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Hall AN, Morton E, Queitsch C. First discovered, long out of sight, finally visible: ribosomal DNA. Trends Genet 2022; 38:587-597. [PMID: 35272860 PMCID: PMC10132741 DOI: 10.1016/j.tig.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 10/18/2022]
Abstract
With the advent of long-read sequencing, previously unresolvable genomic elements are being revisited in an effort to generate fully complete reference genomes. One such element is ribosomal DNA (rDNA), the highly conserved genomic region that encodes rRNAs. Genomic structure and content of the rDNA are variable in both prokarya and eukarya, posing interesting questions about the biology of rDNA. Here, we consider the types of variation observed in rDNA - including locus structure and number, copy number, and sequence variation - and their known phenotypic consequences. With recent advances in long-read sequencing technology, incorporating the full rDNA sequence into reference genomes is within reach. This knowledge will have important implications for understanding rDNA biology within the context of cell physiology and whole-organism phenotypes.
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Lambert M, Benmoussa A, Diallo I, Ouellet-Boutin K, Dorval V, Majeau N, Joly-Beauparlant C, Droit A, Bergeron A, Têtu B, Fradet Y, Pouliot F, Provost P. Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA. Int J Mol Sci 2021; 22:9757. [PMID: 34575920 PMCID: PMC8467515 DOI: 10.3390/ijms22189757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/02/2021] [Accepted: 09/05/2021] [Indexed: 12/17/2022] Open
Abstract
Using a modified RNA-sequencing (RNA-seq) approach, we discovered a new family of unusually short RNAs mapping to ribosomal RNA 5.8S, which we named dodecaRNAs (doRNAs), according to the number of core nucleotides (12 nt) their members contain. Using a new quantitative detection method that we developed, we confirmed our RNA-seq data and determined that the minimal core doRNA sequence and its 13-nt variant C-doRNA (doRNA with a 5' Cytosine) are the two most abundant doRNAs, which, together, may outnumber microRNAs. The C-doRNA/doRNA ratio is stable within species but differed between species. doRNA and C-doRNA are mainly cytoplasmic and interact with heterogeneous nuclear ribonucleoproteins (hnRNP) A0, A1 and A2B1, but not Argonaute 2. Reporter gene activity assays suggest that C-doRNA may function as a regulator of Annexin II receptor (AXIIR) expression. doRNAs are differentially expressed in prostate cancer cells/tissues and may control cell migration. These findings suggest that unusually short RNAs may be more abundant and important than previously thought.
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Affiliation(s)
- Marine Lambert
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Abderrahim Benmoussa
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Idrissa Diallo
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Katheryn Ouellet-Boutin
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Véronique Dorval
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
| | - Nathalie Majeau
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
| | - Charles Joly-Beauparlant
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Molecular Medicine, Université Laval, Quebec City, QC G1V 4G2, Canada
| | - Arnaud Droit
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Molecular Medicine, Université Laval, Quebec City, QC G1V 4G2, Canada
| | - Alain Bergeron
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Surgery, Université Laval, Quebec City, QC G1R 2J6, Canada
| | - Bernard Têtu
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Yves Fradet
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Surgery, Université Laval, Quebec City, QC G1R 2J6, Canada
| | - Frédéric Pouliot
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Surgery, Université Laval, Quebec City, QC G1R 2J6, Canada
| | - Patrick Provost
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
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Pellegrino S, Terrosu S, Yusupova G, Yusupov M. Inhibition of the Eukaryotic 80S Ribosome as a Potential Anticancer Therapy: A Structural Perspective. Cancers (Basel) 2021; 13:cancers13174392. [PMID: 34503202 PMCID: PMC8430933 DOI: 10.3390/cancers13174392] [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: 08/10/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 01/16/2023] Open
Abstract
Simple Summary Unravelling the molecular basis of ribosomal inhibition by small molecules is crucial to characterise the function of potential anticancer drugs. After approval of the ribosome inhibitor homoharringtonine for treatment of CML, it became clear that acting on the rate of protein synthesis can be a valuable way to prevent indefinite growth of cancers. The present review discusses the state-of-the-art structural knowledge of the binding modes of inhibitors targeting the cytosolic ribosome, with the ambition of providing not only an overview of what has been achieved so far, but to stimulate further investigations to yield more potent and specific anticancer drugs. Abstract Protein biosynthesis is a vital process for all kingdoms of life. The ribosome is the massive ribonucleoprotein machinery that reads the genetic code, in the form of messenger RNA (mRNA), to produce proteins. The mechanism of translation is tightly regulated to ensure that cell growth is well sustained. Because of the central role fulfilled by the ribosome, it is not surprising that halting its function can be detrimental and incompatible with life. In bacteria, the ribosome is a major target of inhibitors, as demonstrated by the high number of small molecules identified to bind to it. In eukaryotes, the design of ribosome inhibitors may be used as a therapy to treat cancer cells, which exhibit higher proliferation rates compared to healthy ones. Exciting experimental achievements gathered during the last few years confirmed that the ribosome indeed represents a relevant platform for the development of anticancer drugs. We provide herein an overview of the latest structural data that helped to unveil the molecular bases of inhibition of the eukaryotic ribosome triggered by small molecules.
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Affiliation(s)
- Simone Pellegrino
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
- Correspondence: (S.P.); (M.Y.)
| | - Salvatore Terrosu
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France; (S.T.); (G.Y.)
| | - Gulnara Yusupova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France; (S.T.); (G.Y.)
| | - Marat Yusupov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France; (S.T.); (G.Y.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia
- Correspondence: (S.P.); (M.Y.)
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Analysis of Acanthamoeba genotypes from public freshwater sources in Thailand reveals a new genotype, T23 Acanthamoeba bangkokensis sp. nov. Sci Rep 2021; 11:17290. [PMID: 34453084 PMCID: PMC8397737 DOI: 10.1038/s41598-021-96690-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023] Open
Abstract
A survey of Acanthamoeba in 100 public freshwater sources in 28 provinces across Thailand has identified 9 genotypes comprising T2/6, T3-T5, T9, T11, T12, T18 and a novel ‘T23’ among 131 isolates. Sequencing of the near complete 18S rRNA gene of Acanthamoeba of all isolates has shown that the most predominant genotype T4 found in 87 isolates (66.4%) contained 4 subtypes, i.e. T4A, T4B, T4C and T4F, while all isolates assigned to genotype T2/6 belonged to subtype B. Among intron-bearing genotypes, most isolates harbouring genotype T3 contained S516 introns, characterised by 3 distinct variants whilst all genotypes T4A and T5 were intronless. Identical 18S rRNA sequences of Acanthamoeba were identified across regions of the country and four isolates in this study shared the same sequences with those from remote nations, suggesting that some strains have reproductive success in diverse ecological niche. Nucleotide diversity of genotypes T2/6B, T3, T4, T9 and T11 in this study was significantly less than that among global isolates outside Thailand, implying that limited sequence diversity occurred within local populations. A remarkably higher level of nucleotide diversity in genotype T11 than those of other genotypes (0.041 vs. 0.012–0.024) could be due to cryptic subtypes. Recombination breakpoints have been detected within genotypes and subtypes as well as within isolates despite no evidence for sexual and parasexual cycles in the genus Acanthamoeba. Tajima’s D, Fu & Li’s D* and F* statistics revealed significantly negative deviation from neutrality across genotypes and subtypes, implying purifying selection in this locus. The 18S rRNA gene of the novel genotype ‘T23’ displayed 7.82% to 28.44% sequence differences in comparison with all known genotypes. Both Bayesian and maximum likelihood phylogenetic trees have placed genotype T23 as sister to the clade comprising genotypes T10, T12 and T14, all of these possess cyst structure belonging to morphological group III. Hence, Acanthamoeba bangkokensis sp. nov. is proposed for this novel genotype. It is likely that more genotypes of Acanthamoeba remain to be discovered while the evolution of the 18S rRNA gene of this pathogenic-free living amoeba seems to be ongoing.
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Lammel DR, Nüsslein K, Cerri CEP, Veresoglou SD, Rillig MC. Soil biota shift with land use change from pristine rainforest and Savannah (Cerrado) to agriculture in southern Amazonia. Mol Ecol 2021; 30:4899-4912. [PMID: 34297871 DOI: 10.1111/mec.16090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022]
Abstract
Southern Amazonia is currently experiencing extensive land use change from forests to agriculture caused by increased local and global demand for agricultural products. However, little is known about the impacts of deforestation and land use change on soil biota. We investigated two regions in southern Amazonia (rainforest and Savannah/Cerrado biomes), analysing soil biota community turnover based on 16S (Archaea and Bacteria) and 18S rRNA genes (Eukaryotes, including Fungi, Protists and Animalia) and correlating them with soil chemistry and land use intensity. We found that soil biota community structure is driven by land use change in both Cerrado and rainforest. Crop fields approximatively doubled the richness of soil Archaea, Bacteria and Protists. We propose that crop systems not only increase soil pH and fertility, but also create continued disturbance (crop seasons) that stimulates soil diversity, as predicted by the dynamic equilibrium model (DEM) and the intermediate disturbance hypothesis (IDH). Even though agricultural fields had higher soil biota richness, some taxa were suppressed by agriculture (6/31 operational taxonomic units of Archaea, 245/1790 of Bacteria, 12/74 of Animalia, 20/144 of Fungi and 25/310 of Protists). Consequently, land use change in this region should proceed with caution. In the southern Amazonia region of Brazil, current laws require farmers to keep 20%-80% pristine vegetation areas on their property. Our data support the relevance of this law: since there are unique soil taxa under native vegetation, keeping these pristine areas adjacent to the agricultural fields should maximize soil biodiversity protection in these regions.
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Affiliation(s)
- Daniel R Lammel
- Freie Universität Berlin, Institut für Biologie, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Department of Microbiology, University of Massachusetts, Amherst, MA, USA.,ESALQ&CENA, University of São Paulo, Piracicaba, Brazil
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | | | - Stavros D Veresoglou
- Freie Universität Berlin, Institut für Biologie, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Matthias C Rillig
- Freie Universität Berlin, Institut für Biologie, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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Prahl RE, Khan S, Deo RC. The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces. PLoS One 2021; 16:e0253772. [PMID: 34191835 PMCID: PMC8244850 DOI: 10.1371/journal.pone.0253772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/13/2021] [Indexed: 11/19/2022] Open
Abstract
Many fungi require specific growth conditions before they can be identified. Direct environmental DNA sequencing is advantageous, although for some taxa, specific primers need to be used for successful amplification of molecular markers. The internal transcribed spacer region is the preferred DNA barcode for fungi. However, inter- and intra-specific distances in ITS sequences highly vary among some fungal groups; consequently, it is not a solely reliable tool for species delineation. Ampelomyces, mycoparasites of the fungal phytopathogen order Erysiphales, can have ITS genetic differences up to 15%; this may lead to misidentification with other closely related unknown fungi. Indeed, Ampelomyces were initially misidentified as other pycnidial mycoparasites, but subsequent research showed that they differ in pycnidia morphology and culture characteristics. We investigated whether the ITS2 nucleotide content and secondary structure was different between Ampelomyces ITS2 sequences and those unrelated to this genus. To this end, we retrieved all ITS sequences referred to as Ampelomyces from the GenBank database. This analysis revealed that fungal ITS environmental DNA sequences are still being deposited in the database under the name Ampelomyces, but they do not belong to this genus. We also detected variations in the conserved hybridization model of the ITS2 proximal 5.8S and 28S stem from two Ampelomyces strains. Moreover, we suggested for the first time that pseudogenes form in the ITS region of this mycoparasite. A phylogenetic analysis based on ITS2 sequences-structures grouped the environmental sequences of putative Ampelomyces into a different clade from the Ampelomyces-containing clades. Indeed, when conducting ITS2 analysis, resolution of genetic distances between Ampelomyces and those putative Ampelomyces improved. Each clade represented a distinct consensus ITS2 S2, which suggested that different pre-ribosomal RNA (pre-rRNA) processes occur across different lineages. This study recommends the use of ITS2 S2s as an important tool to analyse environmental sequencing and unveiling the underlying evolutionary processes.
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Affiliation(s)
- Rosa E. Prahl
- School of Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia
- * E-mail:
| | - Shahjahan Khan
- School of Sciences, Centre for Health Research, Centre for Applied Climate Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Ravinesh C. Deo
- School of Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia
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Chelomina GN, Rozhkovan KV, Burundukova OL, Gorpenchenko TY, Khrolenko YA, Zhuravlev YN. Age-Dependent and Tissue-Specific Alterations in the rDNA Clusters of the Panax ginseng C. A. Meyer Cultivated Cell Lines. Biomolecules 2020; 10:biom10101410. [PMID: 33036123 PMCID: PMC7599642 DOI: 10.3390/biom10101410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 01/25/2023] Open
Abstract
Long-term cultivation of Panax ginseng cell lines leads to a decreasing synthesis of the biologically active substances used in traditional medicine. To gain insight into the cellular mechanisms which may influence this process, we analyzed variations within the rDNA cluster of the Oriental ginseng cell lines. The cell lines were cultivated for 6 and 24 years; the number of nucleoli and chromosomes was analyzed. The complete 18S rDNA sequences were cloned and sequenced. The nucleotide polymorphism and phylogenetic relations of the sequences were analyzed, and the secondary structures for separate 18S rRNA regions were modeled. The 18S rDNA accumulated mutations during cell cultivation that correlate well with an increase in the number of chromosomes and nucleoli. The patterns of nucleotide diversity are culture-specific and the increasing polymorphism associates with cytosine methylation sites. The secondary structures of some 18S rRNA regions and their interaction can alter during cultivation. The phylogenetic tree topologies are particular for each cell line.The observed alterations in rDNA clusters are associated with a somaclonal variation, leading to changes in the pattern of intracellular synthesis during cell cultivation. The identified divergent rRNAs could provide additional gene expression regulation in P. ginseng cells by forming heterogeneous ribosomes.
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Affiliation(s)
- Galina N. Chelomina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
- Correspondence: ; Tel.: +7-(423)-231-0410
| | - Konstantin V. Rozhkovan
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
- Saint-Petersburg State University Clinic, St. Petersburg 190103, Russia
| | - Olga L. Burundukova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
| | - Tatiana Y. Gorpenchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
| | - Yulia A. Khrolenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
| | - Yuri N. Zhuravlev
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far-Eastern Branch of Russian Academy of Science, Vladivostok 690022, Russia; (K.V.R.); (O.L.B.); (T.Y.G.); (Y.A.K.); (Y.N.Z.)
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Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 2020; 11:14. [PMID: 32714773 PMCID: PMC7353689 DOI: 10.1186/s43008-020-00033-z] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
| | - M. Catherine Aime
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| | - Andrew N. Miller
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970 USA
| | - Hiran A. Ariyawansa
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipe City, Taiwan
| | - Takayuki Aoki
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Agriculture and Food Research Organization, Genetic Resources Center, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Gianluigi Cardinali
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
| | - Pedro W. Crous
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Irina S. Druzhinina
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - David M. Geiser
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802 USA
| | - David L. Hawksworth
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ UK
- Jilin Agricultural University, Changchun, 130118 Jilin Province China
| | - Kevin D. Hyde
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- World Agroforestry Centre, East and Central Asia, Kunming, 650201 Yunnan China
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Rai, 50150 Thailand
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - Peter R. Johnston
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Manaaki Whenua – Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | | | - Elaine Malosso
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Avenida da Engenharia, s/n Cidade Universitária, Recife, PE 50.740-600 Brazil
| | - Tom W. May
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Maarja Öpik
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- University of Tartu, 40 Lai Street, 51 005 Tartu, Estonia
| | - Vincent Robert
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marc Stadler
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marco Thines
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60439 Frankfurt (Main); Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Andrey M. Yurkov
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
| | - Conrad L. Schoch
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
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9
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Garcia S, Wendel JF, Borowska-Zuchowska N, Aïnouche M, Kuderova A, Kovarik A. The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants. FRONTIERS IN PLANT SCIENCE 2020; 11:41. [PMID: 32117380 PMCID: PMC7025596 DOI: 10.3389/fpls.2020.00041] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/13/2020] [Indexed: 05/18/2023]
Abstract
INTRODUCTION Ribosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE) pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for hybridogenic origin of species. Data were obtained from more than 80 plant species, including several well-defined allopolyploids and homoploid hybrids of different evolutionary ages and from widely dispersed taxonomic groups. RESULTS (i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs composed of two or more interconnected loops representing intergenic spacers (IGS). (ii) There was a relationship between graph complexity and locus numbers. (iii) The sequences and lengths of the 5S rDNA units reconstituted in silico from k-mers were congruent with those experimentally determined. (iv) Three-genomic comparative cluster analysis of reads from allopolyploids and progenitor diploids allowed identification of homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) Gossypium and Brachypodium allopolyploids which already exhibit uniparental partial loss of rDNA repeats. (v) Finally, species harboring introgressed genomes exhibit exceptionally complex graph structures. CONCLUSION We found that the cluster graph shapes and graph parameters (k-mer coverage scores and connected component index) well-reflect the organization and intragenomic homogeneity of 5S rDNA repeats. We propose that the analysis of 5S rDNA cluster graphs computed by the RE pipeline together with the cytogenetic analysis might be a reliable approach for the determination of the hybrid or allopolyploid plant species parentage and may also be useful for detecting historical introgression events.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC - Ajuntament de Barcelona), Barcelona, Spain
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Jonathan F. Wendel
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, United States
| | - Natalia Borowska-Zuchowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Malika Aïnouche
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, Rennes, France
| | - Alena Kuderova
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Ales Kovarik
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
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10
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Sulima SO, Dinman JD. The Expanding Riboverse. Cells 2019; 8:cells8101205. [PMID: 31590378 PMCID: PMC6829380 DOI: 10.3390/cells8101205] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/25/2019] [Accepted: 10/03/2019] [Indexed: 12/13/2022] Open
Abstract
Subverting the conventional concept of “the” ribosome, a wealth of information gleaned from recent studies is revealing a much more diverse and dynamic ribosomal reality than has traditionally been thought possible. A diverse array of researchers is collectively illuminating a universe of heterogeneous and adaptable ribosomes harboring differences in composition and regulatory capacity: These differences enable specialization. The expanding universe of ribosomes not only comprises an incredible richness in ribosomal specialization between species, but also within the same tissues and even cells. In this review, we discuss ribosomal heterogeneity and speculate how the emerging understanding of the ribosomal repertoire is impacting the biological sciences today. Targeting pathogen-specific and pathological “diseased” ribosomes promises to provide new treatment options for patients, and potential applications for “designer ribosomes” are within reach. Our deepening understanding of and ability to manipulate the ribosome are establishing both the technological and theoretical foundations for major advances for the 21st century and beyond.
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Affiliation(s)
- Sergey O Sulima
- Biopharmaceutical New Technologies (BioNTech) Corporation, 55131 Mainz, Germany.
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA .
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