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Nowell RW, Rodriguez F, Hecox-Lea BJ, Mark Welch DB, Arkhipova IR, Barraclough TG, Wilson CG. Bdelloid rotifers deploy horizontally acquired biosynthetic genes against a fungal pathogen. Nat Commun 2024; 15:5787. [PMID: 39025839 PMCID: PMC11258130 DOI: 10.1038/s41467-024-49919-1] [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: 05/16/2023] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
Coevolutionary antagonism generates relentless selection that can favour genetic exchange, including transfer of antibiotic synthesis and resistance genes among bacteria, and sexual recombination of disease resistance alleles in eukaryotes. We report an unusual link between biological conflict and DNA transfer in bdelloid rotifers, microscopic animals whose genomes show elevated levels of horizontal gene transfer from non-metazoan taxa. When rotifers were challenged with a fungal pathogen, horizontally acquired genes were over twice as likely to be upregulated as other genes - a stronger enrichment than observed for abiotic stressors. Among hundreds of upregulated genes, the most markedly overrepresented were clusters resembling bacterial polyketide and nonribosomal peptide synthetases that produce antibiotics. Upregulation of these clusters in a pathogen-resistant rotifer species was nearly ten times stronger than in a susceptible species. By acquiring, domesticating, and expressing non-metazoan biosynthetic pathways, bdelloids may have evolved to resist natural enemies using antimicrobial mechanisms absent from other animals.
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Affiliation(s)
- Reuben W Nowell
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Department of Life Sciences, Imperial College London; Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
- Institute of Ecology and Evolution, University of Edinburgh; Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Bette J Hecox-Lea
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - David B Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Timothy G Barraclough
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Department of Life Sciences, Imperial College London; Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Christopher G Wilson
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
- Department of Life Sciences, Imperial College London; Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK.
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2
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Keeling PJ. Horizontal gene transfer in eukaryotes: aligning theory with data. Nat Rev Genet 2024; 25:416-430. [PMID: 38263430 DOI: 10.1038/s41576-023-00688-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 01/25/2024]
Abstract
Horizontal gene transfer (HGT), or lateral gene transfer, is the non-sexual movement of genetic information between genomes. It has played a pronounced part in bacterial and archaeal evolution, but its role in eukaryotes is less clear. Behaviours unique to eukaryotic cells - phagocytosis and endosymbiosis - have been proposed to increase the frequency of HGT, but nuclear genomes encode fewer HGTs than bacteria and archaea. Here, I review the existing theory in the context of the growing body of data on HGT in eukaryotes, which suggests that any increased chance of acquiring new genes through phagocytosis and endosymbiosis is offset by a reduced need for these genes in eukaryotes, because selection in most eukaryotes operates on variation not readily generated by HGT.
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Affiliation(s)
- Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
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3
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Wilson CG, Pieszko T, Nowell RW, Barraclough TG. Recombination in bdelloid rotifer genomes: asexuality, transfer and stress. Trends Genet 2024; 40:422-436. [PMID: 38458877 DOI: 10.1016/j.tig.2024.02.001] [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: 11/03/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
Bdelloid rotifers constitute a class of microscopic animals living in freshwater habitats worldwide. Several strange features of bdelloids have drawn attention: their ability to tolerate desiccation and other stresses, a lack of reported males across the clade despite centuries of study, and unusually high numbers of horizontally acquired, non-metazoan genes. Genome sequencing is transforming our understanding of their lifestyle and its consequences, while in turn providing wider insights about recombination and genome organisation in animals. Many questions remain, not least how to reconcile apparent genomic signatures of sex with the continued absence of reported males, why bdelloids have so many horizontally acquired genes, and how their remarkable ability to survive stress interacts with recombination and other genomic processes.
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Affiliation(s)
- Christopher G Wilson
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
| | - Tymoteusz Pieszko
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Reuben W Nowell
- Institute of Ecology and Evolution, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
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4
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Moris VC, Bruneau L, Berthe J, Heuskin AC, Penninckx S, Ritter S, Weber U, Durante M, Danchin EGJ, Hespeels B, Doninck KV. Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga. BMC Biol 2024; 22:11. [PMID: 38273318 PMCID: PMC10809525 DOI: 10.1186/s12915-023-01807-8] [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: 08/18/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The remarkable resistance to ionizing radiation found in anhydrobiotic organisms, such as some bacteria, tardigrades, and bdelloid rotifers has been hypothesized to be incidental to their desiccation resistance. Both stresses produce reactive oxygen species and cause damage to DNA and other macromolecules. However, this hypothesis has only been investigated in a few species. RESULTS In this study, we analyzed the transcriptomic response of the bdelloid rotifer Adineta vaga to desiccation and to low- (X-rays) and high- (Fe) LET radiation to highlight the molecular and genetic mechanisms triggered by both stresses. We identified numerous genes encoding antioxidants, but also chaperones, that are constitutively highly expressed, which may contribute to the protection of proteins against oxidative stress during desiccation and ionizing radiation. We also detected a transcriptomic response common to desiccation and ionizing radiation with the over-expression of genes mainly involved in DNA repair and protein modifications but also genes with unknown functions that were bdelloid-specific. A distinct transcriptomic response specific to rehydration was also found, with the over-expression of genes mainly encoding Late Embryogenesis Abundant proteins, specific heat shock proteins, and glucose repressive proteins. CONCLUSIONS These results suggest that the extreme resistance of bdelloid rotifers to radiation might indeed be a consequence of their capacity to resist complete desiccation. This study paves the way to functional genetic experiments on A. vaga targeting promising candidate proteins playing central roles in radiation and desiccation resistance.
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Affiliation(s)
- Victoria C Moris
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium.
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium.
| | - Lucie Bruneau
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Jérémy Berthe
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Anne-Catherine Heuskin
- Namur Research Institute for Life Sciences (NARILIS), Laboratory of Analysis By Nuclear Reactions (LARN), University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Sébastien Penninckx
- Medical Physics Department, Institut Jules Bordet - Université Libre de Bruxelles, 90 Rue Meylemeersch, 1070, Brussels, Belgium
| | - Sylvia Ritter
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Uli Weber
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Marco Durante
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 06903, Sophia Antipolis, France
| | - Boris Hespeels
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium
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Weaver RJ, McDonald AE. Mitochondrial alternative oxidase across the tree of life: Presence, absence, and putative cases of lateral gene transfer. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:149003. [PMID: 37557975 DOI: 10.1016/j.bbabio.2023.149003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
The alternative oxidase (AOX) is a terminal oxidase in the electron transport system that plays a role in mitochondrial bioenergetics. The past 20 years of research shows AOX has a wide yet patchy distribution across the tree of life. AOX has been suggested to have a role in stress tolerance, growth, and development in plants, but less is known about its function in other groups, including animals. In this study, we analyzed the taxonomic distribution of AOX across >2800 species representatives from prokaryotes and eukaryotes and developed a standardized workflow for finding and verifying the authenticity of AOX sequences. We found that AOX is limited to proteobacteria among prokaryotes, but is widely distributed in eukaryotes, with the highest prevalence in plants, fungi, and protists. AOX is present in many invertebrates, but is absent in others including most arthropods, and is absent from vertebrates. We found aberrant AOX sequences associated with some animal groups. Some of these aberrant AOXs were contaminants, but we also found putative cases of lateral gene transfer of AOX from fungi and protists to nematodes, springtails, fungus gnats, and rotifers. Our findings provide a robust and detailed analysis of the distribution of AOX and a method for identifying and verifying putative AOX sequences, which will be useful as more sequence data becomes available on public repositories.
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Affiliation(s)
- Ryan J Weaver
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
| | - Allison E McDonald
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada.
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6
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Ribes-Navarro A, Kabeya N, Castro LFC, Gomes-dos-Santos A, Fonseca MM, Alberts-Hubatsch H, Hontoria F, Navarro JC, Monroig Ó. Examination of gammarid transcriptomes reveals a widespread occurrence of key metabolic genes from epibiont bdelloid rotifers in freshwater species. Open Biol 2023; 13:230196. [PMID: 37875161 PMCID: PMC10597677 DOI: 10.1098/rsob.230196] [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: 06/23/2023] [Accepted: 09/19/2023] [Indexed: 10/26/2023] Open
Abstract
Previous data revealed the unexpected presence of genes encoding for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthetic enzymes in transcriptomes from freshwater gammarids but not in marine species, even though closely related species were compared. This study aimed to clarify the origin and occurrence of selected LC-PUFA biosynthesis gene markers across all published gammarid transcriptomes. Through systematic searches, we confirmed the widespread occurrence of sequences from seven elongases and desaturases involved in LC-PUFA biosynthesis, in transcriptomes from freshwater gammarids but not marine species, and clarified that such occurrence is independent from the gammarid species and geographical origin. The phylogenetic analysis established that the retrieved elongase and desaturase sequences were closely related to bdelloid rotifers, confirming that multiple transcriptomes from freshwater gammarids contain contaminating rotifers' genetic material. Using the Adineta steineri genome, we investigated the genomic location and exon-intron organization of the elongase and desaturase genes, establishing they are all genome-anchored and, importantly, identifying instances of horizontal gene transfer. Finally, we provide compelling evidence demonstrating Bdelloidea desaturases and elongases enable these organisms to perform all the reactions for de novo biosynthesis of PUFA and, from them, LC-PUFA, an advantageous trait when considering the low abundance of these essential nutrients in freshwater environments.
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Affiliation(s)
- Alberto Ribes-Navarro
- Instituto de Acuicultura Torre de la Sal (IATS), CSIC, 12595 Ribera de Cabanes, Castellón, Spain
| | - Naoki Kabeya
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato, Tokyo, Japan
| | - L. Filipe C. Castro
- CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua do Campo Alegre S/N, 4169-007 Porto, Portugal
| | - André Gomes-dos-Santos
- CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Miguel M. Fonseca
- CIMAR/CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Hilke Alberts-Hubatsch
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Francisco Hontoria
- Instituto de Acuicultura Torre de la Sal (IATS), CSIC, 12595 Ribera de Cabanes, Castellón, Spain
| | - Juan C. Navarro
- Instituto de Acuicultura Torre de la Sal (IATS), CSIC, 12595 Ribera de Cabanes, Castellón, Spain
| | - Óscar Monroig
- Instituto de Acuicultura Torre de la Sal (IATS), CSIC, 12595 Ribera de Cabanes, Castellón, Spain
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7
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Milner DS, Galindo LJ, Irwin NAT, Richards TA. Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes. Annu Rev Microbiol 2023; 77:45-66. [PMID: 36944262 DOI: 10.1146/annurev-micro-032421-115538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, the ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire.
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Affiliation(s)
- David S Milner
- Department of Biology, University of Oxford, Oxford, United Kingdom;
| | | | - Nicholas A T Irwin
- Department of Biology, University of Oxford, Oxford, United Kingdom;
- Merton College, University of Oxford, Oxford, United Kingdom
| | - Thomas A Richards
- Department of Biology, University of Oxford, Oxford, United Kingdom;
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8
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Suring W, Hoogduin D, Le Ngoc G, Brouwer A, van Straalen NM, Roelofs D. Nonribosomal Peptide Synthetases in Animals. Genes (Basel) 2023; 14:1741. [PMID: 37761881 PMCID: PMC10531068 DOI: 10.3390/genes14091741] [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: 07/23/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are a class of cytosolic enzymes that synthesize a range of bio-active secondary metabolites including antibiotics and siderophores. They are widespread among both prokaryotes and eukaryotes but are considered rare among animals. Recently, several novel NRPS genes have been described in nematodes, schistosomes, and arthropods, which led us to investigate how prevalent NRPS genes are in the animal kingdom. We screened 1059 sequenced animal genomes and showed that NRPSs were present in 7 out of the 19 phyla analyzed. A phylogenetic analysis showed that the identified NRPSs form clades distinct from other adenylate-forming enzymes that contain similar domains such as fatty acid synthases. NRPSs show a remarkably scattered distribution over the animal kingdom. They are especially abundant in rotifers and nematodes. In rotifers, we found a large variety of domain architectures and predicted substrates. In the nematode Plectus sambesii, we identified the beta-lactam biosynthesis genes L-δ-(α-aminoadipoyl)-L-cysteinyl-D-valine synthetase, isopenicillin N synthase, and deacetoxycephalosporin C synthase that catalyze the formation of beta-lactam antibiotics in fungi and bacteria. These genes are also present in several species of Collembola, but not in other hexapods analyzed so far. In conclusion, our survey showed that NRPS genes are more abundant and widespread in animals than previously known.
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Affiliation(s)
- Wouter Suring
- A-LIFE Ecology and Evolution, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
- Department of Academy Technology & Innovation, NHL Stenden University of Applied Sciences, Rengerslaan 8-10, 8917 DD Leeuwarden, The Netherlands
| | - Dylan Hoogduin
- A-LIFE Ecology and Evolution, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| | - Giang Le Ngoc
- A-LIFE Ecology and Evolution, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
- Biomedical Primate Research Centre, Lange Kleiweg 161, 2282 GJ Rijswijk, The Netherlands
| | - Abraham Brouwer
- BioDetection Systems, Science Park 406, 1098 XH Amsterdam, The Netherlands
| | - Nico M. van Straalen
- A-LIFE Ecology and Evolution, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| | - Dick Roelofs
- A-LIFE Ecology and Evolution, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
- Keygene N.V., Agro Business Park 90, 6708 PW Wageningen, The Netherlands
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9
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Stick R, Peter A. CaaX-less lamins: Lophotrochozoa provide a glance at the playground of evolution. PROTOPLASMA 2023; 260:741-756. [PMID: 36102949 PMCID: PMC10125929 DOI: 10.1007/s00709-022-01809-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/01/2022] [Indexed: 05/05/2023]
Abstract
Nuclear lamins are the main components of the nuclear lamina in many eukaryotes. They are members of the intermediate filament (IF) protein family. Lamins differ from cytoplasmic IF proteins by the presence of a nuclear localisation sequence (NLS) and a C-terminal tetrapeptide, the CaaX motif. The CaaX motif is target of post-translational modifications including isoprenylation, proteolytic processing, and carboxyl-methylation. These modifications, in conjunction with the NLS, direct lamins to the inner nuclear membrane where they assemble into filaments. Lamins lacking a CaaX motif are unable to associate independently with nuclear membranes and remain in the nucleoplasm. So far, three species have been reported to exclusively express CaaX-less lamins. All three belong to the lophotrochozoan lineage. To find out whether they represent rare exceptions, we analysed lamins of representatives of 17 lophotrochozoan phyla. Here we report that all four clades of Rotifera as well as individual taxa of Mollusca and Annelida lack CaaX-lamins, but express lamins with alternative C-termini. Of note, the respective mollusc and annelid groups occupy very different phylogenetic ranks. Most of these alternative C-termini are rich in aromatic residues. A possible function of these residues in membrane association is discussed. Alternative splicing of terebellid lamin transcripts gives rise to two lamin variants, one with a CaaX motif and one with an alternative C-terminus. A similar situation is found in Arenicolidae, Opheliidae, Capitellidae, and Echiura. This points a way, how the switch from lamins carrying a CaaX motif to lamins with alternative C-termini may have occurred.
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Affiliation(s)
- Reimer Stick
- Department of Cell Biology, University of Bremen, P.O. Box 330440, 28334, Bremen, Germany.
| | - Annette Peter
- Department of Cell Biology, University of Bremen, P.O. Box 330440, 28334, Bremen, Germany
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10
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Hespeels B, Fontaneto D, Cornet V, Penninckx S, Berthe J, Bruneau L, Larrick JW, Rapport E, Bailly J, Debortoli N, Iakovenko N, Janko K, Heuskin AC, Lucas S, Hallet B, Van Doninck K. Back to the roots, desiccation and radiation resistances are ancestral characters in bdelloid rotifers. BMC Biol 2023; 21:72. [PMID: 37024917 PMCID: PMC10080820 DOI: 10.1186/s12915-023-01554-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/27/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Bdelloid rotifers are micro-invertebrates distributed worldwide, from temperate latitudes to the most extreme areas of the planet like Antarctica or the Atacama Desert. They have colonized any habitat where liquid water is temporarily available, including terrestrial environments such as soils, mosses, and lichens, tolerating desiccation and other types of stress such as high doses of ionizing radiation (IR). It was hypothesized that bdelloid desiccation and radiation resistance may be attributed to their potential ability to repair DNA double-strand breaks (DSBs). Here, these properties are investigated and compared among nine bdelloid species collected from both mild and harsh habitats, addressing the correlation between the ability of bdelloid rotifers to survive desiccation and their capacity to repair massive DNA breakage in a phylogenetically explicit context. Our research includes both specimens isolated from habitats that experience frequent desiccation (at least 1 time per generation), and individuals sampled from habitats that rarely or never experienced desiccation. RESULTS Our analysis reveals that DNA repair prevails in somatic cells of both desiccation-tolerant and desiccation-sensitive bdelloid species after exposure to X-ray radiation. Species belonging to both categories are able to withstand high doses of ionizing radiation, up to 1000 Gy, without experiencing any negative effects on their survival. However, the fertility of two desiccation-sensitive species, Rotaria macrura and Rotaria rotatoria, was more severely impacted by low doses of radiation than that of desiccation-resistant species. Surprisingly, the radioresistance of desiccation-resistant species is not related to features of their original habitat. Indeed, bdelloids isolated from Atacama Desert or Antarctica were not characterized by a higher radioresistance than species found in more temperate environments. CONCLUSIONS Tolerance to desiccation and radiation are supported as ancestral features of bdelloid rotifers, with a group of species of the genus Rotaria having lost this trait after colonizing permanent water habitats. Together, our results provide a comprehensive overview of the evolution of desiccation and radiation resistance among bdelloid rotifers.
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Affiliation(s)
- Boris Hespeels
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium.
| | - Diego Fontaneto
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania Pallanza, Italy
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics AS CR, Rumburská 89, Liběchov, 277 21, Czech Republic
| | - Valérie Cornet
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium
| | - Sébastien Penninckx
- Medical Physics Department, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Jérémy Berthe
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
- Research Unit in Molecular Biology and Evolution, DBO, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Lucie Bruneau
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - James W Larrick
- Panorama Research Institute, Sunnyvale, CA, USA
- SETI Institute, Mountain View, CA, USA
| | - Eloïse Rapport
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Jérémie Bailly
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Nicolas Debortoli
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Nataliia Iakovenko
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics AS CR, Rumburská 89, Liběchov, 277 21, Czech Republic
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, CZ - 165 21 Praha 6, Suchdol, Czech Republic
- Faculty of Science, University of Ostrava, Chittussiho 10, 71000, Ostrava, Czech Republic
| | - Karel Janko
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics AS CR, Rumburská 89, Liběchov, 277 21, Czech Republic
- Faculty of Science, University of Ostrava, Chittussiho 10, 71000, Ostrava, Czech Republic
| | - Anne-Catherine Heuskin
- Laboratory of Analysis by Nuclear Reactions (LARN), Namur Research Institute for Life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Stéphane Lucas
- Laboratory of Analysis by Nuclear Reactions (LARN), Namur Research Institute for Life Sciences (Narilis), University of Namur, Namur, Belgium
| | - Bernard Hallet
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, B-1348, Louvain-la-Neuve, Belgium
| | - Karine Van Doninck
- Research Unit in Environmental and Evolutionary Biology (URBE), Laboratory of Evolutionary Genetics and Ecology (LEGE), NAmur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment (ILEE), University of Namur, Namur, Belgium.
- Research Unit in Molecular Biology and Evolution, DBO, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium.
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11
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Wang D, Meng Y, Meng F. Genome-centric metagenomics insights into functional divergence and horizontal gene transfer of denitrifying bacteria in anammox consortia. WATER RESEARCH 2022; 224:119062. [PMID: 36116192 DOI: 10.1016/j.watres.2022.119062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/21/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Denitrifying bacteria with high abundances in anammox communities play crucial roles in achieving stable anammox-based systems. Despite the relative constant composition of denitrifying bacteria, their functional diversity remains to be explored in anammox communities. Herein, a total of 77 high-quality metagenome-assembled genomes (MAGs) of denitrifying bacteria were recovered from the anammox community in a full-scale swine wastewater treatment plant. Among these microbes, a total of 26 MAGs were affiliated with the seven dominant denitrifying genera that have total abundances higher than 1%. A meta-analysis of these species suggested that external organics reduced the abundances of genus Ignavibacterium and species MAG.305 of UTPRO2 in anammox communities. Comparative genome analysis revealed functional divergence across different denitrifying bacteria, largely owing to their distinct capabilities for carbohydrate (including endogenous and exogenous) utilization and vitamin (e.g., pantothenate and thiamine) biosynthesis. Serval microbes in this system contained fewer genes encoding biotin, pantothenate and methionine biosynthesis compared with their related species from other habitats. In addition, the genes encoding energy production and conversion (73 genes) and inorganic ion transport (53 genes) putatively transferred from other species to denitrifying bacteria, while these denitrifying bacteria (especially genera UTPRO2 and SCN-69-89) likely donated the genes encoding nutrients (e.g., inorganic ion and amino acid) transporter (64 genes) for other members to utilize new metabolites. Collectively, these findings highlighted the functional divergence of these denitrifying bacteria and speculated that the genetic interactions within anammox communities through horizontal gene transfer may be one of the reasons for their functional divergence.
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Affiliation(s)
- Depeng Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Yabing Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China.
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12
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Yoshida Y, Tanaka S. Deciphering the Biological Enigma-Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the Chironomid Polypedilum vanderplanki. INSECTS 2022; 13:557. [PMID: 35735894 PMCID: PMC9224920 DOI: 10.3390/insects13060557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023]
Abstract
Anhydrobiosis, an ametabolic dehydrated state triggered by water loss, is observed in several invertebrate lineages. Anhydrobiotes revive when rehydrated, and seem not to suffer the ultimately lethal cell damage that results from severe loss of water in other organisms. Here, we review the biochemical and genomic evidence that has revealed the protectant molecules, repair systems, and maintenance pathways associated with anhydrobiosis. We then introduce two lineages in which anhydrobiosis has evolved independently: Tardigrada, where anhydrobiosis characterizes many species within the phylum, and the genus Polypedilum, where anhydrobiosis occurs in only two species. Finally, we discuss the complexity of the evolution of anhydrobiosis within invertebrates based on current knowledge, and propose perspectives to enhance the understanding of anhydrobiosis.
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Affiliation(s)
- Yuki Yoshida
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Sae Tanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Institute for Advanced Biosciences, Keio University, 341-1 Mizukami, Tsuruoka 997-0052, Japan
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13
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Datki Z, Sinka R, Galik B, Galik-Olah Z. Particle-dependent reproduction and exogenic biopolymer secretion of protozoa co-cultured rotifers. Int J Biol Macromol 2022; 211:669-677. [PMID: 35588974 DOI: 10.1016/j.ijbiomac.2022.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/24/2022] [Accepted: 05/03/2022] [Indexed: 11/30/2022]
Abstract
The rotifer-specific exogenic biopolymer, named Rotimer and its related molecular processes are affected by physical and chemical factors (e.g., temperature, pH or metal ions); however, the study of biological influences (e.g., the presence protozoa) concerning the particle-dependent reproduction (egg laying) and 'biopolymer producing capacity' (BPC) of rotifers is the objective of the present work. Non-planktonic rotifer species (Philodina acuticornis, Adineta vaga, Euchlanis dilatata, and Lecane bulla) were studied in paired micrometazoa-protozoa co-cultures involving Paramecium, Diplonema, and Amoeba. These protozoa can be beneficial food sources, enhancing reproduction, or even toxic factors for the above-mentioned animals, but can also function as particle-like mechanical stimulators. Furthermore, current studies reveal that bdelloids, similarly to monogonants, produce filamentous exudate; moreover, the body of bdelloids is covered by their exudate, unlike that of monogonants, especially in the case of A. vaga. A mathematical formula was developed as an improved version of a previously published viability marker to characterize the BPC and the relative amount of produced exudate in different conditions. Rotifer species secreting biopolymers appear to be a general trait indicating a common evolutionary background (e.g., calcium- and particle dependency) of such molecules; therefore, the BPC becomes an experiential sublethal influencing marker to these micrometazoans.
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Affiliation(s)
- Zsolt Datki
- Micro-In Vivo Research Laboratory, Interdisciplinary Research, Development and Innovation Centre of Excellence, University of Szeged, Dugonics ter 13. H-6720 Szeged, Hungary.
| | - Rita Sinka
- Department of Genetics, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Hungary
| | - Bence Galik
- Bioinformatics Research Group, Bioinformatics and Sequencing Core Facility, Szentagothai Research Centre, University of Pecs, Ifjusag u. 20, H-7624 Pecs, Hungary; Department of Clinical Molecular Biology, Medical University of Bialystok, ul.Jana Kilinskiego 1, 15-089 Bialystok, Poland
| | - Zita Galik-Olah
- Micro-In Vivo Research Laboratory, Interdisciplinary Research, Development and Innovation Centre of Excellence, University of Szeged, Dugonics ter 13. H-6720 Szeged, Hungary
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14
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Foe VE. Does the Pachytene Checkpoint, a Feature of Meiosis, Filter Out Mistakes in Double-Strand DNA Break Repair and as a side-Effect Strongly Promote Adaptive Speciation? Integr Org Biol 2022; 4:obac008. [PMID: 36827645 PMCID: PMC8998493 DOI: 10.1093/iob/obac008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This essay aims to explain two biological puzzles: why eukaryotic transcription units are composed of short segments of coding DNA interspersed with long stretches of non-coding (intron) DNA, and the near ubiquity of sexual reproduction. As is well known, alternative splicing of its coding sequences enables one transcription unit to produce multiple variants of each encoded protein. Additionally, padding transcription units with non-coding DNA (often many thousands of base pairs long) provides a readily evolvable way to set how soon in a cell cycle the various mRNAs will begin being expressed and the total amount of mRNA that each transcription unit can make during a cell cycle. This regulation complements control via the transcriptional promoter and facilitates the creation of complex eukaryotic cell types, tissues, and organisms. However, it also makes eukaryotes exceedingly vulnerable to double-strand DNA breaks, which end-joining break repair pathways can repair incorrectly. Transcription units cover such a large fraction of the genome that any mis-repair producing a reorganized chromosome has a high probability of destroying a gene. During meiosis, the synaptonemal complex aligns homologous chromosome pairs and the pachytene checkpoint detects, selectively arrests, and in many organisms actively destroys gamete-producing cells with chromosomes that cannot adequately synapse; this creates a filter favoring transmission to the next generation of chromosomes that retain the parental organization, while selectively culling those with interrupted transcription units. This same meiotic checkpoint, reacting to accidental chromosomal reorganizations inflicted by error-prone break repair, can, as a side effect, provide a mechanism for the formation of new species in sympatry. It has been a long-standing puzzle how something as seemingly maladaptive as hybrid sterility between such new species can arise. I suggest that this paradox is resolved by understanding the adaptive importance of the pachytene checkpoint, as outlined above.
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15
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First Insights into the Repertoire of Secretory Lectins in Rotifers. Mar Drugs 2022; 20:md20020130. [PMID: 35200659 PMCID: PMC8878817 DOI: 10.3390/md20020130] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 02/06/2023] Open
Abstract
Due to their high biodiversity and adaptation to a mutable and challenging environment, aquatic lophotrochozoan animals are regarded as a virtually unlimited source of bioactive molecules. Among these, lectins, i.e., proteins with remarkable carbohydrate-recognition properties involved in immunity, reproduction, self/nonself recognition and several other biological processes, are particularly attractive targets for biotechnological research. To date, lectin research in the Lophotrochozoa has been restricted to the most widespread phyla, which are the usual targets of comparative immunology studies, such as Mollusca and Annelida. Here we provide the first overview of the repertoire of the secretory lectin-like molecules encoded by the genomes of six target rotifer species: Brachionus calyciflorus, Brachionus plicatilis, Proales similis (class Monogononta), Adineta ricciae, Didymodactylos carnosus and Rotaria sordida (class Bdelloidea). Overall, while rotifer secretory lectins display a high molecular diversity and belong to nine different structural classes, their total number is significantly lower than for other groups of lophotrochozoans, with no evidence of lineage-specific expansion events. Considering the high evolutionary divergence between rotifers and the other major sister phyla, their widespread distribution in aquatic environments and the ease of their collection and rearing in laboratory conditions, these organisms may represent interesting targets for glycobiological studies, which may allow the identification of novel carbohydrate-binding proteins with peculiar biological properties.
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16
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van Dijk B, Bertels F, Stolk L, Takeuchi N, Rainey PB. Transposable elements promote the evolution of genome streamlining. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200477. [PMID: 34839699 PMCID: PMC8628081 DOI: 10.1098/rstb.2020.0477] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/30/2021] [Indexed: 12/25/2022] Open
Abstract
Eukaryotes and prokaryotes have distinct genome architectures, with marked differences in genome size, the ratio of coding/non-coding DNA, and the abundance of transposable elements (TEs). As TEs replicate independently of their hosts, the proliferation of TEs is thought to have driven genome expansion in eukaryotes. However, prokaryotes also have TEs in intergenic spaces, so why do prokaryotes have small, streamlined genomes? Using an in silico model describing the genomes of single-celled asexual organisms that coevolve with TEs, we show that TEs acquired from the environment by horizontal gene transfer can promote the evolution of genome streamlining. The process depends on local interactions and is underpinned by rock-paper-scissors dynamics in which populations of cells with streamlined genomes beat TEs, which beat non-streamlined genomes, which beat streamlined genomes, in continuous and repeating cycles. Streamlining is maladaptive to individual cells, but improves lineage viability by hindering the proliferation of TEs. Streamlining does not evolve in sexually reproducing populations because recombination partially frees TEs from the deleterious effects they cause. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
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Affiliation(s)
- Bram van Dijk
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Frederic Bertels
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Lianne Stolk
- Theoretical Biology, Department of Biology, Utrecht University, The Netherlands
| | - Nobuto Takeuchi
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paul B. Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL, CNRS, Paris, France
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17
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Orús-Alcalde A, Lu TM, Børve A, Hejnol A. The evolution of the metazoan Toll receptor family and its expression during protostome development. BMC Ecol Evol 2021; 21:208. [PMID: 34809567 PMCID: PMC8609888 DOI: 10.1186/s12862-021-01927-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 10/21/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Toll-like receptors (TLRs) play a crucial role in immunity and development. They contain leucine-rich repeat domains, one transmembrane domain, and one Toll/IL-1 receptor domain. TLRs have been classified into V-type/scc and P-type/mcc TLRs, based on differences in the leucine-rich repeat domain region. Although TLRs are widespread in animals, detailed phylogenetic studies of this gene family are lacking. Here we aim to uncover TLR evolution by conducting a survey and a phylogenetic analysis in species across Bilateria. To discriminate between their role in development and immunity we furthermore analyzed stage-specific transcriptomes of the ecdysozoans Priapulus caudatus and Hypsibius exemplaris, and the spiralians Crassostrea gigas and Terebratalia transversa. RESULTS We detected a low number of TLRs in ecdysozoan species, and multiple independent radiations within the Spiralia. V-type/scc and P-type/mcc type-receptors are present in cnidarians, protostomes and deuterostomes, and therefore they emerged early in TLR evolution, followed by a loss in xenacoelomorphs. Our phylogenetic analysis shows that TLRs cluster into three major clades: clade α is present in cnidarians, ecdysozoans, and spiralians; clade β in deuterostomes, ecdysozoans, and spiralians; and clade γ is only found in spiralians. Our stage-specific transcriptome and in situ hybridization analyses show that TLRs are expressed during development in all species analyzed, which indicates a broad role of TLRs during animal development. CONCLUSIONS Our findings suggest that a clade α TLR gene (TLR-Ca) and a clade β/γ TLR gene (TLR-Cβ/γ) were already present in the cnidarian-bilaterian common ancestor. However, although TLR-Ca was conserved in cnidarians, TLR-Cβ/γ was lost during the early evolution of these taxa. Moreover, TLR-Cβ/γ duplicated to generate TLR-Cβ and TLR-Cγ in the lineage to the last common protostome-deuterostome ancestor. TLR-Ca, TLR-Cβ and TLR-Cγ further expanded generating the three major TLR clades. While all three clades radiated in several spiralian lineages, specific TLRs clades have been presumably lost in other lineages. Furthermore, the expression of the majority of these genes during protostome ontogeny suggests a likely role in development.
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Affiliation(s)
- Andrea Orús-Alcalde
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Tsai-Ming Lu
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Aina Børve
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway.
- Department of Biological Sciences, University of Bergen, Bergen, Norway.
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18
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Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E, Arora R, Cariou M, Cruaud C, Gaudray FR, Gilbert C, Guiglielmoni N, Hespeels B, Kozlowski DKL, Labadie K, Limasset A, Llirós M, Marbouty M, Terwagne M, Virgo J, Cordaux R, Danchin EGJ, Hallet B, Koszul R, Lenormand T, Flot JF, Van Doninck K. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. SCIENCE ADVANCES 2021; 7:eabg4216. [PMID: 34613768 PMCID: PMC8494291 DOI: 10.1126/sciadv.abg4216] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability to repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing a well-assembled reference genome is a critical step to developing an understanding of the effects of long-term asexuality and DNA breakage on genome evolution. To this end, we present the first high-quality chromosome-level genome assemblies for the bdelloid Adineta vaga, composed of six pairs of homologous (diploid) chromosomes with a footprint of paleotetraploidy. The observed large-scale losses of heterozygosity are signatures of recombination between homologous chromosomes, either during mitotic DNA double-strand break repair or when resolving programmed DNA breaks during a modified meiosis. Dynamic subtelomeric regions harbor more structural diversity (e.g., chromosome rearrangements, transposable elements, and haplotypic divergence). Our results trigger the reappraisal of potential meiotic processes in bdelloid rotifers and help unravel the factors underlying their long-term asexual evolutionary success.
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Affiliation(s)
- Paul Simion
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
| | - Jitendra Narayan
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Antoine Houtain
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Alessandro Derzelle
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
- Collège Doctoral, Sorbonne Université, F-75005 Paris, France
| | - Emilien Nicolas
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Rohan Arora
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Marie Cariou
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | | | - Clément Gilbert
- Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, CNRS, IRD, UMR, 91198 Gif-sur-Yvette, France
| | - Nadège Guiglielmoni
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Boris Hespeels
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Djampa K. L. Kozlowski
- INRAE, Université Côte-d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis 06903, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Antoine Limasset
- Université de Lille, CNRS, UMR 9189 - CRIStAL, 59655 Villeneuve-d’Ascq, France
| | - Marc Llirós
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Institut d’Investigació Biomédica de Girona, Malalties Digestives i Microbiota, 17190 Salt, Spain
| | - Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
| | - Matthieu Terwagne
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Julie Virgo
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Richard Cordaux
- Ecologie et Biologie des interactions, Université de Poitiers, UMR CNRS 7267, 5 rue Albert Turpain, 86073 Poitiers, France
| | - Etienne G. J. Danchin
- INRAE, Université Côte-d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis 06903, France
| | - Bernard Hallet
- LIBST, Université Catholique de Louvain (UCLouvain), Croix du Sud 4/5, Louvain-la-Neuve 1348, Belgium
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
| | - Thomas Lenormand
- CEFE, Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Jean-Francois Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels - (IB), Brussels 1050, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
| | - Karine Van Doninck
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
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19
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Biodiversity-based development and evolution: the emerging research systems in model and non-model organisms. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1236-1280. [PMID: 33893979 DOI: 10.1007/s11427-020-1915-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/16/2021] [Indexed: 02/07/2023]
Abstract
Evolutionary developmental biology, or Evo-Devo for short, has become an established field that, broadly speaking, seeks to understand how changes in development drive major transitions and innovation in organismal evolution. It does so via integrating the principles and methods of many subdisciplines of biology. Although we have gained unprecedented knowledge from the studies on model organisms in the past decades, many fundamental and crucially essential processes remain a mystery. Considering the tremendous biodiversity of our planet, the current model organisms seem insufficient for us to understand the evolutionary and physiological processes of life and its adaptation to exterior environments. The currently increasing genomic data and the recently available gene-editing tools make it possible to extend our studies to non-model organisms. In this review, we review the recent work on the regulatory signaling of developmental and regeneration processes, environmental adaptation, and evolutionary mechanisms using both the existing model animals such as zebrafish and Drosophila, and the emerging nonstandard model organisms including amphioxus, ascidian, ciliates, single-celled phytoplankton, and marine nematode. In addition, the challenging questions and new directions in these systems are outlined as well.
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20
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Matriano DM, Alegado RA, Conaco C. Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta. Sci Rep 2021; 11:5993. [PMID: 33727612 PMCID: PMC7971027 DOI: 10.1038/s41598-021-85259-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 02/28/2021] [Indexed: 01/31/2023] Open
Abstract
Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible roles in the evolution of animal multicellularity remains unexplored. We identified at least 175 candidate HGTs in the genome of the colonial choanoflagellate Salpingoeca rosetta using sequence-based tests. The majority of these were orthologous to genes in bacterial and microalgal lineages, yet displayed genomic features consistent with the rest of the S. rosetta genome-evidence of ancient acquisition events. Putative functions include enzymes involved in amino acid and carbohydrate metabolism, cell signaling, and the synthesis of extracellular matrix components. Functions of candidate HGTs may have contributed to the ability of choanoflagellates to assimilate novel metabolites, thereby supporting adaptation, survival in diverse ecological niches, and response to external cues that are possibly critical in the evolution of multicellularity in choanoflagellates.
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Affiliation(s)
- Danielle M Matriano
- Marine Science Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Rosanna A Alegado
- Department of Oceanography, Hawai'i Sea Grant, Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Manoa, Honolulu, USA
| | - Cecilia Conaco
- Marine Science Institute, University of the Philippines, Diliman, Quezon City, Philippines.
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21
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Nowell RW, Wilson CG, Almeida P, Schiffer PH, Fontaneto D, Becks L, Rodriguez F, Arkhipova IR, Barraclough TG. Evolutionary dynamics of transposable elements in bdelloid rotifers. eLife 2021; 10:e63194. [PMID: 33543711 PMCID: PMC7943196 DOI: 10.7554/elife.63194] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/04/2021] [Indexed: 12/17/2022] Open
Abstract
Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates in which males are thus far unknown. Contrary to expectations, we find a variety of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms. Instead, we find that that TE content evolves relatively slowly in bdelloids and that gene families involved in RNAi-mediated TE suppression have undergone significant expansion, which might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.
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Affiliation(s)
- Reuben W Nowell
- Department of Zoology, University of OxfordOxfordUnited Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscot, BerkshireUnited Kingdom
| | - Christopher G Wilson
- Department of Zoology, University of OxfordOxfordUnited Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscot, BerkshireUnited Kingdom
| | - Pedro Almeida
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscot, BerkshireUnited Kingdom
- Division of Biosciences, University College LondonLondonUnited Kingdom
| | - Philipp H Schiffer
- Institute of Zoology, Section Developmental Biology, University of Cologne, KölnWormlabGermany
| | - Diego Fontaneto
- National Research Council of Italy, Water Research InstituteVerbania PallanzaItaly
| | - Lutz Becks
- Community Dynamics Group, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary BiologyPlönGermany
- Aquatic Ecology and Evolution, University of KonstanzKonstanzGermany
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MAUnited States
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MAUnited States
| | - Timothy G Barraclough
- Department of Zoology, University of OxfordOxfordUnited Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscot, BerkshireUnited Kingdom
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22
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Vakhrusheva OA, Mnatsakanova EA, Galimov YR, Neretina TV, Gerasimov ES, Naumenko SA, Ozerova SG, Zalevsky AO, Yushenova IA, Rodriguez F, Arkhipova IR, Penin AA, Logacheva MD, Bazykin GA, Kondrashov AS. Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga. Nat Commun 2020; 11:6421. [PMID: 33339818 PMCID: PMC7749112 DOI: 10.1038/s41467-020-19614-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 10/23/2020] [Indexed: 01/08/2023] Open
Abstract
Sexual reproduction is almost ubiquitous among extant eukaryotes. As most asexual lineages are short-lived, abandoning sex is commonly regarded as an evolutionary dead end. Still, putative anciently asexual lineages challenge this view. One of the most striking examples are bdelloid rotifers, microscopic freshwater invertebrates believed to have completely abandoned sexual reproduction tens of Myr ago. Here, we compare whole genomes of 11 wild-caught individuals of the bdelloid rotifer Adineta vaga and present evidence that some patterns in its genetic variation are incompatible with strict clonality and lack of genetic exchange. These patterns include genotype proportions close to Hardy-Weinberg expectations within loci, lack of linkage disequilibrium between distant loci, incongruent haplotype phylogenies across the genome, and evidence for hybridization between divergent lineages. Analysis of triallelic sites independently corroborates these findings. Our results provide evidence for interindividual genetic exchange and recombination in A. vaga, a species previously thought to be anciently asexual.
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Affiliation(s)
- Olga A Vakhrusheva
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation.
| | - Elena A Mnatsakanova
- Department of General Ecology and Hydrobiology, Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
| | - Yan R Galimov
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, 119334, Russian Federation
| | - Tatiana V Neretina
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
| | - Evgeny S Gerasimov
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, 119435, Russian Federation
| | - Sergey A Naumenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, 02115, USA
| | - Svetlana G Ozerova
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, 119334, Russian Federation
- Medkvadrat, Moscow, 115409, Russian Federation
| | - Arthur O Zalevsky
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
| | - Maria D Logacheva
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
| | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
| | - Alexey S Kondrashov
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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23
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Horizontal Gene Transfer in Eukaryotes: Not if, but How Much? Trends Genet 2020; 36:915-925. [DOI: 10.1016/j.tig.2020.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022]
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24
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Abe T, Akazawa Y, Toyoda A, Niki H, Baba T. Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes. Front Microbiol 2020; 11:1486. [PMID: 32719664 PMCID: PMC7350273 DOI: 10.3389/fmicb.2020.01486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/08/2020] [Indexed: 02/05/2023] Open
Abstract
Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, particularly in the absence of information on donor sequences. As an alternative to phylogeny-based methods that rely on sequence alignments, we have developed an alignment-free clustering method on the basis of an unsupervised neural network “Batch-Learning Self-Organizing Map (BLSOM)” in which sequence fragments are clustered based solely on oligonucleotide similarity without taxonomical information, to detect HGT candidates and their origin in entire genomes. By mapping the microbial genomic sequences on large-scale BLSOMs constructed with nearly all prokaryotic genomes, HGT candidates can be identified, and their origin assigned comprehensively, even for microbial genomes that exhibit high novelty. By focusing on two types of Alphaproteobacteria, specifically psychrotolerant Sphingomonas strains from an Antarctic lake, we detected HGT candidates using BLSOM and found higher proportions of HGT candidates from organisms belonging to Betaproteobacteria in the genomes of these two Antarctic strains compared with those of continental strains. Further, an origin difference was noted in the HGT candidates found in the two Antarctic strains. Although their origins were highly diversified, gene functions related to the cell wall or membrane biogenesis were shared among the HGT candidates. Moreover, analyses of amino acid frequency suggested that housekeeping genes and some HGT candidates of the Antarctic strains exhibited different characteristics to other continental strains. Lys, Ser, Thr, and Val were the amino acids found to be increased in the Antarctic strains, whereas Ala, Arg, Glu, and Leu were decreased. Our findings strongly suggest a low-temperature adaptation process for microbes that may have arisen convergently as an independent evolutionary strategy in each Antarctic strain. Hence, BLSOM analysis could serve as a powerful tool in not only detecting HGT candidates and their origins in entire genomes, but also in providing novel perspectives into the environmental adaptations of microbes.
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Affiliation(s)
- Takashi Abe
- Department of Information Engineering, Faculty of Engineering, Niigata University, Niigata, Japan
| | - Yu Akazawa
- Department of Information Engineering, Faculty of Engineering, Niigata University, Niigata, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan.,Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, National Institute of Genetics, Mishima, Japan
| | - Tomoya Baba
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan.,Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Tokyo, Japan
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25
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Li X, Fang C, Zhao JP, Zhou XY, Ni Z, Niu DK. Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer. BMC Genomics 2020; 21:452. [PMID: 32611311 PMCID: PMC7329468 DOI: 10.1186/s12864-020-06865-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 06/23/2020] [Indexed: 12/04/2022] Open
Abstract
Background Although horizontal gene transfer (HGT) is a widely accepted force in the evolution of prokaryotic genomes, its role in the evolution of eukaryotic genomes remains hotly debated. Some bdelloid rotifers that are resistant to extreme desiccation and radiation undergo a very high level of HGT, whereas in another desiccation-resistant invertebrate, the tardigrade, the pattern does not exist. Overall, the DNA double-strand breaks (DSBs) induced by prolonged desiccation have been postulated to open a gateway to the nuclear genome for exogenous DNA integration and thus to facilitate the HGT process, thereby enhancing the rate of endosymbiotic DNA transfer (EDT). Results We first surveyed the abundance of nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs) in five eukaryotes that are highly resistant to desiccation: the bdelloid rotifers Adineta vaga and Adineta ricciae, the tardigrade Ramazzottius varieornatus, and the resurrection plants Dorcoceras hygrometricum and Selaginella tamariscina. Excessive NUMTs or NUPTs were not detected. Furthermore, we compared 24 groups of desiccation-tolerant organisms with their relatively less desiccation-tolerant relatives but did not find a significant difference in NUMT/NUPT contents. Conclusions Desiccation may induce DSBs, but it is unlikely to dramatically increase the frequency of exogenous sequence integration in most eukaryotes. The capture of exogenous DNA sequences is possible only when DSBs are repaired through a subtype of non-homologous end joining, named alternative end joining (alt-EJ). Due to the deleterious effects of the resulting insertion mutations, alt-EJ is less frequently initiated than other mechanisms.
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Affiliation(s)
- Xixi Li
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Cheng Fang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jun-Peng Zhao
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiao-Yu Zhou
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Zhihua Ni
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.,College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Deng-Ke Niu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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26
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Mauer K, Hellmann SL, Groth M, Fröbius AC, Zischler H, Hankeln T, Herlyn H. The genome, transcriptome, and proteome of the fish parasite Pomphorhynchus laevis (Acanthocephala). PLoS One 2020; 15:e0232973. [PMID: 32574180 PMCID: PMC7310846 DOI: 10.1371/journal.pone.0232973] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/24/2020] [Indexed: 01/05/2023] Open
Abstract
Thorny-headed worms (Acanthocephala) are endoparasites exploiting Mandibulata (Arthropoda) and Gnathostomata (Vertebrata). Despite their world-wide occurrence and economic relevance as a pest, genome and transcriptome assemblies have not been published before. However, such data might hold clues for a sustainable control of acanthocephalans in animal production. For this reason, we present the first draft of an acanthocephalan nuclear genome, besides the mitochondrial one, using the fish parasite Pomphorhynchus laevis (Palaeacanthocephala) as a model. Additionally, we have assembled and annotated the transcriptome of this species and the proteins encoded. A hybrid assembly of long and short reads resulted in a near-complete P. laevis draft genome of ca. 260 Mb, comprising a large repetitive portion of ca. 63%. Numbers of transcripts and translated proteins (35,683) were within the range of other members of the Rotifera-Acanthocephala clade. Our data additionally demonstrate a significant reorganization of the acanthocephalan gene repertoire. Thus, more than 20% of the usually conserved metazoan genes were lacking in P. laevis. Ontology analysis of the retained genes revealed many connections to the incorporation of carotinoids. These are probably taken up via the surface together with lipids, thus accounting for the orange coloration of P. laevis. Furthermore, we found transcripts and protein sequences to be more derived in P. laevis than in rotifers from Monogononta and Bdelloidea. This was especially the case in genes involved in energy metabolism, which might reflect the acanthocephalan ability to use the scarce oxygen in the host intestine for respiration and simultaneously carry out fermentation. Increased plasticity of the gene repertoire through the integration of foreign DNA into the nuclear genome seems to be another underpinning factor of the evolutionary success of acanthocephalans. In any case, energy-related genes and their proteins may be considered as candidate targets for the acanthocephalan control.
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Affiliation(s)
- Katharina Mauer
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sören Lukas Hellmann
- Molecular Genetics and Genomic Analysis Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Marco Groth
- CF DNA sequencing, Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Andreas C. Fröbius
- Molecular Andrology, Biomedical Research Center Seltersberg (BFS), Justus Liebig University Gießen, Gießen, Germany
| | - Hans Zischler
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Thomas Hankeln
- Molecular Genetics and Genomic Analysis Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Holger Herlyn
- Anthropology, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
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27
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Emamalipour M, Seidi K, Zununi Vahed S, Jahanban-Esfahlan A, Jaymand M, Majdi H, Amoozgar Z, Chitkushev LT, Javaheri T, Jahanban-Esfahlan R, Zare P. Horizontal Gene Transfer: From Evolutionary Flexibility to Disease Progression. Front Cell Dev Biol 2020; 8:229. [PMID: 32509768 PMCID: PMC7248198 DOI: 10.3389/fcell.2020.00229] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/17/2020] [Indexed: 12/11/2022] Open
Abstract
Flexibility in the exchange of genetic material takes place between different organisms of the same or different species. This phenomenon is known to play a key role in the genetic, physiological, and ecological performance of the host. Exchange of genetic materials can cause both beneficial and/or adverse biological consequences. Horizontal gene transfer (HGT) or lateral gene transfer (LGT) as a general mechanism leads to biodiversity and biological innovations in nature. HGT mediators are one of the genetic engineering tools used for selective introduction of desired changes in the genome for gene/cell therapy purposes. HGT, however, is crucial in development, emergence, and recurrence of various human-related diseases, such as cancer, genetic-, metabolic-, and neurodegenerative disorders and can negatively affect the therapeutic outcome by promoting resistant forms or disrupting the performance of genome editing toolkits. Because of the importance of HGT and its vital physio- and pathological roles, here the variety of HGT mechanisms are reviewed, ranging from extracellular vesicles (EVs) and nanotubes in prokaryotes to cell-free DNA and apoptotic bodies in eukaryotes. Next, we argue that HGT plays a role both in the development of useful features and in pathological states associated with emerging and recurrent forms of the disease. A better understanding of the different HGT mediators and their genome-altering effects/potentials may pave the way for the development of more effective therapeutic and diagnostic regimes.
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Affiliation(s)
- Melissa Emamalipour
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khaled Seidi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hasan Majdi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zohreh Amoozgar
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - L T Chitkushev
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, United States.,Health Informatics Lab, Metropolitan College, Boston University, Boston, MA, United States
| | - Tahereh Javaheri
- Health Informatics Lab, Metropolitan College, Boston University, Boston, MA, United States
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland.,Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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28
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Gerdol M, Sollitto M, Pallavicini A, Castellano I. The complex evolutionary history of sulfoxide synthase in ovothiol biosynthesis. Proc Biol Sci 2019; 286:20191812. [PMID: 31771466 DOI: 10.1098/rspb.2019.1812] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Sulfoxide synthases are enzymes involved in the biosynthesis of small sulfur-containing natural products. Their enzymatic activity represents a unique sulfur transfer strategy in nature that is the insertion of a sulfur atom on the imidazole ring of histidine. To date, only two enzymes are known to carry out this function: the sulfoxide synthase EgtB, involved in the biosynthesis of ergothioneine in fungi and bacteria, and the 5-histidylcysteine sulfoxide synthase OvoA, involved in the biosynthesis of ovothiols, found in the eggs and biological fluids of marine invertebrates, some proteobacteria and protists. In particular, ovothiols, thanks to their unique redox properties, are probably the most intriguing marine sulfur-containing molecules. Although they have long been considered as cellular protective molecules, new evidence suggest that their biological activities and ecological role might be more complex than originally thought. Here, we investigate the evolutionary history of OvoA in Metazoa, reporting its monophyletic ancient origins, which could be traced back to the latest common ancestor of Choanozoa. Nevertheless, we show that OvoA is missing in several major extant taxa and we discuss this patchy distribution in the light of the massive genome reduction events documented in Metazoa. We also highlight two interesting cases of secondary acquisition through horizontal gene transfer, which occurred in hydrozoans and bdelloid rotifers. The evolutionary success of this metabolic pathway is probably ascribable to its role in the maintenance of cellular redox homeostasis, which enables organisms to survive in different environmental niches.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Marco Sollitto
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Trieste, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Immacolata Castellano
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
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29
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Kaczmarek Ł, Roszkowska M, Fontaneto D, Jezierska M, Pietrzak B, Wieczorek R, Poprawa I, Kosicki JZ, Karachitos A, Kmita H. Staying young and fit? Ontogenetic and phylogenetic consequences of animal anhydrobiosis. J Zool (1987) 2019. [DOI: 10.1111/jzo.12677] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ł. Kaczmarek
- Department of Animal Taxonomy and Ecology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
| | - M. Roszkowska
- Department of Animal Taxonomy and Ecology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
- Department of Bioenergetics Institute of Molecular Biology and Biotechnology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
| | - D. Fontaneto
- National Research Council Water Research Institute (CNR‐IRSA) Verbania Italy
| | - M. Jezierska
- Department of Animal Histology and Embryology University of Silesia in Katowice Katowice Poland
| | - B. Pietrzak
- Department of Hydrobiology Faculty of Biology Biological and Chemical Research Centre University of Warsaw Warszawa Poland
| | - R. Wieczorek
- Faculty of Chemistry University of Warsaw Warsaw Poland
| | - I. Poprawa
- Department of Animal Histology and Embryology University of Silesia in Katowice Katowice Poland
| | - J. Z. Kosicki
- Department of Avian Biology and Ecology Faculty of Biology Adam Mickiewicz University Poznan Poznań Poland
| | - A. Karachitos
- Department of Bioenergetics Institute of Molecular Biology and Biotechnology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
| | - H. Kmita
- Department of Bioenergetics Institute of Molecular Biology and Biotechnology Faculty of Biology Adam Mickiewicz University in Poznan Poznań Poland
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30
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Fontaneto D. Long-distance passive dispersal in microscopic aquatic animals. MOVEMENT ECOLOGY 2019; 7:10. [PMID: 30962931 PMCID: PMC6434837 DOI: 10.1186/s40462-019-0155-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/05/2019] [Indexed: 05/21/2023]
Abstract
Given their dormancy capability (long-term resistant stages) and their ability to colonise and reproduce, microscopic aquatic animals have been suggested having cosmopolitan distribution. Their dormant stages may be continuously moved by mobile elements through the entire planet to any suitable habitat, preventing the formation of biogeographical patterns. In this review, I will go through the evidence we have on the most common microscopic aquatic animals, namely nematodes, rotifers, and tardigrades, for each of the assumptions allowing long-distance dispersal (dormancy, viability, and reproduction) and all the evidence we have for transportation, directly from surveys of dispersing stages, and indirectly from the outcome of successful dispersal in biogeographical and phylogeographical studies. The current knowledge reveals biogeographical patterns also for microscopic organisms, with species-specific differences in ecological features that make some taxa indeed cosmopolitan with the potential for long-distance dispersal, but others with restricted geographic distributions.
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Affiliation(s)
- Diego Fontaneto
- National Research Council of Italy, Water Research Institute, Largo Tonolli 50, 28922 Verbania Pallanza, Italy
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31
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Immediate and heritable costs of desiccation on the life history of the bdelloid rotifer Philodina roseola. ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-018-0379-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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32
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Hecox-Lea BJ, Mark Welch DB. Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers. BMC Evol Biol 2018; 18:177. [PMID: 30486781 PMCID: PMC6264785 DOI: 10.1186/s12862-018-1288-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 11/02/2018] [Indexed: 11/26/2022] Open
Abstract
Background Bdelloid rotifers are the oldest, most diverse and successful animal taxon for which males, hermaphrodites, and traditional meiosis are unknown. Their degenerate tetraploid genome, with 2–4 copies of most loci, includes thousands of genes acquired from all domains of life by horizontal transfer. Many bdelloid species thrive in ephemerally aquatic habitats by surviving desiccation at any life stage with no loss of fecundity or lifespan. Their unique genomic diversity and the intense selective pressure of desiccation provide an exceptional opportunity to study the evolution of diversity and novelty in genes involved in DNA repair. Results We used genomic data and RNA-Seq of the desiccation process in the bdelloid Adineta vaga to characterize DNA damage reversal, translesion synthesis, and the major DNA repair pathways: base, nucleotide, and alternate excision repair, mismatch repair (MMR), and double strand break repair by homologous recombination (HR) and classical non-homologous end joining (NHEJ). We identify multiple horizontally transferred DNA damage response genes otherwise unknown in animals (AlkD, Fpg, LigK UVDE), and the presence of genes often considered vertebrate specific, particularly in the NHEJ complex and X family polymerases. While 75–100% of genes involved in MMR and HR are present in 0–2 copies, genes involved in NHEJ, which are present in only a single copy in nearly all other animals, are retained in 3–8 copies. We present structural predictions and expression evidence of neo- or sub-functionalization of multiple copy genes involved in NHEJ and other repair processes. Conclusion The horizontally-acquired genes and duplicated genes in BER and NHEJ suggest resilience to oxidative damage is conferred in part by increased DNA damage recognition and efficient end repair capabilities. The pattern of gene loss and retention in MMR and HR may facilitate recombination and gene conversion between divergent sequences, thus providing at least some of the benefits of sex. The unique retention and divergence of duplicates genes in NHEJ may be facilitated by the lack of efficient selection in the absence of meiotic recombination and independent assortment, and may contribute to the evolutionary success of bdelloids. Electronic supplementary material The online version of this article (10.1186/s12862-018-1288-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bette J Hecox-Lea
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.,Department of Biology, Northeastern University, Boston, MA, USA
| | - David B Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
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Hand SC, Moore DS, Patil Y. Challenges during diapause and anhydrobiosis: Mitochondrial bioenergetics and desiccation tolerance. IUBMB Life 2018; 70:1251-1259. [PMID: 30369011 DOI: 10.1002/iub.1953] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 11/11/2022]
Abstract
In preparation for the onset of environmental challenges like overwintering, food limitation, anoxia, or water stress, many invertebrates and certain killifish enter diapause. Diapause is a developmentally-programed dormancy characterized by suppression of development and metabolism. For embryos of Artemia franciscana (brine shrimp), the metabolic arrest is profound. These gastrula-stage embryos depress oxidative metabolism by ~99% during diapause and survive years of severe desiccation in a state termed anhydrobiosis. Trehalose is the sole fuel source for this developmental stage. Mitochondrial function during diapause is downregulated primarily by restricting substrate supply, as a result of inhibiting key enzymes of carbohydrate metabolism. Because proton conductance across the inner membrane is not decreased during diapause, the inference is that membrane potential must be compromised. In the absence of any intervention, the possibility exists that the F1 Fo ATP synthase and the adenine nucleotide translocator may reverse, leading to wholesale hydrolysis of cellular ATP. Studies with anhydrobiotes like A. franciscana are revealing multiple traits useful for improving desiccation tolerance that include the expression and accumulation late embryogenesis abundant (LEA) proteins and trehalose. LEA proteins are intrinsically disordered in aqueous solution but gain secondary structure (predominantly α-helix) as water is removed. These protective agents stabilize biological structures including lipid bilayers and mitochondria during severe water stress. © 2018 IUBMB Life, 70(12):1251-1259, 2018.
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Affiliation(s)
- Steven C Hand
- Department of Biological Sciences, Division of Cellular Developmental and Integrative Biology, Louisiana State University, LA, USA
| | - Daniel S Moore
- Department of Biological Sciences, Division of Cellular Developmental and Integrative Biology, Louisiana State University, LA, USA
| | - Yuvraj Patil
- Department of Biological Sciences, Division of Cellular Developmental and Integrative Biology, Louisiana State University, LA, USA
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Liu C, Liu B, Zhang Y, Jiang F, Ren Y, Li S, Wang H, Fan W. Ancient horizontally transferred genes in the genome of California two-spot octopus, Octopus bimaculoides. Gene 2018; 667:34-44. [PMID: 29738840 DOI: 10.1016/j.gene.2018.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 04/10/2018] [Accepted: 05/02/2018] [Indexed: 11/28/2022]
Abstract
Horizontal gene transfer (HGT), a mechanism that shares genetic material between the host and donor from separated offspring branches, has been described as a means of producing novel and beneficial phenotypes for the host organisms. However, in molluscs, the second most diverse group, the existence of HGT is still controversial. In the present study, 12 HGT genes were identified from California two-spot octopus Octopus bimaculoides based on a similarity search, phylogenetic construction, gene composition analysis and PCR (Polymerase Chain Reaction) validation. Based on the phylogenetic topologies, ten HGT genes were identified to have been transferred into the possible molluscan ancestor, possibly before its radiation. Furthermore, most of the donor organisms were predicted to be familiar bacteria in marine environments. These horizontally transferred genes were under a strong negative selection and could be transcribed in octopus functionally. The predicted biochemical functions of these genes include metabolism, neurotransmission, immune defense and tissue integrity. Seven Zn-metalloproteinases were validated as the main type of HGT genes in octopus with divergent motif composition, intron presence and phylogenetic relationship to the endogenous ones. Furthermore, the functions of Zn-metalloproteinase were predicted to be responsible for immune defense and tissue remolding. Three HGT genes were distributed mainly in the nervous system and were predicted to regulate the neurotransmission through glia-neuronal interactions. The results collectively indicated the existence of HGT in molluscs and its potential contribution to the evolution of octopus with regards to functional innovation and adaptability.
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Affiliation(s)
- Conghui Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| | - Bo Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yan Zhang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Fan Jiang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuwei Ren
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Shuqu Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Hengchao Wang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Wei Fan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
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Plant Desiccation Tolerance and its Regulation in the Foliage of Resurrection “Flowering-Plant” Species. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8080146] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The majority of flowering-plant species can survive complete air-dryness in their seed and/or pollen. Relatively few species (‘resurrection plants’) express this desiccation tolerance in their foliage. Knowledge of the regulation of desiccation tolerance in resurrection plant foliage is reviewed. Elucidation of the regulatory mechanism in resurrection grasses may lead to identification of genes that can improve stress tolerance and yield of major crop species. Well-hydrated leaves of resurrection plants are desiccation-sensitive and the leaves become desiccation tolerant as they are drying. Such drought-induction of desiccation tolerance involves changes in gene-expression causing extensive changes in the complement of proteins and the transition to a highly-stable quiescent state lasting months to years. These changes in gene-expression are regulated by several interacting phytohormones, of which drought-induced abscisic acid (ABA) is particularly important in some species. Treatment with only ABA induces desiccation tolerance in vegetative tissue of Borya constricta Churchill. and Craterostigma plantagineum Hochstetter. but not in the resurrection grass Sporobolus stapfianus Gandoger. Suppression of drought-induced senescence is also important for survival of drying. Further research is needed on the triggering of the induction of desiccation tolerance, on the transition between phases of protein synthesis and on the role of the phytohormone, strigolactone and other potential xylem-messengers during drying and rehydration.
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Cross-Contamination Explains "Inter and Intraspecific Horizontal Genetic Transfers" between Asexual Bdelloid Rotifers. Curr Biol 2018; 28:2436-2444.e14. [PMID: 30017483 DOI: 10.1016/j.cub.2018.05.070] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/07/2017] [Accepted: 05/23/2018] [Indexed: 11/22/2022]
Abstract
A few metazoan lineages are thought to have persisted for millions of years without sexual reproduction. If so, they would offer important clues to the evolutionary paradox of sex itself [1, 2]. Most "ancient asexuals" are subject to ongoing doubt because extant populations continue to invest in males [3-9]. However, males are famously unknown in bdelloid rotifers, a class of microscopic invertebrates comprising hundreds of species [10-12]. Bdelloid genomes have acquired an unusually high proportion of genes from non-metazoans via horizontal transfer [13-17]. This well-substantiated finding has invited speculation [13] that homologous horizontal transfer between bdelloid individuals also may occur, perhaps even "replacing" sex [14]. In 2016, Current Biology published an article claiming to supply evidence for this idea. Debortoli et al. [18] sampled rotifers from natural populations and sequenced one mitochondrial and four nuclear loci. Species assignments were incongruent among loci for several samples, which was interpreted as evidence of "interspecific horizontal genetic transfers." Here, we use sequencing chromatograms supplied by the authors to demonstrate that samples treated as individuals actually contained two or more highly divergent mitochondrial and ribosomal sequences, revealing cross-contamination with DNA from multiple animals of different species. Other chromatograms indicate contamination with DNA from conspecific animals, explaining genetic and genomic evidence for "intraspecific horizontal exchanges" reported in the same study. Given the clear evidence of contamination, the data and findings of Debortoli et al. [18] provide no reliable support for their conclusions that DNA is transferred horizontally between or within bdelloid species.
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Hernandez AM, Ryan JF. Horizontally transferred genes in the ctenophore Mnemiopsis leidyi. PeerJ 2018; 6:e5067. [PMID: 29922518 PMCID: PMC6005172 DOI: 10.7717/peerj.5067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/04/2018] [Indexed: 12/16/2022] Open
Abstract
Horizontal gene transfer (HGT) has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that HGT between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.
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Affiliation(s)
- Alexandra M Hernandez
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
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Nowell RW, Almeida P, Wilson CG, Smith TP, Fontaneto D, Crisp A, Micklem G, Tunnacliffe A, Boschetti C, Barraclough TG. Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species. PLoS Biol 2018; 16:e2004830. [PMID: 29689044 PMCID: PMC5916493 DOI: 10.1371/journal.pbio.2004830] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 03/19/2018] [Indexed: 12/22/2022] Open
Abstract
Bdelloid rotifers are a class of microscopic invertebrates that have existed for millions of years apparently without sex or meiosis. They inhabit a variety of temporary and permanent freshwater habitats globally, and many species are remarkably tolerant of desiccation. Bdelloids offer an opportunity to better understand the evolution of sex and recombination, but previous work has emphasised desiccation as the cause of several unusual genomic features in this group. Here, we present high-quality whole-genome sequences of 3 bdelloid species: Rotaria macrura and R. magnacalcarata, which are both desiccation intolerant, and Adineta ricciae, which is desiccation tolerant. In combination with the published assembly of A. vaga, which is also desiccation tolerant, we apply a comparative genomics approach to evaluate the potential effects of desiccation tolerance and asexuality on genome evolution in bdelloids. We find that ancestral tetraploidy is conserved among all 4 bdelloid species, but homologous divergence in obligately aquatic Rotaria genomes is unexpectedly low. This finding is contrary to current models regarding the role of desiccation in shaping bdelloid genomes. In addition, we find that homologous regions in A. ricciae are largely collinear and do not form palindromic repeats as observed in the published A. vaga assembly. Consequently, several features interpreted as genomic evidence for long-term ameiotic evolution are not general to all bdelloid species, even within the same genus. Finally, we substantiate previous findings of high levels of horizontally transferred nonmetazoan genes in both desiccating and nondesiccating bdelloid species and show that this unusual feature is not shared by other animal phyla, even those with desiccation-tolerant representatives. These comparisons call into question the proposed role of desiccation in mediating horizontal genetic transfer.
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Affiliation(s)
- Reuben W. Nowell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom
| | - Pedro Almeida
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom
| | - Christopher G. Wilson
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom
| | - Thomas P. Smith
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom
| | - Diego Fontaneto
- National Research Council of Italy, Institute of Ecosystem Study, Verbania Pallanza, Italy
| | - Alastair Crisp
- Department of Chemical Engineering and Biotechnology, West Cambridge Site, University of Cambridge, Cambridge, United Kingdom
| | - Gos Micklem
- Department of Genetics, Cambridge Systems Biology Centre, Downing Site, University of Cambridge, Cambridge, United Kingdom
| | - Alan Tunnacliffe
- Department of Chemical Engineering and Biotechnology, West Cambridge Site, University of Cambridge, Cambridge, United Kingdom
| | - Chiara Boschetti
- Department of Chemical Engineering and Biotechnology, West Cambridge Site, University of Cambridge, Cambridge, United Kingdom
- School of Biological and Marine Sciences, Plymouth University, Portland Square Building, Plymouth, United Kingdom
| | - Timothy G. Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom
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Leger MM, Eme L, Stairs CW, Roger AJ. Demystifying Eukaryote Lateral Gene Transfer (Response to Martin 2017 DOI: 10.1002/bies.201700115). Bioessays 2018; 40:e1700242. [DOI: 10.1002/bies.201700242] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/06/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Michelle M. Leger
- Institute of Evolutionary Biology (CSIC-UPF); Pg. Marítim de la Barceloneta, Barcelona ES 08003 Spain
| | - Laura Eme
- Department of Cell and Molecular Biology; Science for Life Laboratory; Uppsala University; Box 596, Uppsala SE 751 25 Sweden
| | - Courtney W. Stairs
- Department of Cell and Molecular Biology; Science for Life Laboratory; Uppsala University; Box 596, Uppsala SE 751 25 Sweden
| | - Andrew J. Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics; Department of Biochemistry and Molecular Biology; Dalhousie University; P.O. Box 15000, Halifax CAN B3H 4R2 Nova Scotia Canada
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40
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41
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Rancurel C, Legrand L, Danchin EGJ. Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Genes (Basel) 2017; 8:E248. [PMID: 28961181 PMCID: PMC5664098 DOI: 10.3390/genes8100248] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/22/2017] [Accepted: 09/22/2017] [Indexed: 11/22/2022] Open
Abstract
Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr. Alienness parses BLAST results against public libraries to rapidly identify candidate HGT in any genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any National Center for Biotechnology Information (NCBI) protein library. The user defines recipient (e.g., Metazoa) and donor (e.g., bacteria, fungi) branches of interest in the NCBI taxonomy. Based on the best BLAST E-values of candidate donor and recipient taxa, Alienness calculates an Alien Index (AI) for each query protein. An AI > 0 indicates a better hit to candidate donor than recipient taxa and a possible HGT. Higher AI represent higher gap of E-values between candidate donor and recipient and a more likely HGT. We confirmed the accuracy of Alienness on phylogenetically confirmed HGT of non-metazoan origin in plant-parasitic nematodes. Alienness scans whole proteomes to rapidly identify possible HGT in any species of interest and thus fosters exploration of HGT more easily and largely across the tree of life.
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Affiliation(s)
- Corinne Rancurel
- INRA, CNRS, ISA, Université Côte d'Azur, 06903 Sophia Antipolis Cedex, France.
| | - Ludovic Legrand
- LIPM, INRA, CNRS, Université de Toulouse, 31326 Castanet-Tolosan Cedex, France.
| | - Etienne G J Danchin
- INRA, CNRS, ISA, Université Côte d'Azur, 06903 Sophia Antipolis Cedex, France.
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42
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Drezen JM, Gauthier J, Josse T, Bézier A, Herniou E, Huguet E. Foreign DNA acquisition by invertebrate genomes. J Invertebr Pathol 2017; 147:157-168. [DOI: 10.1016/j.jip.2016.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/09/2016] [Accepted: 09/14/2016] [Indexed: 12/14/2022]
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43
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Ram Y, Hadany L. Condition-dependent sex: who does it, when and why? Philos Trans R Soc Lond B Biol Sci 2016; 371:20150539. [PMID: 27619702 PMCID: PMC5031623 DOI: 10.1098/rstb.2015.0539] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2016] [Indexed: 01/09/2023] Open
Abstract
We review the phenomenon of condition-dependent sex-where individuals' condition affects the likelihood that they will reproduce sexually rather than asexually. In recent years, condition-dependent sex has been studied both theoretically and empirically. Empirical results in microbes, fungi and plants support the theoretical prediction that negative condition-dependent sex, in which individuals in poor condition are more likely to reproduce sexually, can be evolutionarily advantageous under a wide range of settings. Here, we review the evidence for condition-dependent sex and its potential implications for the long-term survival and adaptability of populations. We conclude by asking why condition-dependent sex is not more commonly observed, and by considering generalizations of condition-dependent sex that might apply even for obligate sexuals.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Yoav Ram
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Lilach Hadany
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 6997801, Israel
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Torralba D, Baixauli F, Sánchez-Madrid F. Mitochondria Know No Boundaries: Mechanisms and Functions of Intercellular Mitochondrial Transfer. Front Cell Dev Biol 2016; 4:107. [PMID: 27734015 PMCID: PMC5039171 DOI: 10.3389/fcell.2016.00107] [Citation(s) in RCA: 260] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/14/2016] [Indexed: 12/25/2022] Open
Abstract
Mitochondria regulate multiple cell processes, including calcium signaling, apoptosis and cell metabolism. Mitochondria contain their own circular genome encoding selected subunits of the oxidative phosphorylation complexes. Recent findings reveal that, in addition to being maternally inherited, mitochondria can traverse cell boundaries and thus be horizontally transferred between cells. Although, the physiological relevance of this phenomenon is still under debate, mitochondria uptake rescues mitochondrial respiration defects in recipient cells and regulates signaling, proliferation or chemotherapy resistance in vitro and in vivo. In this review, we outline the pathophysiological consequences of horizontal mitochondrial transfer and offer a perspective on the cellular and molecular mechanisms mediating their intercellular transmission, including tunneling nanotubes, extracellular vesicles, cellular fusion, and GAP junctions. The physiological relevance of mitochondrial transfer and the potential therapeutic application of this exchange for treating mitochondrial-related diseases are discussed.
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Affiliation(s)
- Daniel Torralba
- Signaling and Inflammation Program, Centro Nacional Investigaciones CardiovascularesMadrid, Spain; Servicio de Inmunología, Instituto Investigación Sanitaria Princesa, Universidad Autonoma de MadridMadrid, Spain
| | - Francesc Baixauli
- Signaling and Inflammation Program, Centro Nacional Investigaciones CardiovascularesMadrid, Spain; Servicio de Inmunología, Instituto Investigación Sanitaria Princesa, Universidad Autonoma de MadridMadrid, Spain
| | - Francisco Sánchez-Madrid
- Signaling and Inflammation Program, Centro Nacional Investigaciones CardiovascularesMadrid, Spain; Servicio de Inmunología, Instituto Investigación Sanitaria Princesa, Universidad Autonoma de MadridMadrid, Spain
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Evidence Supporting the Uptake and Genomic Incorporation of Environmental DNA in the "Ancient Asexual" Bdelloid Rotifer Philodina roseola. Life (Basel) 2016; 6:life6030038. [PMID: 27608044 PMCID: PMC5041014 DOI: 10.3390/life6030038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 08/08/2016] [Accepted: 08/30/2016] [Indexed: 11/17/2022] Open
Abstract
Increasing evidence suggests that bdelloid rotifers regularly undergo horizontal gene transfer, apparently as a surrogate mechanism of genetic exchange in the absence of true sexual reproduction, in part because of their ability to withstand desiccation. We provide empirical support for this latter hypothesis using the bdelloid Philodina roseola, which we demonstrate to readily internalize environmental DNA in contrast to a representative monogonont rotifer (Brachionus rubens), which, like other monogononts, is facultative sexual and cannot withstand desiccation. In addition, environmental DNA that was more similar to the host DNA was retained more often and for a longer period of time. Indirect evidence (increased variance in the reproductive output of the untreated F1 generation) suggests that environmental DNA can be incorporated into the genome during desiccation and is thus heritable. Our observed fitness effects agree with sexual theory and also occurred when the animals were desiccated in groups (thereby acting as DNA donors), but not individually, indicating the mechanism could occur in nature. Thus, although DNA uptake and its genomic incorporation appears proximally related to anhydrobiosis in bdelloids, it might also facilitate accidental genetic exchange with closely related taxa, thereby maintaining higher levels of genetic diversity than is otherwise expected for this group of "ancient asexuals".
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46
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A functional difference between native and horizontally acquired genes in bdelloid rotifers. Gene 2016; 590:186-91. [PMID: 27312952 DOI: 10.1016/j.gene.2016.06.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 06/02/2016] [Accepted: 06/06/2016] [Indexed: 02/06/2023]
Abstract
The form of RNA processing known as SL trans-splicing involves the transfer of a short conserved sequence, the spliced leader (SL), from a noncoding SL RNA to the 5' ends of mRNA molecules. SL trans-splicing occurs in several animal taxa, including bdelloid rotifers (Rotifera, Bdelloidea). One striking feature of these aquatic microinvertebrates is the large proportion of foreign genes, i.e. those acquired by horizontal gene transfer from other organisms, in their genomes. However, whether such foreign genes behave similarly to native genes has not been tested in bdelloids or any other animal. We therefore used a combination of experimental and computational methods to examine whether transcripts of foreign genes in bdelloids were SL trans-spliced, like their native counterparts. We found that many foreign transcripts contain SLs, use similar splice acceptor sequences to native genes, and are able to undergo alternative trans-splicing. However, a significantly lower proportion of foreign mRNAs contains SL sequences than native transcripts. This demonstrates a novel functional difference between foreign and native genes in bdelloids and suggests that SL trans-splicing is not essential for the expression of foreign genes, but is acquired during their domestication.
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Jensen L, Grant JR, Laughinghouse HD, Katz LA. Assessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa. Evolution 2016; 70:1322-33. [DOI: 10.1111/evo.12935] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/04/2016] [Accepted: 04/19/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Lindy Jensen
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
- Current Address: Department of Molecular and Integrative Physiology; University of Michigan; Ann Arbor Michigan 48109
| | - Jessica R. Grant
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
| | | | - Laura A. Katz
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
- Program in Organismic and Evolutionary Biology; University of Massachusetts; Amherst Massachusetts 01003
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Reply to Bemm et al. and Arakawa: Identifying foreign genes in independent Hypsibius dujardini genome assemblies. Proc Natl Acad Sci U S A 2016; 113:E3058-61. [PMID: 27173900 DOI: 10.1073/pnas.1601149113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, Maroon H, Thomas F, Aboobaker AA, Blaxter M. No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. Proc Natl Acad Sci U S A 2016; 113:5053-5058. [PMID: 27035985 DOI: 10.1101/033464] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper [Boothby TC, et al. (2015) Proc Natl Acad Sci USA 112(52):15976-15981], the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT) and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini As expected from whole-organism DNA sampling, our raw data contained reads from nontarget genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria and 0.2% strong candidates for fHGT from nonmetazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1-2% of genes and that the proposal that one-sixth of tardigrade genes originate from functional HGT events is an artifact of undetected contamination.
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Affiliation(s)
- Georgios Koutsovoulos
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Sujai Kumar
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom; The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Lewis Stevens
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Jennifer Daub
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Claire Conlon
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Habib Maroon
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Fran Thomas
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Aziz A Aboobaker
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
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Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, Maroon H, Thomas F, Aboobaker AA, Blaxter M. No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. Proc Natl Acad Sci U S A 2016; 113:5053-8. [PMID: 27035985 PMCID: PMC4983863 DOI: 10.1073/pnas.1600338113] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper [Boothby TC, et al. (2015) Proc Natl Acad Sci USA 112(52):15976-15981], the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT) and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini As expected from whole-organism DNA sampling, our raw data contained reads from nontarget genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria and 0.2% strong candidates for fHGT from nonmetazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1-2% of genes and that the proposal that one-sixth of tardigrade genes originate from functional HGT events is an artifact of undetected contamination.
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Affiliation(s)
- Georgios Koutsovoulos
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Sujai Kumar
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom; The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Lewis Stevens
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Jennifer Daub
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Claire Conlon
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Habib Maroon
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Fran Thomas
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Aziz A Aboobaker
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
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