages obtained by single-cell sequencing from environmental samples and show with a phylogenomic approach that rozellids form a monophyletic group that is sister to microsporidians, corroborating the previously proposed phylum Rozellomycota. Whereas no mitochondrial genes coding for the respiratory Complex I could be found, we discovered a gene coding for a nucleotide phosphate transporter in one of the three draft genomes. The scattered absence of Complex I genes and scattered presence of nucleotide transporter genes across diverse microsporidian and rozellid lineages suggest that these adaptations to a parasitic lifestyle, which reduce the parasite's capability to synthesize ATP but enables it to steal ATP from its host, evolved independently in microsporidians and rozellids.
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Affiliation(s)
- Pauline C. Thomé
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Iker Irisarri
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature Hamburg, Hamburg, Germany
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Michael T. Monaghan
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Jürgen F. H. Strassert
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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43
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Cao W, Wu LY, Xia XY, Chen X, Wang ZX, Pan XM. A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins. Sci Rep 2023; 13:20304. [PMID: 37985846 PMCID: PMC10662474 DOI: 10.1038/s41598-023-47496-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023] Open
Abstract
Because of the limited effectiveness of prevailing phylogenetic methods when applied to highly divergent protein sequences, the phylogenetic analysis problem remains challenging. Here, we propose a sequence-based evolutionary distance algorithm termed sequence distance (SD), which innovatively incorporates site-to-site correlation within protein sequences into the distance estimation. In protein superfamilies, SD can effectively distinguish evolutionary relationships both within and between protein families, producing phylogenetic trees that closely align with those based on structural information, even with sequence identity less than 20%. SD is highly correlated with the similarity of the protein structure, and can calculate evolutionary distances for thousands of protein pairs within seconds using a single CPU, which is significantly faster than most protein structure prediction methods that demand high computational resources and long run times. The development of SD will significantly advance phylogenetics, providing researchers with a more accurate and reliable tool for exploring evolutionary relationships.
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Affiliation(s)
- Wei Cao
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lu-Yun Wu
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xia-Yu Xia
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiang Chen
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhi-Xin Wang
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Xian-Ming Pan
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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44
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Kapli P, Kotari I, Telford MJ, Goldman N, Yang Z. DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies. Syst Biol 2023; 72:1119-1135. [PMID: 37366056 PMCID: PMC10627555 DOI: 10.1093/sysbio/syad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Indexed: 06/28/2023] Open
Abstract
Inference of deep phylogenies has almost exclusively used protein rather than DNA sequences based on the perception that protein sequences are less prone to homoplasy and saturation or to issues of compositional heterogeneity than DNA sequences. Here, we analyze a model of codon evolution under an idealized genetic code and demonstrate that those perceptions may be misconceptions. We conduct a simulation study to assess the utility of protein versus DNA sequences for inferring deep phylogenies, with protein-coding data generated under models of heterogeneous substitution processes across sites in the sequence and among lineages on the tree, and then analyzed using nucleotide, amino acid, and codon models. Analysis of DNA sequences under nucleotide-substitution models (possibly with the third codon positions excluded) recovered the correct tree at least as often as analysis of the corresponding protein sequences under modern amino acid models. We also applied the different data-analysis strategies to an empirical dataset to infer the metazoan phylogeny. Our results from both simulated and real data suggest that DNA sequences may be as useful as proteins for inferring deep phylogenies and should not be excluded from such analyses. Analysis of DNA data under nucleotide models has a major computational advantage over protein-data analysis, potentially making it feasible to use advanced models that account for among-site and among-lineage heterogeneity in the nucleotide-substitution process in inference of deep phylogenies.
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Affiliation(s)
- Paschalia Kapli
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
| | - Ioanna Kotari
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, 1210, Austria
| | - Maximilian J Telford
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
| | - Nick Goldman
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ziheng Yang
- Department of Genetics, University College London, Gower Street, London WC1E 6BT, UK
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45
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Roberts WR, Ruck EC, Downey KM, Pinseel E, Alverson AJ. Resolving Marine-Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance. Syst Biol 2023; 72:984-997. [PMID: 37335140 DOI: 10.1093/sysbio/syad038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 06/02/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023] Open
Abstract
Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats worldwide. We generated a phylogenomic data set of genomes and transcriptomes for 59 diatom taxa to resolve freshwater transitions in one lineage, the Thalassiosirales. Although most parts of the species tree were consistently resolved with strong support, we had difficulties resolving a Paleocene radiation, which affected the placement of one freshwater lineage. This and other parts of the tree were characterized by high levels of gene tree discordance caused by incomplete lineage sorting and low phylogenetic signal. Despite differences in species trees inferred from concatenation versus summary methods and codons versus amino acids, traditional methods of ancestral state reconstruction supported six transitions into freshwaters, two of which led to subsequent species diversification. Evidence from gene trees, protein alignments, and diatom life history together suggest that habitat transitions were largely the product of homoplasy rather than hemiplasy, a condition where transitions occur on branches in gene trees not shared with the species tree. Nevertheless, we identified a set of putatively hemiplasious genes, many of which have been associated with shifts to low salinity, indicating that hemiplasy played a small but potentially important role in freshwater adaptation. Accounting for differences in evolutionary outcomes, in which some taxa became locked into freshwaters while others were able to return to the ocean or become salinity generalists, might help further distinguish different sources of adaptive mutation in freshwater diatoms.
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Affiliation(s)
- Wade R Roberts
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Elizabeth C Ruck
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Kala M Downey
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Eveline Pinseel
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
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46
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Brabec J, Salomaki ED, Kolísko M, Scholz T, Kuchta R. The evolution of endoparasitism and complex life cycles in parasitic platyhelminths. Curr Biol 2023; 33:4269-4275.e3. [PMID: 37729914 DOI: 10.1016/j.cub.2023.08.064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/05/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023]
Abstract
Within flatworms, the vast majority of parasitism is innate to Neodermata, the most derived and diversified group of the phylum Platyhelminthes.1,2 The four major lineages of Neodermata maintain various combinations of life strategies.3 They include both externally (ecto-) and internally feeding (endo-) parasites. Some lineages complete their life cycles directly by infecting a single host, whereas others succeed only through serial infections of multiple hosts of various vertebrate and invertebrate groups. Food sources and modes of digestion add further combinatorial layers to the often incompletely understood mosaic of neodermatan life histories. Their evolutionary trajectories have remained molecularly unresolved because of conflicting evolutionary inferences and a lack of genomic data.4 Here, we generated transcriptomes for nine early branching neodermatan representatives and performed detailed phylogenomic analyses to address these critical gaps. Polyopisthocotylea, mostly hematophagous ectoparasites, form a group with the mostly hematophagous but endoparasitic trematodes (Trematoda), rather than sharing a common ancestor with Monopisthocotylea, ectoparasitic epithelial feeders. Phylogenetic placement of the highly specialized endoparasitic Cestoda alters depending on the model. Regardless of this uncertainty, this study brings an unconventional perspective on the evolution of platyhelminth parasitism, rejecting a common origin for the endoparasitic lifestyle intrinsic to cestodes and trematodes. Instead, our data indicate that complex life cycles and invasion of vertebrates' gut lumen, the hallmark features of these parasites, evolved independently within Neodermata. We propose the demise of the traditionally recognized class Monogenea and the promotion of its two subclasses to the class level as Monopisthocotyla new class and Polyopisthocotyla new class.
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Affiliation(s)
- Jan Brabec
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice 37005, Czech Republic.
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice 37005, Czech Republic; Center for Computational Biology of Human Disease and Center for Computation and Visualization, Brown University, 180 George St, Providence, RI 02906, USA
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice 37005, Czech Republic
| | - Tomáš Scholz
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice 37005, Czech Republic
| | - Roman Kuchta
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice 37005, Czech Republic
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Dai M, He SL, Chen B, Li TJ. Phylogeny of Rhynchium and Its Related Genera (Hymenoptera: Eumeninae) Based on Universal Single-Copy Orthologs and Ultraconserved Elements. INSECTS 2023; 14:775. [PMID: 37754743 PMCID: PMC10532281 DOI: 10.3390/insects14090775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]
Abstract
The subfamily Eumeninae is a large group of fierce predatory insects that prey mainly on the larvae of Lepidoptera pests. Because of the highly similar morphologies of the genus Rhynchium and its related genera in the subfamily, including Rhynchium Spinola, Allorhynchium van der Vecht, Anterhynchium de Saussure, Pararrhynchium de Saussure, it is essential to delineate their relationships. A previous phylogenetic analysis based on mitochondrial genomes suggested the inconsistent relationships of these genera under traditional classification based on morphological characters. In this study, we first used single-copy orthologs [USCO] and ultraconserved elements [UCE] extracted from 10 newly sequenced low-coverage whole genomes to resolve the phylogenetic relationships of the above genera. The newly sequenced genomes are 152.99 Mb to 211.49 Mb in size with high completeness (BUSCO complete: 91.5-95.6%) and G + C content (36.31-38.76%). Based on extracted 5811 USCOs and 2312 UCEs, the phylogenetic relationships of Rhynchium and its related genera were: ((Allorhynchium + Lissodynerus) + (Pararrhynchium + (Anterhynchium + (Dirhynchium + Rhynchium)))), which was consistent with the mitochondrial genome results. The results supported the genus Rhynchium as monophyletic, whereas Anterhynchium was recovered as paraphyletic, with Anterhynchium (Dirhynchium) as a sister to Rhynchium and hence deserving generic status; In addition, in the genus Pararrhynchium, P. septemfasciatus feanus and P. venkataramani were separated, not clustered on a branch, just as P. septemfasciatus feanus was not together with P. striatum based on mitochondrial genomes. Since Lissodynerus septemfasciatus, the type species of the genus Lissodynerus, was transferred to Pararrhynchium, it is considered that the genus Lissodynerus should be restituted as a valid genus, not a synonym of Pararrhynchium.
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Affiliation(s)
| | | | | | - Ting-Jing Li
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Science, Chongqing Normal University, Chongqing 401331, China; (M.D.); (S.-L.H.); (B.C.)
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48
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Bailey NP, Shao Y, Du S, Foster PG, Fettweis J, Hall N, Wang Z, Hirt RP. Evolutionary conservation of Trichomonas-mycoplasma symbiosis across the host species barrier. Front Microbiol 2023; 14:1242275. [PMID: 37808290 PMCID: PMC10557491 DOI: 10.3389/fmicb.2023.1242275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction The protozoan parasite Trichomonas vaginalis is the most common cellular sexually transmitted disease in humans, and the closely related species Trichomonas gallinae is an avian parasite of ecological and economic importance. Phylogenetic evidence suggests T. vaginalis arose during bird to human transmission of a T. gallinae-like ancestor. Trichomonas vaginalis shares a strong clinical association with the independent sexually transmitted pathogen Metamycoplasma (formerly Mycoplasma) hominis, and the uncultured bacterium "Candidatus Malacoplasma (formerly Mycoplasma) girerdii," with the latter association being an order of magnitude stronger. Both bacterial species have been shown to profoundly influence T. vaginalis growth, energy production and virulence-associated mechanisms. Methods Evidence for a novel Malacoplasma sp. was discovered by in vivo Illumina metatranscriptomics sequencing of the T. gallinae-infected pigeon mouth. We leveraged published 16S rDNA profiling data from digestive tract of 12 healthy and 24 T. gallinae-infected pigeons to investigate association between the novel Malacoplasma sp. and T. gallinae. We utilised Illumina metagenomics sequencing targeted to pigeon oral and crop samples infected with the novel Malacoplasma sp. to generate its full-length genome sequence. Sequence similarity network analysis was used to compare annotated proteins from the novel Malacoplasma sp. with a range of other related species. Results Here we present evidence for a novel Malacoplasma species, related to "Ca. M. girerdii," that is strongly associated with T. gallinae in the upper digestive tract of domestic pigeons. Analysis of the genome sequence revealed gene features apparently specific to a Trichomonas-symbiotic Malacoplasma lineage. Discussion These data support a model of long-term association between Trichomonas and Malacoplasma spp. that has been conserved across diversification of the Trichomonas lineage and the host species barrier from birds to human.
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Affiliation(s)
- Nicholas P. Bailey
- Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Yuxin Shao
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shaodua Du
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | | | | | - Neil Hall
- Earlham Institute, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Zheng Wang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Robert P. Hirt
- Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
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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] [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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50
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Farrell AA, Nesbø CL, Zhaxybayeva O. Early Divergence and Gene Exchange Highways in the Evolutionary History of Mesoaciditogales. Genome Biol Evol 2023; 15:evad156. [PMID: 37616556 PMCID: PMC10476701 DOI: 10.1093/gbe/evad156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
The placement of a nonhyperthermophilic order Mesoaciditogales as the earliest branching clade within the Thermotogota phylum challenges the prevailing hypothesis that the last common ancestor of Thermotogota was a hyperthermophile. Yet, given the long branch leading to the only two Mesoaciditogales described to date, the phylogenetic position of the order may be due to the long branch attraction artifact. By testing various models and applying data recoding in phylogenetic reconstructions, we observed that early branching of Mesoaciditogales within Thermotogota is strongly supported by the conserved marker genes assumed to be vertically inherited. However, based on the taxonomic content of 1,181 gene families and a phylogenetic analysis of 721 gene family trees, we also found that a substantial number of Mesoaciditogales genes are more closely related to species from the order Petrotogales. These genes contribute to coenzyme transport and metabolism, fatty acid biosynthesis, genes known to respond to heat and cold stressors, and include many genes of unknown functions. The Petrotogales comprise moderately thermophilic and mesophilic species with similar temperature tolerances to that of Mesoaciditogales. Our findings hint at extensive horizontal gene transfer (HGT) between, or parallel independent gene gains by, the two ecologically similar lineages and suggest that the exchanged genes may be important for adaptation to comparable temperature niches.
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Affiliation(s)
- Anne A Farrell
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Camilla L Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire, USA
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