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Morard R, Darling KF, Weiner AKM, Hassenrück C, Vanni C, Cordier T, Henry N, Greco M, Vollmar NM, Milivojevic T, Rahman SN, Siccha M, Meilland J, Jonkers L, Quillévéré F, Escarguel G, Douady CJ, de Garidel-Thoron T, de Vargas C, Kucera M. The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton. Biol Rev Camb Philos Soc 2024; 99:1218-1241. [PMID: 38351434 DOI: 10.1111/brv.13065] [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: 08/31/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 07/06/2024]
Abstract
The nature and extent of diversity in the plankton has fascinated scientists for over a century. Initially, the discovery of many new species in the remarkably uniform and unstructured pelagic environment appeared to challenge the concept of ecological niches. Later, it became obvious that only a fraction of plankton diversity had been formally described, because plankton assemblages are dominated by understudied eukaryotic lineages with small size that lack clearly distinguishable morphological features. The high diversity of the plankton has been confirmed by comprehensive metabarcoding surveys, but interpretation of the underlying molecular taxonomies is hindered by insufficient integration of genetic diversity with morphological taxonomy and ecological observations. Here we use planktonic foraminifera as a study model and reveal the full extent of their genetic diversity and investigate geographical and ecological patterns in their distribution. To this end, we assembled a global data set of ~7600 ribosomal DNA sequences obtained from morphologically characterised individual foraminifera, established a robust molecular taxonomic framework for the observed diversity, and used it to query a global metabarcoding data set covering ~1700 samples with ~2.48 billion reads. This allowed us to extract and assign 1 million reads, enabling characterisation of the structure of the genetic diversity of the group across ~1100 oceanic stations worldwide. Our sampling revealed the existence of, at most, 94 distinct molecular operational taxonomic units (MOTUs) at a level of divergence indicative of biological species. The genetic diversity only doubles the number of formally described species identified by morphological features. Furthermore, we observed that the allocation of genetic diversity to morphospecies is uneven. Only 16 morphospecies disguise evolutionarily significant genetic diversity, and the proportion of morphospecies that show genetic diversity increases poleward. Finally, we observe that MOTUs have a narrower geographic distribution than morphospecies and that in some cases the MOTUs belonging to the same morphospecies (cryptic species) have different environmental preferences. Overall, our analysis reveals that even in the light of global genetic sampling, planktonic foraminifera diversity is modest and finite. However, the extent and structure of the cryptic diversity reveals that genetic diversification is decoupled from morphological diversification, hinting at different mechanisms acting at different levels of divergence.
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Affiliation(s)
- Raphaël Morard
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Kate F Darling
- School of GeoSciences, University of Edinburgh, Edinburgh, EH9 3JW, UK
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Agnes K M Weiner
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, Bergen, 5007, Norway
| | - Christiane Hassenrück
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Seestrasse 15, Warnemünde, 18119, Germany
| | - Chiara Vanni
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Tristan Cordier
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, Bergen, 5007, Norway
| | - Nicolas Henry
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, Roscoff, 29680, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, 75016, France
| | - Mattia Greco
- Institut de Ciències del Mar, Passeig Marítim de la Barceloneta, Barcelona, 37-49, Spain
| | - Nele M Vollmar
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, Bergen, 5007, Norway
| | - Tamara Milivojevic
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Shirin Nurshan Rahman
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Michael Siccha
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Julie Meilland
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Lukas Jonkers
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Frédéric Quillévéré
- Univ Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS, UMR CNRS 5276 LGL-TPE, Villeurbanne, F-69622, France
| | - Gilles Escarguel
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, F-69622, France
| | - Christophe J Douady
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, F-69622, France
- Institut Universitaire de France, Paris, France
| | | | - Colomban de Vargas
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, Roscoff, 29680, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR7144, Place Georges Teissier, Roscoff, 29680, France
| | - Michal Kucera
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
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Agmon I. Three Biopolymers and Origin of Life Scenarios. Life (Basel) 2024; 14:277. [PMID: 38398786 PMCID: PMC10890401 DOI: 10.3390/life14020277] [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: 12/28/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
To track down the possible roots of life, various models for the initial living system composed of different combinations of the three extant biopolymers, RNA, DNA, and proteins, are presented. The suitability of each molecular set is assessed according to its ability to emerge autonomously, sustain, and evolve continuously towards life as we know it. The analysis incorporates current biological knowledge gained from high-resolution structural data and large sequence datasets, together with experimental results concerned with RNA replication and with the activity demonstrated by standalone constructs of the ribosomal Peptidyl Transferase Center region. The scrutiny excludes the DNA-protein combination and assigns negligible likelihood to the existence of an RNA-DNA world, as well as to an RNA world that contained a replicase made of RNA. It points to the precedence of an RNA-protein system, whose model of emergence suggests specific processes whereby a coded proto-ribosome ribozyme, specifically aminoacylated proto-tRNAs and a proto-polymerase enzyme, could have autonomously emerged, cross-catalyzing the formation of each other. This molecular set constitutes a feasible starting point for a continuous evolutionary path, proceeding via natural processes from the inanimate matter towards life as we know it.
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Affiliation(s)
- Ilana Agmon
- Institute for Advanced Studies in Theoretical Chemistry, Schulich Faculty of Chemistry, Technion—Israel Institute of Technology, Haifa 3200003, Israel;
- Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 9190401, Israel
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Lis JA. Molecular Apomorphies in the Secondary and Tertiary Structures of Length-Variable Regions (LVRs) of 18S rRNA Shed Light on the Systematic Position of the Family Thaumastellidae (Hemiptera: Heteroptera: Pentatomoidea). Int J Mol Sci 2023; 24:ijms24097758. [PMID: 37175465 PMCID: PMC10178826 DOI: 10.3390/ijms24097758] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
The SSU nrDNA, a small subunit of the nuclear ribosomal DNA (coding 18S rRNA), is one of the most frequently sequenced genes in molecular studies in Hexapoda. In insects, including true bugs (Hemiptera: Heteroptera), only its primary structures (i.e., aligned sequences) are predominantly used in phylogenetic reconstructions. It is known that including RNA secondary structures in the alignment procedure is essential for improving accuracy and robustness in phylogenetic tree reconstruction. Moreover, local plasticity in rRNAs might impact their tertiary structures and corresponding functions. To determine the systematic position of Thaumastellidae within the superfamily Pentatomoidea, the secondary and-for the first time among all Hexapoda-tertiary structures of 18S rRNAs in twelve pentatomoid families were compared and analysed. Results indicate that the shapes of the secondary and tertiary structures of the length-variable regions (LVRs) in the 18S rRNA are phylogenetically highly informative. Based on these results, it is suggested that the Thaumastellidae is maintained as an independent family within the superfamily Pentatomoidea, rather than as a part of the family Cydnidae. Moreover, the analyses indicate a close relationship between Sehirinae and Parastrachiidae, expressed in morpho-molecular synapomorphies in the predicted secondary and tertiary structures of the length-variable region L (LVR L).
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Affiliation(s)
- Jerzy A Lis
- Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland
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4
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Chia MA, Ameh I, George KC, Balogun EO, Akinyemi SA, Lorenzi AS. Genetic Diversity of Microcystin Producers (Cyanobacteria) and Microcystin Congeners in Aquatic Resources across Africa: A Review Paper. TOXICS 2022; 10:772. [PMID: 36548605 PMCID: PMC9783101 DOI: 10.3390/toxics10120772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Microcystins are produced by multifaceted organisms called cyanobacteria, which are integral to Africa's freshwater environments. The excessive proliferation of cyanobacteria caused by rising temperature and eutrophication leads to the production and release of copious amounts of microcystins, requiring critical management and control approaches to prevent the adverse environmental and public health problems associated with these bioactive metabolites. Despite hypotheses reported to explain the phylogeography and mechanisms responsible for cyanobacterial blooms in aquatic water bodies, many aspects are scarcely understood in Africa due to the paucity of investigations and lack of uniformity of experimental methods. Due to a lack of information and large-scale studies, cyanobacteria occurrence and genetic diversity are seldom reported in African aquatic ecosystems. This review covers the diversity and geographical distribution of potential microcystin-producing and non-microcystin-producing cyanobacterial taxa in Africa. Molecular analyses using housekeeping genes (e.g., 16S rRNA, ITS, rpoC1, etc.) revealed significant sequence divergence across several cyanobacterial strains from East, North, West, and South Africa, but the lack of uniformity in molecular markers employed made continent-wise phylogenetic comparisons impossible. Planktothrix agardhii, Microcystis aeruginosa, and Cylindrospermopsis raciborskii (presently known as Raphidiopsis raciborskii) were the most commonly reported genera. Potential microcystin (MCs)-producing cyanobacteria were detected using mcy genes, and several microcystin congeners were recorded. Studying cyanobacteria species from the African continent is urgent to effectively safeguard public and environmental health because more than 80% of the continent has no data on these important microorganisms and their bioactive secondary metabolites.
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Affiliation(s)
- Mathias Ahii Chia
- Department of Botany, Ahmadu Bello University, Zaria 810107, Nigeria
| | - Ilu Ameh
- Department of Biochemistry, Ahmadu Bello University, Zaria 810107, Nigeria
- African Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria 810107, Nigeria
| | - Korie Chibuike George
- Department of Biochemistry, Ahmadu Bello University, Zaria 810107, Nigeria
- African Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria 810107, Nigeria
| | | | | | - Adriana Sturion Lorenzi
- Department of Cellular Biology, Institute of Biological Sciences, University of Brasília—UnB, Brasília 70910-900, Brazil
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Sultanov D, Hochwagen A. Varying strength of selection contributes to the intragenomic diversity of rRNA genes. Nat Commun 2022; 13:7245. [PMID: 36434003 PMCID: PMC9700816 DOI: 10.1038/s41467-022-34989-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022] Open
Abstract
Ribosome biogenesis in eukaryotes is supported by hundreds of ribosomal RNA (rRNA) gene copies that are encoded in the ribosomal DNA (rDNA). The multiple copies of rRNA genes are thought to have low sequence diversity within one species. Here, we present species-wide rDNA sequence analysis in Saccharomyces cerevisiae that challenges this view. We show that rDNA copies in this yeast are heterogeneous, both among and within isolates, and that many variants avoided fixation or elimination over evolutionary time. The sequence diversity landscape across the rDNA shows clear functional stratification, suggesting different copy-number thresholds for selection that contribute to rDNA diversity. Notably, nucleotide variants in the most conserved rDNA regions are sufficiently deleterious to exhibit signatures of purifying selection even when present in only a small fraction of rRNA gene copies. Our results portray a complex evolutionary landscape that shapes rDNA sequence diversity within a single species and reveal unexpectedly strong purifying selection of multi-copy genes.
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Affiliation(s)
- Daniel Sultanov
- grid.137628.90000 0004 1936 8753Department of Biology, New York University, New York, NY 10003 USA
| | - Andreas Hochwagen
- grid.137628.90000 0004 1936 8753Department of Biology, New York University, New York, NY 10003 USA
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6
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Hassler HB, Probert B, Moore C, Lawson E, Jackson RW, Russell BT, Richards VP. Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies. MICROBIOME 2022; 10:104. [PMID: 35799218 PMCID: PMC9264627 DOI: 10.1186/s40168-022-01295-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/23/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable phylogenetic signal are accumulating. Here, we compare core gene phylogenies to phylogenies constructed using core gene concatenations to estimate the strength of signal for the 16S rRNA gene, its hypervariable regions, and all core genes at the intra- and inter-genus levels. Specifically, we perform four intra-genus analyses (Clostridium, n = 65; Legionella, n = 47; Staphylococcus, n = 36; and Campylobacter, n = 17) and one inter-genus analysis [41 core genera of the human gut microbiome (31 families, 17 orders, and 12 classes), n = 82]. RESULTS At both taxonomic levels, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the gene showed one of the lowest levels of concordance with the core genome phylogeny (50.7% average). Concordance for hypervariable regions was lower still, with entropy masking providing little to no benefit. A major factor influencing concordance was SNP count, which showed a positive logarithmic association. Using this relationship, we determined that 690 ± 110 SNPs were required for 80% concordance (average 16S rRNA gene SNP count was 254). We also found a wide range in 16S-23S-5S rRNA operon copy number among genomes (1-27). At the inter-genus level, concordance for the whole 16S rRNA gene was markedly higher (73.8% - 10th out of 49 loci); however, the most concordant hypervariable regions (V4, V3-V4, and V1-V2) ranked in the third quartile (62.5 to 60.0%). CONCLUSIONS Ramifications of a poor phylogenetic performance for the 16S rRNA gene are far reaching. For example, in addition to incorrect species/strain delineation and phylogenetic inference, it has the potential to confound community diversity metrics if phylogenetic information is incorporated - for example, with popular approaches such as Faith's phylogenetic diversity and UniFrac. Our results highlight the problematic nature of these approaches and their use (along with entropy masking) is discouraged. Lastly, the wide range in 16S rRNA gene copy number among genomes also has a strong potential to confound diversity metrics. Video Abstract.
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Affiliation(s)
- Hayley B. Hassler
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Brett Probert
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Carson Moore
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Elizabeth Lawson
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | | | - Brook T. Russell
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634 USA
| | - Vincent P. Richards
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
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7
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Corsaro D. Insights into Microsporidia Evolution from Early Diverging Microsporidia. EXPERIENTIA SUPPLEMENTUM (2012) 2022; 114:71-90. [PMID: 35543999 DOI: 10.1007/978-3-030-93306-7_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microsporidia have drastically modified genomes and cytology resulting from their high level of adaptation to intracytoplasmic parasitism. Their origins, which had long remained enigmatic, were placed within the line of Rozella, a primitive endoparasitic chytrid. These origins became more and more refined with the discovery of various parasites morphologically similar to the primitive lines of microsporidia (Metchnikovellids and Chytridiopsids) but which possess fungal-like genomes and functional mitochondria. These various parasites turn out to be distinct missing links between a large assemblage of chytrid-like rozellids and the true microsporidians, which are actually a very evolved branch of the rozellids themselves. The question of how to consider the historically known Microsporidia and the various microsporidia-like organisms within paraphyletic rozellids is discussed.
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Affiliation(s)
- Daniele Corsaro
- CHLAREAS Chlamydia Research Association, Vandoeuvre-lès-Nancy, France.
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8
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Chen CK, Cheng R, Demeter J, Chen J, Weingarten-Gabbay S, Jiang L, Snyder MP, Weissman JS, Segal E, Jackson PK, Chang HY. Structured elements drive extensive circular RNA translation. Mol Cell 2021; 81:4300-4318.e13. [PMID: 34437836 PMCID: PMC8567535 DOI: 10.1016/j.molcel.2021.07.042] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 06/03/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022]
Abstract
The human genome encodes tens of thousands circular RNAs (circRNAs) with mostly unknown functions. Circular RNAs require internal ribosome entry sites (IRES) if they are to undergo translation without a 5' cap. Here, we develop a high-throughput screen to systematically discover RNA sequences that can direct circRNA translation in human cells. We identify more than 17,000 endogenous and synthetic sequences as candidate circRNA IRES. 18S rRNA complementarity and a structured RNA element positioned on the IRES are important for driving circRNA translation. Ribosome profiling and peptidomic analyses show extensive IRES-ribosome association, hundreds of circRNA-encoded proteins with tissue-specific distribution, and antigen presentation. We find that circFGFR1p, a protein encoded by circFGFR1 that is downregulated in cancer, functions as a negative regulator of FGFR1 oncoprotein to suppress cell growth during stress. Systematic identification of circRNA IRES elements may provide important links among circRNA regulation, biological function, and disease.
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Affiliation(s)
- Chun-Kan Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ran Cheng
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jin Chen
- Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shira Weingarten-Gabbay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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9
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Paskerova GG, Miroliubova TS, Valigurová A, Janouškovec J, Kováčiková M, Diakin A, Sokolova YY, Mikhailov KV, Aleoshin VV, Simdyanov TG. Evidence from the resurrected family Polyrhabdinidae Kamm, 1922 (Apicomplexa: Gregarinomorpha) supports the epimerite, an attachment organelle, as a major eugregarine innovation. PeerJ 2021; 9:e11912. [PMID: 34616591 PMCID: PMC8450007 DOI: 10.7717/peerj.11912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 07/14/2021] [Indexed: 11/21/2022] Open
Abstract
Background Gregarines are a major group of apicomplexan parasites of invertebrates. The gregarine classification is largely incomplete because it relies primarily on light microscopy, while electron microscopy and molecular data in the group are fragmentary and often do not overlap. A key characteristic in gregarine taxonomy is the structure and function of their attachment organelles (AOs). AOs have been commonly classified as “mucrons” or “epimerites” based on their association with other cellular traits such as septation. An alternative proposal focused on the AOs structure, functional role, and developmental fate has recently restricted the terms “mucron” to archigregarines and “epimerite” to eugregarines. Methods Light microscopy and scanning and transmission electron microscopy, molecular phylogenetic analyses of ribosomal RNA genes. Results We obtained the first data on fine morphology of aseptate eugregarines Polyrhabdina pygospionis and Polyrhabdina cf. spionis, the type species. We demonstrate that their AOs differ from the mucron in archigregarines and represent an epimerite structurally resembling that in other eugregarines examined using electron microscopy. We then used the concatenated ribosomal operon DNA sequences (SSU, 5.8S, and LSU rDNA) of P. pygospionis to explore the phylogeny of eugregarines with a resolution superior to SSU rDNA alone. The obtained phylogenies show that the Polyrhabdina clade represents an independent, deep-branching family in the Ancoroidea clade within eugregarines. Combined, these results lend strong support to the hypothesis that the epimerite is a synapomorphic innovation of eugregarines. Based on these findings, we resurrect the family Polyrhabdinidae Kamm, 1922 and erect and diagnose the family Trollidiidae fam. n. within the superfamily Ancoroidea Simdyanov et al., 2017. Additionally, we re-describe the characteristics of P. pygospionis, emend the diagnoses of the genus Polyrhabdina, the family Polyrhabdinidae, and the superfamily Ancoroidea.
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Affiliation(s)
- Gita G Paskerova
- Department of Invertebrate Zoology, Faculty of Biology, St Petersburg State University, St Petersburg, Russia
| | - Tatiana S Miroliubova
- Laboratory for Fauna and Systematics of Parasites, Center for Parasitology, Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russian Federation
| | - Andrea Valigurová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jan Janouškovec
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - Magdaléna Kováčiková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Andrei Diakin
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Yuliya Ya Sokolova
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russian Federation
| | - Kirill V Mikhailov
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir V Aleoshin
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Timur G Simdyanov
- Department of Invertebrate Zoology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
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10
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Bininda-Emonds ORP. 18S rRNA variability maps reveal three highly divergent, conserved motifs within Rotifera. BMC Ecol Evol 2021; 21:118. [PMID: 34112085 PMCID: PMC8194223 DOI: 10.1186/s12862-021-01845-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 18S rRNA is a major component of the small subunit of the eukaryotic ribosome and an important phylogenetic marker for many groups, often to the point of being the only marker available for some. A core structure across eukaryotes exists for this molecule that can help to inform about its evolution in different groups. Using an alignment of 18S rDNA for Rotifera as traditionally recognized (=Bdelloidea, Monogononta, and Seisonacea, but not Acanthocephala), I fitted sequences for three exemplar species (Adineta vaga, Brachionus plicatilis, and Seison nebaliae, respectively) to the core structure and used these maps to reveal patterns of evolution for the remainder of this diverse group of microscopic animals. RESULTS The obtained variability maps of the 18S rRNA molecule revealed a pattern of high diversity among the three major rotifer clades coupled with strong conservation within each of bdelloids and monogononts. A majority of individual sites (ca. 60%) were constant even across rotifers as a whole with variable sites showing only intermediate rates of evolution. Although the three structural maps each showed good agreement with the inferred core structure for eukaryotic 18S rRNA and so were highly similar to one another at the secondary and tertiary levels, the overall pattern is of three highly distinct, but conserved motifs within the group at the primary sequence level. A novel finding was that of a variably expressed deletion at the 3' end of the V3 hypervariable region among some bdelloid species that occasionally extended into and included the pseudoknot structure following this region as well as the central "square" of the 18S rRNA molecule. Compared to other groups, levels of variation and rates of evolution for 18S rRNA in Rotifera roughly matched those for Gastropoda and Acanthocephala, despite increasing evidence for the latter being a clade within Rotifera. CONCLUSIONS The lack of comparative data for comparable groups makes interpretation of the results (i.e., very low variation within each of the three major rotifer clades, but high variation between them) and their potential novelty difficult. However, these findings in combination with the high morphological diversity within rotifers potentially help to explain why no clear consensus has been reached to date with regard to the phylogenetic relationships among the major groups.
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Affiliation(s)
- Olaf R P Bininda-Emonds
- AG Systematics and Evolutionary Biology, IBU-Faculty V, Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky Strasse 9-11, 26111, Oldenburg, Germany.
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11
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Hoshina R, Tsukii Y, Harumoto T, Suzaki T. Characterization of a green Stentor with symbiotic algae growing in an extremely oligotrophic environment and storing large amounts of starch granules in its cytoplasm. Sci Rep 2021; 11:2865. [PMID: 33536497 PMCID: PMC7859197 DOI: 10.1038/s41598-021-82416-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/30/2020] [Indexed: 01/30/2023] Open
Abstract
The genus Stentor is a relatively well-known ciliate owing to its lucid trumpet shape. Stentor pyriformis represents a green, short, and fat Stentor, but it is a little-known species. We investigated 124 ponds and wetlands in Japan and confirmed the presence of S. pyriformis at 23 locations. All these ponds were noticeably oligotrophic. With the improvement of oligotrophic culture conditions, we succeeded in long-term cultivation of three strains of S. pyriformis. The cytoplasm of S. piriformis contains a large number of 1-3 μm refractive granules that turn brown by Lugol's staining. The granules also show a typical Maltese-cross pattern by polarization microscopy, strongly suggesting that the granules are made of amylopectin-rich starch. By analyzing the algal rDNA, it was found that all S. pyriformis symbionts investigated in this study were Chlorella variabilis. This species is known as the symbiont of Paramecium bursaria and is physiologically specialized for endosymbiosis. Genetic discrepancies between C. variabilis of S. pyriformis and P. bursaria may indicate that algal sharing was an old incident. Having symbiotic algae and storing carbohydrate granules in the cytoplasm is considered a powerful strategy for this ciliate to withstand oligotrophic and cold winter environments in highland bogs.
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Affiliation(s)
- Ryo Hoshina
- grid.419056.f0000 0004 1793 2541Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga 526-0829 Japan
| | - Yuuji Tsukii
- grid.257114.40000 0004 1762 1436Laboratory of Biological Science, Hosei University, 2-17-1 Fujimi, Chiyoda-ku, Tokyo 102-8160 Japan
| | - Terue Harumoto
- grid.174568.90000 0001 0059 3836Research Group of Biological Sciences, Division of Natural Sciences, Nara Women’s University, Kitauoya-Nishimachi, Nara 630-8506 Japan
| | - Toshinobu Suzaki
- grid.31432.370000 0001 1092 3077Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501 Japan
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12
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Pediludiella daitoensis gen. et sp. nov. (Scenedesmaceae, Chlorophyceae), a large coccoid green alga isolated from a Loxodes ciliate. Sci Rep 2020; 10:628. [PMID: 31959793 PMCID: PMC6971069 DOI: 10.1038/s41598-020-57423-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/31/2019] [Indexed: 12/30/2022] Open
Abstract
Freshwater protists often harbor unicellular green algae within their cells. In ciliates, possibly because of large host cell sizes and the small size of algal coccoids, a single host cell typically contains more than a hundred algal cells. While surveying such algae-bearing protists on Minami Daito Jima Island in Japan, we found a green Loxodes ciliate (Loxodida, Karyorelictea) that contained one or two dozens of very large coccoid algae. We isolated one of these algae and analyzed its characteristics in detail. A small subunit (SSU) rDNA phylogeny indicated Pseudodidymocystis species (Scenedesmaceae, Chlorophyceae) to be the taxon closest to the alga, although it was clearly separated from this by 39 or more different sites (inclusive of gaps). SSU rRNA structure analyses indicated that these displacements included eight compensatory base changes (CBCs) and seven hemi-CBCs. We therefore concluded that this alga belongs to a separate genus, and described it as Pediludiella daitoensis gen. et sp. nov. The shape of the isolated and cultured P. daitoensis was nearly spherical and reached up to 30 µm in diameter. Chloroplasts were arranged peripherally and often split and elongated. Cells were often vacuolated and possessed a net-like cytoplasm that resembled a football (soccer ball) in appearance, which was reflected in the genus name.
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13
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Morard R, Füllberg A, Brummer GJA, Greco M, Jonkers L, Wizemann A, Weiner AKM, Darling K, Siccha M, Ledevin R, Kitazato H, de Garidel-Thoron T, de Vargas C, Kucera M. Genetic and morphological divergence in the warm-water planktonic foraminifera genus Globigerinoides. PLoS One 2019; 14:e0225246. [PMID: 31805130 PMCID: PMC6894840 DOI: 10.1371/journal.pone.0225246] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 10/31/2019] [Indexed: 11/19/2022] Open
Abstract
The planktonic foraminifera genus Globigerinoides provides a prime example of a species-rich genus in which genetic and morphological divergence are uncorrelated. To shed light on the evolutionary processes that lead to the present-day diversity of Globigerinoides, we investigated the genetic, ecological and morphological divergence of its constituent species. We assembled a global collection of single-cell barcode sequences and show that the genus consists of eight distinct genetic types organized in five extant morphospecies. Based on morphological evidence, we reassign the species Globoturborotalita tenella to Globigerinoides and amend Globigerinoides ruber by formally proposing two new subspecies, G. ruber albus n.subsp. and G. ruber ruber in order to express their subspecies level distinction and to replace the informal G. ruber "white" and G. ruber "pink", respectively. The genetic types within G. ruber and Globigerinoides elongatus show a combination of endemism and coexistence, with little evidence for ecological differentiation. CT-scanning and ontogeny analysis reveal that the diagnostic differences in adult morphologies could be explained by alterations of the ontogenetic trajectories towards final (reproductive) size. This indicates that heterochrony may have caused the observed decoupling between genetic and morphological diversification within the genus. We find little evidence for environmental forcing of either the genetic or the morphological diversification, which allude to biotic interactions such as symbiosis, as the driver of speciation in Globigerinoides.
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Affiliation(s)
- Raphaël Morard
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
- * E-mail:
| | - Angelina Füllberg
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
| | - Geert-Jan A. Brummer
- NIOZ Royal Netherlands Institute for Sea Research, Department of Ocean Systems, and Utrecht University, Den Burg, and Utrecht University, The Netherlands
- Vrije Universiteit Amsterdam, Department of Earth Sciences, Faculty of Science, Amsterdam, The Netherlands
| | - Mattia Greco
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
| | - Lukas Jonkers
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
| | - André Wizemann
- Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Agnes K. M. Weiner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Kate Darling
- School of GeoSciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- School of Geography and Sustainable Development, University of St Andrews, St Andrews, Scotland, United Kingdom
| | - Michael Siccha
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
| | - Ronan Ledevin
- UMR5199 PACEA, Université de Bordeaux, Allée Geoffroy Saint Hilaire, Pessac, France
| | - Hiroshi Kitazato
- Japan Agency for Marine Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | | | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, Roscoff, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Michal Kucera
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, Bremen, Germany
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14
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Qing X, Bik H, Yergaliyev TM, Gu J, Fonderie P, Brown-Miyara S, Szitenberg A, Bert W. Widespread prevalence but contrasting patterns of intragenomic rRNA polymorphisms in nematodes: Implications for phylogeny, species delimitation and life history inference. Mol Ecol Resour 2019; 20:318-332. [PMID: 31721426 DOI: 10.1111/1755-0998.13118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 10/26/2019] [Accepted: 11/07/2019] [Indexed: 01/15/2023]
Abstract
Ribosomal RNA genes have long been a favoured locus in phylogenetic and metabarcoding studies. Within a genome, rRNA loci are organized as tandem repeated arrays and the copies are homogenized through the process of concerted evolution. However, some level of rRNA variation (intragenomic polymorphism) is known to persist and be maintained in the genomes of many species. In nematode worms, the extent of rRNA polymorphism (RP) across species and the evolutionary and life history factors that contribute to the maintenance of intragenomic RP is largely unknown. Here, we present an extensive analysis across 30 terrestrial nematode species representing a range of free-living and parasitic taxa isolated worldwide. Our results indicate that RP is common and widespread, ribosome function appears to be maintained despite mutational changes, and intragenomic variants are stable in the genome and neutrally evolving. However, levels of variation were varied widely across rRNA locus and species, with some taxa observed to lack RP entirely. Higher levels of RP were significantly correlated with shorter generation time and high reproductive rates, and population-level factors may play a role in the geographic and phylogenetic structuring of rRNA variants observed in genera such as Rotylenchulus and Pratylenchus. Although RP did not dramatically impact the clustering and recovery of taxa in mock metabarcoding analyses, the present study has significant implications for global biodiversity estimates of nematode species derived from environmental rRNA amplicon studies, as well as our understanding of the evolutionary and ecological factors shaping genetic diversity across the nematode Tree of Life.
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Affiliation(s)
- Xue Qing
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium.,Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion, Israel
| | - Holly Bik
- Department of Nematology, University of California-Riverside, Riverside, CA, USA
| | - Timur M Yergaliyev
- Dead Sea and Arava Science Center, Dead Sea Branch, Masada National Park, Tamar Regional Council, Tel Aviv, Israel.,A. Baitursynov Kostanay State University, Kostanay, Kazakhstan
| | - Jianfeng Gu
- Technical Center of Ningbo Customs (Ningbo Inspection and Quarantine Science Technology Academy), Ningbo, China
| | - Pamela Fonderie
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sigal Brown-Miyara
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion, Israel
| | - Amir Szitenberg
- Dead Sea and Arava Science Center, Dead Sea Branch, Masada National Park, Tamar Regional Council, Tel Aviv, Israel
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium
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15
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Evidence of Intra-individual SSU Polymorphisms in Dark-spored Myxomycetes (Amoebozoa). Protist 2019; 170:125681. [PMID: 31586669 DOI: 10.1016/j.protis.2019.125681] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 11/24/2022]
Abstract
The nuclear small subunit rRNA gene (SSU or 18S) is a marker frequently used in phylogenetic and barcoding studies in Amoebozoa, including Myxomycetes. Despite its common usage and the confirmed existence of divergent copies of ribosomal genes in other protists, the potential presence of intra-individual SSU variability in Myxomycetes has never been studied before. Here we investigated the pattern of nucleotide polymorphism in the 5' end fragment of SSU by cloning and sequencing a total of 238 variants from eight specimens, each representing a species of the dark-spored orders Stemonitidales and Physarales. After excluding singletons, a relatively low SSU intra-individual variability was found but our data indicate that this might be a widely distributed phenomenon in Myxomycetes as all samples analyzed possessed various ribotypes. To determine if the occurrence of multiple SSU variants within a single specimen has a negative effect on the circumscription of species boundaries, we conducted phylogenetic analyses that revealed that clone variation may be detrimental for inferring phylogenetic relationships among some of the specimens analyzed. Despite that intra-individual variability should be assessed in additional taxa, our results indicate that special care should be taken for species identification when working with closely related species.
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16
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Morard R, Vollmar NM, Greco M, Kucera M. Unassigned diversity of planktonic foraminifera from environmental sequencing revealed as known but neglected species. PLoS One 2019; 14:e0213936. [PMID: 30897140 PMCID: PMC6428320 DOI: 10.1371/journal.pone.0213936] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/04/2019] [Indexed: 11/18/2022] Open
Abstract
Most research on extant planktonic foraminifera has been directed towards larger species (>0.150 mm) which can be easily manipulated, counted and yield enough calcite for geochemical analyses. This has drawn attention towards the macroperforate clade and created an impression of their numerical and ecological dominance. Drawing such conclusions from the study of such “giants” is a dangerous path. There were times in the evolutionary history of planktonic foraminifera when all species were smaller than 0.1 mm and indeed numerous small taxa, mainly from the microperforate clade, have been formally described from the modern plankton. The significance of these small, obscure and neglected species is poorly characterized and their relationship to the newly discovered hyperabundant but uncharacterized lineages of planktonic foraminifera in metabarcoding datasets is unknown. To determine, who is hiding in the metabarcoding datasets, we carried out an extensive sequencing of 18S rDNA targeted at small and obscure species. The sequences of the newly characterized small and obscure taxa match many of the previously uncharacterized lineages found in metabarcoding data. This indicates that most of the modern diversity in planktonic foraminifera has been taxonomically captured, but the role of the small and neglected taxa has been severely underestimated.
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Affiliation(s)
- Raphaël Morard
- MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- * E-mail:
| | - Nele M. Vollmar
- MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Mattia Greco
- MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Michal Kucera
- MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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17
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Filling gaps in the microsporidian tree: rDNA phylogeny of Chytridiopsis typographi (Microsporidia: Chytridiopsida). Parasitol Res 2018; 118:169-180. [DOI: 10.1007/s00436-018-6130-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/23/2018] [Indexed: 12/18/2022]
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18
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Hoef-Emden K. Revision of the Genus Chroomonas HANSGIRG: The Benefits of DNA-containing Specimens. Protist 2018; 169:662-681. [DOI: 10.1016/j.protis.2018.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 11/29/2022]
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19
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Molecular and Morphological Diversity of the Oxymonad Genera Monocercomonoides and Blattamonas gen. nov. Protist 2018; 169:744-783. [DOI: 10.1016/j.protis.2018.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 04/27/2018] [Accepted: 06/25/2018] [Indexed: 11/20/2022]
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20
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Eckert IM, Littlefair JE, Zhang GK, Chain FJ, Crease TJ, Cristescu ME. Bioinformatics for Biomonitoring: Species Detection and Diversity Estimates Across Next-Generation Sequencing Platforms. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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21
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Byrne SJ, Butler CA, Reynolds EC, Dashper SG. Taxonomy of Oral Bacteria. METHODS IN MICROBIOLOGY 2018. [DOI: 10.1016/bs.mim.2018.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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22
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Táborský P, Pánek T, Čepička I. Anaeramoebidae fam. nov., a Novel Lineage of Anaerobic Amoebae and Amoeboflagellates of Uncertain Phylogenetic Position. Protist 2017; 168:495-526. [DOI: 10.1016/j.protis.2017.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 07/17/2017] [Accepted: 07/27/2017] [Indexed: 12/18/2022]
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23
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A New Molecular Approach Based on the Secondary Structure of Ribosomal RNA for Phylogenetic Analysis of Mobilid Ciliates. Curr Microbiol 2017; 75:296-304. [DOI: 10.1007/s00284-017-1379-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
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24
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Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus. Eur J Protistol 2017; 61:92-106. [PMID: 28992523 DOI: 10.1016/j.ejop.2017.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 08/22/2017] [Accepted: 09/08/2017] [Indexed: 11/20/2022]
Abstract
Two new species, Ripella decalvata and R. tribonemae (Amoebozoa, Vannellida), are described and the diversity of known strains assigned to the genus analyzed. Ripella spp. are closely similar to each other in the light microscopic characters and sequences of small-subunit (SSU) ribosomal RNA gene, but differences in the cell coat structure and cytochrome oxidase (COI) gene sequences are more prominent. SSU rRNA in R. platypodia CCAP1589/2, R. decalvata and R. tribonemae demonstrates an unusual pattern of intragenomic variation. Sequencing of multiple molecular clones of this gene produced numerous sequence variants in a number of specific sites. These sites were usually terminal parts of several variable helices in all studied strains. Analysis of all known Ripella strains shows that SSU rRNA sites differing between strains of different origin are mainly restricted to these areas of the gene. There are only two sites, which differ between strains, but not within genomes. This intragenomic variability of the SSU rRNA gene, seemingly characteristic of all Ripella spp., was never reported to be so extensive in Amoebozoa. The data obtained show another example of complex organization of rRNA gene cluster in protists and emphasize caution needed when interpreting the metagenomic data based on this marker.
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25
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Qing X, Slos D, Claeys M, Bert W. Ultrastructural, phylogenetic and rRNA secondary structural analysis of a new nematode (Nematoda: Tylenchomorpha) from mushroom with recovery of intestinal crystals. ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2017.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Mikhailov KV, Simdyanov TG, Aleoshin VV. Genomic Survey of a Hyperparasitic Microsporidian Amphiamblys sp. (Metchnikovellidae). Genome Biol Evol 2017; 9:454-467. [PMID: 27694476 PMCID: PMC5381614 DOI: 10.1093/gbe/evw235] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2016] [Indexed: 12/18/2022] Open
Abstract
Metchnikovellidae are a group of unusual microsporidians that lack some of the defining ultrastructural features characteristic of derived Microsporidia and are thought to be one of their earliest-branching lineages. The basal position of metchnikovellids was never confirmed by molecular phylogeny in published research, and thus far no genomic data for this group were available. In this work, we obtain a partial genome of metchnikovellid Amphiamblys sp. using multiple displacement amplification, next-generation sequencing, and metagenomic binning approaches. The partial genome, which we estimate to be close to 90% complete, displays genome compaction on par with gene-dense microsporidian genomes, but contains an unusual repertoire of unique repeat elements. Phylogenetic analyses of multigene datasets place Amphiamblys sp. as the first branch of the microsporidian lineage following the divergence of a mitochondriate microsporidian Mitosporidium. We find evidence for a mitochondrial remnant presumably functionally equivalent to a mitosome in Amphiamblys sp. and the common enzymatic complement for microsporidian anaerobic metabolism. Comparative genomic analyses identify the conservation of components for clathrin vesicle formation as one of the key features distinguishing the metchnikovellid from its highly derived relatives. The presented data confirm the notion of Metchnikovellidae as a less derived microsporidian group, and provide an additional stepping stone for reconstruction of an evolutionary transition from the early diverging parasitic fungi to derived Microsporidia.
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Affiliation(s)
- Kirill V. Mikhailov
- A.N. Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Timur G. Simdyanov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Vladimir V. Aleoshin
- A.N. Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
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27
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Plotkin A, Voigt O, Willassen E, Rapp HT. Molecular phylogenies challenge the classification of Polymastiidae (Porifera, Demospongiae) based on morphology. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0301-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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Morard R, Escarguel G, Weiner AKM, André A, Douady CJ, Wade CM, Darling KF, Ujiié Y, Seears HA, Quillévéré F, de Garidel-Thoron T, de Vargas C, Kucera M. Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera. Syst Biol 2016; 65:925-40. [PMID: 27073250 DOI: 10.1093/sysbio/syw031] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/04/2016] [Indexed: 11/12/2022] Open
Abstract
Investigations of biodiversity, biogeography, and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many groups of organisms, morphologically defined species often disguise considerable genetic diversity, which may be indicative of the existence of cryptic species. The diversity hidden by morphological species can be disentangled through genetic surveys, which also provide access to data on the ecological distribution of genetically circumscribed units. These units can be identified by unique DNA sequence motifs and allow studies of evolutionary and ecological processes at different levels of divergence. However, the nomenclature of genetically circumscribed units within morphological species is not regulated and lacks stability. This represents a major obstacle to efforts to synthesize and communicate data on genetic diversity for multiple stakeholders. We have been confronted with such an obstacle in our work on planktonic foraminifera, where the stakeholder community is particularly diverse, involving geochemists, paleoceanographers, paleontologists, and biologists, and the lack of stable nomenclature beyond the level of formal morphospecies prevents effective transfer of knowledge. To circumvent this problem, we have designed a stable, reproducible, and flexible nomenclature system for genetically circumscribed units, analogous to the principles of a formal nomenclature system. Our system is based on the definition of unique DNA sequence motifs collocated within an individual, their typification (in analogy with holotypes), utilization of their hierarchical phylogenetic structure to define levels of divergence below that of the morphospecies, and a set of nomenclature rules assuring stability. The resulting molecular operational taxonomic units remain outside the domain of current nomenclature codes, but are linked to formal morphospecies as regulated by the codes. Subsequently, we show how this system can be applied to classify genetically defined units using the SSU rDNA marker in planktonic foraminifera and we highlight its potential use for other groups of organisms where similarly high levels of connectivity between molecular and formal taxonomies can be achieved.
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Affiliation(s)
- Raphaël Morard
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany,
| | - Gilles Escarguel
- Université de Lyon; UMR5023 Ecologie des Hydrosystémes Naturels et Anthropisés; Universiteì Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Agnes K M Weiner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany, Japan Agency for Marine Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Kanagawa, Japan
| | - Aurore André
- Université de Reims-Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, Batiment 18, 51100 REIMS, France
| | - Christophe J Douady
- Université de Lyon; UMR5023 Ecologie des Hydrosystémes Naturels et Anthropisés; Universiteì Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France, Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
| | - Christopher M Wade
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Kate F Darling
- School of GeoSciences, University of Edinburgh, Edinburgh EH9 3JW, UK, School of Geography and GeoSciences, University of St Andrews, Fife KY16 9AL, UK
| | - Yurika Ujiié
- Department of Biology, Shinshu University, Asahi3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Heidi A Seears
- Department of Biology, Gilmer Hall, University of Virginia, 485 McCormick Road, Charlottesville, VA 22904, USA
| | - Frédéric Quillévéré
- Univ Lyon, Université Lyon 1, ENS de Lyon, CNRS, UMR 5276 LGL-TPE, F-69622 Villeurbanne, France
| | - Thibault de Garidel-Thoron
- Centre Européen de Recherche et d'Enseignement de Géosciences de l'Environnement, Centre National de la Recherche Scientifique, et Aix-Marseille Université, Aix-en-Provence, France
| | - Colomban de Vargas
- Centre National de la Recherche Scientifique, UMR 7144, EPEP, Station Biologique de Roscoff, 29680 Roscoff, France, and Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Michal Kucera
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany
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Molecular identification of Entamoeba species in savanna woodland chimpanzees (Pan troglodytes schweinfurthii). Parasitology 2016; 143:741-8. [PMID: 26935395 DOI: 10.1017/s0031182016000263] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
To address the molecular diversity and occurrence of pathogenic species of the genus Entamoeba spp. in wild non-human primates (NHP) we conducted molecular-phylogenetic analyses on Entamoeba from wild chimpanzees living in the Issa Valley, Tanzania. We compared the sensitivity of molecular [using a genus-specific polymerase chain reaction (PCR)] and coproscopic detection (merthiolate-iodine-formaldehyde concentration) of Entamoeba spp. We identified Entamoeba spp. in 72 chimpanzee fecal samples (79%) subjected to species-specific PCRs for six Entamoeba species/groups (Entamoeba histolytica, Entamoeba nuttalli, Entamoeba dispar, Entamoeba moshkovskii, Entamoeba coli and Entamoeba polecki ST2). We recorded three Entamoeba species: E. coli (47%), E. dispar (16%), Entamoeba hartmanni (51%). Coproscopically, we could only distinguish the cysts of complex E. histolytica/dispar/moshkovskii/nuttalli and E. coli. Molecular prevalence of entamoebas was higher than the prevalence based on the coproscopic examination. Our molecular phylogenies showed that sequences of E. dispar and E. coli from Issa chimpanzees are closely related to sequences from humans and other NHP from GenBank. The results showed that wild chimpanzees harbour Entamoeba species similar to those occurring in humans; however, no pathogenic species were detected. Molecular-phylogenetic methods are critical to improve diagnostics of entamoebas in wild NHP and for determining an accurate prevalence of Entamoeba species.
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Pereira TJ, Baldwin JG. Contrasting evolutionary patterns of 28S and ITS rRNA genes reveal high intragenomic variation in Cephalenchus (Nematoda): Implications for species delimitation. Mol Phylogenet Evol 2016; 98:244-60. [PMID: 26926945 DOI: 10.1016/j.ympev.2016.02.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/20/2016] [Accepted: 02/20/2016] [Indexed: 01/05/2023]
Abstract
Concerted evolution is often assumed to be the evolutionary force driving multi-family genes, including those from ribosomal DNA (rDNA) repeat, to complete homogenization within a species, although cases of non-concerted evolution have been also documented. In this study, sequence variation of 28S and ITS ribosomal RNA (rRNA) genes in the genus Cephalenchus is assessed at three different levels, intragenomic, intraspecific, and interspecific. The findings suggest that not all Cephalenchus species undergo concerted evolution. High levels of intraspecific polymorphism, mostly due to intragenomic variation, are found in Cephalenchus sp1 (BRA-01). Secondary structure analyses of both rRNA genes and across different species show a similar substitution pattern, including mostly compensatory (CBC) and semi-compensatory (SBC) base changes, thus suggesting the functionality of these rRNA copies despite the variation found in some species. This view is also supported by low sequence variation in the 5.8S gene in relation to the flanking ITS-1 and ITS-2 as well as by the existence of conserved motifs in the former gene. It is suggested that potential cross-fertilization in some Cephalenchus species, based on inspection of female reproductive system, might contribute to both intragenomic and intraspecific polymorphism of their rRNA genes. These results reinforce the potential implications of intragenomic and intraspecific genetic diversity on species delimitation, especially in biodiversity studies based solely on metagenetic approaches. Knowledge of sequence variation will be crucial for accurate species diversity estimation using molecular methods.
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Affiliation(s)
- Tiago José Pereira
- Department of Nematology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA.
| | - James Gordon Baldwin
- Department of Nematology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA.
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31
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Caetano-Anollés G, Caetano-Anollés D. Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology. Comput Struct Biotechnol J 2015; 13:427-47. [PMID: 27096056 PMCID: PMC4823900 DOI: 10.1016/j.csbj.2015.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/16/2015] [Accepted: 07/19/2015] [Indexed: 12/11/2022] Open
Abstract
Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101W. Peabody Drive, Urbana, IL 61801, USA; C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Derek Caetano-Anollés
- C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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Zhang Y, Zhao YJ, Wang Q, Tang FH. New Comparative Analysis Based on the Secondary Structure of SSU-rRNA Gene Reveals the Evolutionary Trend and the Family-Genus Characters of Mobilida (Ciliophora, Peritrichia). Curr Microbiol 2015; 71:259-67. [DOI: 10.1007/s00284-015-0848-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 04/22/2015] [Indexed: 10/23/2022]
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Brown EA, Chain FJJ, Crease TJ, MacIsaac HJ, Cristescu ME. Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities? Ecol Evol 2015; 5:2234-51. [PMID: 26078859 PMCID: PMC4461424 DOI: 10.1002/ece3.1485] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 11/25/2022] Open
Abstract
DNA metabarcoding is a promising method for describing communities and estimating biodiversity. This approach uses high-throughput sequencing of targeted markers to identify species in a complex sample. By convention, sequences are clustered at a predefined sequence divergence threshold (often 3%) into operational taxonomic units (OTUs) that serve as a proxy for species. However, variable levels of interspecific marker variation across taxonomic groups make clustering sequences from a phylogenetically diverse dataset into OTUs at a uniform threshold problematic. In this study, we use mock zooplankton communities to evaluate the accuracy of species richness estimates when following conventional protocols to cluster hypervariable sequences of the V4 region of the small subunit ribosomal RNA gene (18S) into OTUs. By including individually tagged single specimens and "populations" of various species in our communities, we examine the impact of intra- and interspecific diversity on OTU clustering. Communities consisting of single individuals per species generated a correspondence of 59-84% between OTU number and species richness at a 3% divergence threshold. However, when multiple individuals per species were included, the correspondence between OTU number and species richness dropped to 31-63%. Our results suggest that intraspecific variation in this marker can often exceed 3%, such that a single species does not always correspond to one OTU. We advocate the need to apply group-specific divergence thresholds when analyzing complex and taxonomically diverse communities, but also encourage the development of additional filtering steps that allow identification of artifactual rRNA gene sequences or pseudogenes that may generate spurious OTUs.
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Affiliation(s)
- Emily A Brown
- Department of Biology, McGill University1205 Docteur Penfield, Montreal, Quebec, Canada, H3A 1B1
- Great Lakes Institute for Environmental Research, University of WindsorWindsor, Ontario, Canada, N9B 3P4
| | - Frédéric J J Chain
- Department of Biology, McGill University1205 Docteur Penfield, Montreal, Quebec, Canada, H3A 1B1
| | - Teresa J Crease
- Department of Integrative Biology, University of Guelph50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - Hugh J MacIsaac
- Great Lakes Institute for Environmental Research, University of WindsorWindsor, Ontario, Canada, N9B 3P4
| | - Melania E Cristescu
- Department of Biology, McGill University1205 Docteur Penfield, Montreal, Quebec, Canada, H3A 1B1
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Wang J, Wang F, Chu L, Wang H, Zhong Z, Liu Z, Gao J, Duan H. High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin. PLoS One 2014; 9:e112812. [PMID: 25401703 PMCID: PMC4234628 DOI: 10.1371/journal.pone.0112812] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 10/19/2014] [Indexed: 12/21/2022] Open
Abstract
Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs) in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution.
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Affiliation(s)
- Jiali Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- Institute of Shandong River Wetlands, Laiwu, China
| | - Fang Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- * E-mail:
| | - Limin Chu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- College of Hydrology and Water Resource, Hohai University, Nanjing, China
| | - Hao Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Zhiping Zhong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhipei Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Li M, Ponce-Gordo F, Grim JN, Wang C, Nilsen F. New insights into the molecular phylogeny of Balantidium (Ciliophora, Vetibuliferida) based on the analysis of new sequences of species from fish hosts. Parasitol Res 2014; 113:4327-33. [DOI: 10.1007/s00436-014-4195-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/23/2014] [Indexed: 11/30/2022]
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36
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Pánek T, Simpson AG, Hampl V, Čepička I. Creneis carolina gen. et sp. nov. (Heterolobosea), a Novel Marine Anaerobic Protist with Strikingly Derived Morphology and Life Cycle. Protist 2014; 165:542-67. [DOI: 10.1016/j.protis.2014.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/05/2014] [Accepted: 05/28/2014] [Indexed: 11/29/2022]
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37
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Caisová L, Melkonian M. Evolution of helix formation in the ribosomal Internal Transcribed Spacer 2 (ITS2) and its significance for RNA secondary structures. J Mol Evol 2014; 78:324-37. [PMID: 24908393 DOI: 10.1007/s00239-014-9625-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 05/19/2014] [Indexed: 01/25/2023]
Abstract
Helices are the most common elements of RNA secondary structure. Despite intensive investigations of various types of RNAs, the evolutionary history of the formation of new helices (novel helical structures) remains largely elusive. Here, by studying the nuclear ribosomal Internal Transcribed Spacer 2 (ITS2), a fast-evolving part of the eukaryotic nuclear ribosomal operon, we identify two possible types of helix formation: one type is "dichotomous helix formation"--transition from one large helix to two smaller helices by invagination of the apical part of a helix, which significantly changes the shape of the original secondary structure but does not increase its complexity (i.e., the total length of the RNA). An alternative type is "lateral helix formation"--origin of an extra helical region by the extension of a bulge loop or a spacer in a multi-helix loop of the original helix, which does not disrupt the pre-existing structure but increases RNA size. Moreover, we present examples from the RNA sequence literature indicating that both types of helix formation may have implications for RNA evolution beyond ITS2.
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Affiliation(s)
- Lenka Caisová
- Universität zu Köln, Biozentrum Köln, Botanisches Institut, Zülpicher Str. 47b, 50674, Köln, Germany,
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38
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Hadziavdic K, Lekang K, Lanzen A, Jonassen I, Thompson EM, Troedsson C. Characterization of the 18S rRNA gene for designing universal eukaryote specific primers. PLoS One 2014; 9:e87624. [PMID: 24516555 PMCID: PMC3917833 DOI: 10.1371/journal.pone.0087624] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 11/18/2013] [Indexed: 12/03/2022] Open
Abstract
High throughput sequencing technology has great promise for biodiversity studies. However, an underlying assumption is that the primers used in these studies are universal for the prokaryotic or eukaryotic groups of interest. Full primer universality is difficult or impossible to achieve and studies using different primer sets make biodiversity comparisons problematic. The aim of this study was to design and optimize universal eukaryotic primers that could be used as a standard in future biodiversity studies. Using the alignment of all eukaryotic sequences from the publicly available SILVA database, we generated a full characterization of variable versus conserved regions in the 18S rRNA gene. All variable regions within this gene were analyzed and our results suggested that the V2, V4 and V9 regions were best suited for biodiversity assessments. Previously published universal eukaryotic primers as well as a number of self-designed primers were mapped to the alignment. Primer selection will depend on sequencing technology used, and this study focused on the 454 pyrosequencing GS FLX Titanium platform. The results generated a primer pair yielding theoretical matches to 80% of the eukaryotic and 0% of the prokaryotic sequences in the SILVA database. An empirical test of marine sediments using the AmpliconNoise pipeline for analysis of the high throughput sequencing data yielded amplification of sequences for 71% of all eukaryotic phyla with no isolation of prokaryotic sequences. To our knowledge this is the first characterization of the complete 18S rRNA gene using all eukaryotes present in the SILVA database, providing a robust test for universal eukaryotic primers. Since both in silico and empirical tests using high throughput sequencing retained high inclusion of eukaryotic phyla and exclusion of prokaryotes, we conclude that these primers are well suited for assessing eukaryote diversity, and can be used as a standard in biodiversity studies.
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Affiliation(s)
| | - Katrine Lekang
- Department of Biology, University of Bergen, Bergen, Norway
| | - Anders Lanzen
- Department of Biology, University of Bergen, Bergen, Norway
- Uni Computing, Uni Research AS, Bergen, Norway
- Department of Ecology and Natural Resources, NEIKER-Tecnalia, Derio, Spain
| | - Inge Jonassen
- Uni Computing, Uni Research AS, Bergen, Norway
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Eric M. Thompson
- Department of Biology, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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Mallatt J, Chittenden KD. The GC content of LSU rRNA evolves across topological and functional regions of the ribosome in all three domains of life. Mol Phylogenet Evol 2014; 72:17-30. [PMID: 24394731 DOI: 10.1016/j.ympev.2013.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 11/28/2013] [Accepted: 12/24/2013] [Indexed: 12/21/2022]
Abstract
Large-subunit rRNA is the ribozyme that catalyzes protein synthesis by translation, and many of its features vary along a deep-to-superficial gradient. By measuring the G+C proportions in this rRNA in all three domains of life (60 bacteria, 379 eukaryote, and 23 archaean sequences), we tested whether the proportion of GC nucleotides varies along this in-out gradient. The rRNA regions used were several zones identified by Bokov and Steinberg (2009) as being arranged from deep to superficial within the LSU. To the Bokov-Steinberg zones, we added the most superficial zone of all, the divergent domains (expansion segments), which are greatly enlarged in eukaryotes. Regression lines constructed from the hundreds of species of organisms revealed the expected in-out gradient, showing that species with high %GC (or high %AT) in their rRNA distribute more of these abundant nucleotides into the peripheral zones. This could be explained by the evolutionary rates of replacement of all nucleotides (A, C, G, T), because these latter rates are fastest at the periphery and slowest near the conserved core. As an overall explanation, we propose that when extrinsic factors (whole-genome nucleotide composition, or environmental temperature) demand the percentage of GC in the rRNA of a species be high or low, then the deep-lying zones are buffered against GC variation because they are the slowest to evolve. The deep, conserved zones are also the most involved in translation, hinting that stabilizing selection there prevents a high GC variability that would diminish LSU rRNA's core functions. We found only a few domain-specific trends in rRNA-GC distribution, which relate to many Archaea living at high temperatures or to the highly complex genes and adaptations of Eukaryota. Use of rRNA sequences in molecular phylogenetic studies, for reconstructing the relationships of organisms across the tree of life, requires accurate models of how rRNA evolves. The demonstration that GC distributes in regular patterns across rRNA regions can improve these tree-reconstruction models in the future and should yield phylogenies of greater accuracy.
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Affiliation(s)
- Jon Mallatt
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States.
| | - Kevin D Chittenden
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States
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Oakeson KF, Gil R, Clayton AL, Dunn DM, von Niederhausern AC, Hamil C, Aoyagi A, Duval B, Baca A, Silva FJ, Vallier A, Jackson DG, Latorre A, Weiss RB, Heddi A, Moya A, Dale C. Genome degeneration and adaptation in a nascent stage of symbiosis. Genome Biol Evol 2014; 6:76-93. [PMID: 24407854 PMCID: PMC3914690 DOI: 10.1093/gbe/evt210] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Symbiotic associations between animals and microbes are ubiquitous in nature, with an estimated 15% of all insect species harboring intracellular bacterial symbionts. Most bacterial symbionts share many genomic features including small genomes, nucleotide composition bias, high coding density, and a paucity of mobile DNA, consistent with long-term host association. In this study, we focus on the early stages of genome degeneration in a recently derived insect-bacterial mutualistic intracellular association. We present the complete genome sequence and annotation of Sitophilus oryzae primary endosymbiont (SOPE). We also present the finished genome sequence and annotation of strain HS, a close free-living relative of SOPE and other insect symbionts of the Sodalis-allied clade, whose gene inventory is expected to closely resemble the putative ancestor of this group. Structural, functional, and evolutionary analyses indicate that SOPE has undergone extensive adaptation toward an insect-associated lifestyle in a very short time period. The genome of SOPE is large in size when compared with many ancient bacterial symbionts; however, almost half of the protein-coding genes in SOPE are pseudogenes. There is also evidence for relaxed selection on the remaining intact protein-coding genes. Comparative analyses of the whole-genome sequence of strain HS and SOPE highlight numerous genomic rearrangements, duplications, and deletions facilitated by a recent expansion of insertions sequence elements, some of which appear to have catalyzed adaptive changes. Functional metabolic predictions suggest that SOPE has lost the ability to synthesize several essential amino acids and vitamins. Analyses of the bacterial cell envelope and genes encoding secretion systems suggest that these structures and elements have become simplified in the transition to a mutualistic association.
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Affiliation(s)
- Kelly F. Oakeson
- Department of Biology, University of Utah
- *Corresponding author: E-mail:
| | - Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | | | | | | | - Cindy Hamil
- Department of Human Genetics, University of Utah
| | - Alex Aoyagi
- Department of Human Genetics, University of Utah
| | - Brett Duval
- Department of Human Genetics, University of Utah
| | | | - Francisco J. Silva
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | - Agnès Vallier
- INSA-Lyon, INRA, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, France
| | | | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana FISABIO – Salud Pública, Valencia, Spain
| | | | - Abdelaziz Heddi
- INSA-Lyon, INRA, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, France
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana FISABIO – Salud Pública, Valencia, Spain
| | - Colin Dale
- Department of Biology, University of Utah
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Smith WA, Oakeson KF, Johnson KP, Reed DL, Carter T, Smith KL, Koga R, Fukatsu T, Clayton DH, Dale C. Phylogenetic analysis of symbionts in feather-feeding lice of the genus Columbicola: evidence for repeated symbiont replacements. BMC Evol Biol 2013; 13:109. [PMID: 23725492 PMCID: PMC3724504 DOI: 10.1186/1471-2148-13-109] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 05/24/2013] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Many groups of insects have obligate bacterial symbionts that are vertically transmitted. Such associations are typically characterized by the presence of a monophyletic group of bacteria living in a well-defined host clade. In addition the phylogeny of the symbiotic bacteria is typically congruent with that of the host, signifying co-speciation. Here we show that bacteria living in a single genus of feather lice, Columbicola (Insecta: Phthiraptera), present an exception to this typical pattern. RESULTS The phylogeny of Columbicola spp. symbionts revealed the presence of three candidate clades, with the most species-rich clade having a comb-like topology with very short internodes and long terminal branches. Evolutionary simulations indicate that this topology is characteristic of a process of repeated symbiont replacement over a brief time period. The two remaining candidate clades in our study exhibit high levels of nucleotide substitution, suggesting accelerated molecular evolution due to relaxed purifying selection or smaller effective population size, which is typical of many vertically transmitted insect symbionts. Representatives of the fast-evolving and slow-evolving symbiont lineages exhibit the same localization, migration, and transmission patterns in their hosts, implying direct replacement. CONCLUSIONS Our findings suggest that repeated, independent symbiont replacements have taken place over the course of the relatively recent radiation of Columbicola spp. These results are compatible with the notion that lice and other insects have the capability to acquire novel symbionts through the domestication of progenitor strains residing in their local environment.
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Affiliation(s)
- Wendy A Smith
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Kelly F Oakeson
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, University of Illinois, 1816 S. Oak Street, Champaign, IL 61820, USA
| | - David L Reed
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Tamar Carter
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Kari L Smith
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Ryuichi Koga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
| | - Dale H Clayton
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Colin Dale
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
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42
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Kudryavtsev A, Pawlowski J. Squamamoeba japonica n. g. n. sp. (Amoebozoa): A Deep-sea Amoeba from the Sea of Japan with a Novel Cell Coat Structure. Protist 2013; 164:13-23. [DOI: 10.1016/j.protis.2012.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 03/27/2012] [Accepted: 07/19/2012] [Indexed: 11/28/2022]
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43
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The nuclear 18S ribosomal RNA gene as a source of phylogenetic information in the genus Taenia. Parasitol Res 2012. [DOI: 10.1007/s00436-012-3199-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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44
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Pánek T, Silberman JD, Yubuki N, Leander BS, Cepicka I. Diversity, Evolution and Molecular Systematics of the Psalteriomonadidae, the Main Lineage of Anaerobic/Microaerophilic Heteroloboseans (Excavata: Discoba). Protist 2012; 163:807-31. [DOI: 10.1016/j.protis.2011.11.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 10/19/2011] [Accepted: 11/01/2011] [Indexed: 12/01/2022]
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45
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Harding T, Brown MW, Plotnikov A, Selivanova E, Park JS, Gunderson JH, Baumgartner M, Silberman JD, Roger AJ, Simpson AGB. Amoeba stages in the deepest branching heteroloboseans, including Pharyngomonas: evolutionary and systematic implications. Protist 2012; 164:272-86. [PMID: 23021907 DOI: 10.1016/j.protis.2012.08.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 08/16/2012] [Accepted: 08/23/2012] [Indexed: 11/30/2022]
Abstract
The taxon Heterolobosea (Excavata) is a major group of protists well known for its diversity of life stages. Most are amoebae capable of transforming into flagellates (amoeboflagellates), while others are known solely as flagellates or solely as amoebae. The deepest-branching heterolobosean taxon confirmed previously, Pharyngomonas, was generally assumed to be a pure flagellate, suggesting that the amoeba form arose later in the evolution of Heterolobosea sensu lato. Here we report that multiple isolates of Pharyngomonas are actually amoeboflagellates that also have cyst stages, with only amoebae transforming into cysts. The amoeba form of Pharyngomonas showed heterolobosean characteristics (e. g. eruptive movement), but also possessed unusual morphological features like slow-flowing crenulated hyaline crescents with conical subpseudopodia, finger-like projections and branching posterior extensions. Furthermore, phylogenetic analyses of 18S ribosomal RNA gene sequences that included two undescribed species of amoebae showed that Pharyngomonas is not the only deep-branching heterolobosean to possess an amoeba stage. These results suggest that possession of an amoeba stage was ancestral for Heterolobosea, unifying this taxon as a group of species with amoeba stages in their lifecycle or derived from organisms with such stages.
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Affiliation(s)
- Tommy Harding
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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46
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Mallatt J, Craig CW, Yoder MJ. Nearly complete rRNA genes from 371 Animalia: Updated structure-based alignment and detailed phylogenetic analysis. Mol Phylogenet Evol 2012; 64:603-17. [DOI: 10.1016/j.ympev.2012.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 05/15/2012] [Accepted: 05/17/2012] [Indexed: 12/30/2022]
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47
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Ovchinnikov S, Masta SE. Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias. BMC Evol Biol 2012; 12:31. [PMID: 22409411 PMCID: PMC3325882 DOI: 10.1186/1471-2148-12-31] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 03/12/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes. RESULTS We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis.The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13 mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites. CONCLUSION The well-supported phylogenetic placement of pseudoscorpions as sister to Acariformes differs from some previous analyses based on morphology. However, these two lineages share multiple molecular evolutionary traits, including substantial mitochondrial genome rearrangements, extensive nucleotide substitution, and loss of helices in their inferred tRNA and rRNA structures.
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Affiliation(s)
- Sergey Ovchinnikov
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207, USA
| | - Susan E Masta
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207, USA
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Harish A, Caetano-Anollés G. Ribosomal history reveals origins of modern protein synthesis. PLoS One 2012; 7:e32776. [PMID: 22427882 PMCID: PMC3299690 DOI: 10.1371/journal.pone.0032776] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Accepted: 01/30/2012] [Indexed: 02/06/2023] Open
Abstract
The origin and evolution of the ribosome is central to our understanding of the cellular world. Most hypotheses posit that the ribosome originated in the peptidyl transferase center of the large ribosomal subunit. However, these proposals do not link protein synthesis to RNA recognition and do not use a phylogenetic comparative framework to study ribosomal evolution. Here we infer evolution of the structural components of the ribosome. Phylogenetic methods widely used in morphometrics are applied directly to RNA structures of thousands of molecules and to a census of protein structures in hundreds of genomes. We find that components of the small subunit involved in ribosomal processivity evolved earlier than the catalytic peptidyl transferase center responsible for protein synthesis. Remarkably, subunit RNA and proteins coevolved, starting with interactions between the oldest proteins (S12 and S17) and the oldest substructure (the ribosomal ratchet) in the small subunit and ending with the rise of a modern multi-subunit ribosome. Ancestral ribonucleoprotein components show similarities to in vitro evolved RNA replicase ribozymes and protein structures in extant replication machinery. Our study therefore provides important clues about the chicken-or-egg dilemma associated with the central dogma of molecular biology by showing that ribosomal history is driven by the gradual structural accretion of protein and RNA structures. Most importantly, results suggest that functionally important and conserved regions of the ribosome were recruited and could be relics of an ancient ribonucleoprotein world.
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Affiliation(s)
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana-Champaign, Illinois, United States of America
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Intra-genomic ribosomal RNA polymorphism and morphological variation in Elphidium macellum suggests inter-specific hybridization in foraminifera. PLoS One 2012; 7:e32373. [PMID: 22393402 PMCID: PMC3290570 DOI: 10.1371/journal.pone.0032373] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 01/28/2012] [Indexed: 11/19/2022] Open
Abstract
Elphidium macellum is a benthic foraminifer commonly found in the Patagonian fjords. To test whether its highly variable morphotypes are ecophenotypes or different genotypes, we analysed 70 sequences of the SSU rRNA gene from 25 specimens. Unexpectedly, we identified 11 distinct ribotypes, with up to 5 ribotypes co-occurring within the same specimen. The ribotypes differ by varying blocks of sequence located at the end of stem-loop motifs in the three expansion segments specific to foraminifera. These changes, distinct from typical SNPs and indels, directly affect the structure of the expansion segments. Their mosaic distribution suggests that ribotypes originated by recombination of two or more clusters of ribosomal genes. We propose that this expansion segment polymorphism (ESP) could originate from hybridization of morphologically different populations of Patagonian Elphidium. We speculate that the complex geological history of Patagonia enhanced divergence of coastal foraminiferal species and contributed to increasing genetic and morphological variation.
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50
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Marin B. Nested in the Chlorellales or independent class? Phylogeny and classification of the Pedinophyceae (Viridiplantae) revealed by molecular phylogenetic analyses of complete nuclear and plastid-encoded rRNA operons. Protist 2011; 163:778-805. [PMID: 22192529 DOI: 10.1016/j.protis.2011.11.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 11/02/2011] [Accepted: 11/05/2011] [Indexed: 01/30/2023]
Abstract
The class Pedinophyceae was established for asymmetric uniflagellate green algae, and was originally considered as an ancestral lineage of viridiplants. However, analyses of 71 concatenated plastid proteins [Turmel et al. (2009): Mol. Biol. Evol. 26: 2317-2331] recovered Pedinomonas within the Chlorellales (Trebouxiophyceae), thereby questioning the Pedinophyceae as an independent class. For the present study, complete nuclear and plastid-encoded rRNA operon sequences have been determined for 37 taxa of green algae including 6 members of the Pedinophyceae, providing 9272 aligned nucleotide positions. Phylogenies using both rRNA operons consistently rejected any relationship between Pedinophyceae and the Chlorellales. Instead, the Pedinophyceae were significantly resolved as sister of all phycoplast-containing 'core' chlorophytes, i.e. Chlorodendrophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Reinvestigation of plastid proteins discovered biased phylogenetic signal among protein partitions, indicating the published Pedinomonas + Chlorellales association as likely artificial. Marine pedinophytes (Resultomonas and Marsupiomonas; Marsupiomonadales ord. nov.), formed a sister clade to the order Pedinomonadales, occurring in freshwater and soil habitats. Synapomorphies in rRNA secondary structures were integrated in taxonomic diagnoses of the Pedinophyceae and were also used for BLAST searches targeting environmental sequence databases. The latter approach revealed conserved habitat preferences for the Marsupiomonadales and Pedinomonadales, and identified several novel pedinophyte lineages.
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Affiliation(s)
- Birger Marin
- Biozentrum Köln, Botanisches Institut, Universität zu Köln, Zülpicher Str. 47b, 50674 Köln, Germany.
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