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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: cellular, genomic and metabolic complexity. Biol Rev Camb Philos Soc 2020; 95:1198-1232. [PMID: 32301582 PMCID: PMC7539958 DOI: 10.1111/brv.12605] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022]
Abstract
The question of how phenotypic and genomic complexity are inter-related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental Sciences, Universitat Pompeu Fabra (UPF)Dr. Aiguader 88, 08003BarcelonaSpain
- ICREAPg. Lluís Companys 23, 08010BarcelonaSpain
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Marghalani AM, Althumali IM, Yousef LM, Alharthi MA, Alahmari ZS, Kabel AM. Coronavirus disease 2019 (COVID-19): Insights into the recent trends and the role of the primary care in diabetic patients. J Family Med Prim Care 2020; 9:3843-3847. [PMID: 33110777 PMCID: PMC7586637 DOI: 10.4103/jfmpc.jfmpc_683_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/10/2020] [Accepted: 07/01/2020] [Indexed: 01/04/2023] Open
Abstract
Diseases with viral etiology continue to emerge in the last years and may represent serious problems that affect various aspects of life. Coronaviruses are a large family of RNA viruses that cause illness affecting the respiratory tract ranging from common cold to severe respiratory distress syndrome. In the last weeks of 2019, enormous cases of unexplained pneumonia were reported in China. Few days later, a novel type of coronavirus was identified as the causative agent of these cases and the disease was named as coronavirus disease 2019 (COVID-19) by the World Health Organization. The disease was rapidly spreading in China and all over the world and now it is considered as pandemic catastrophe. It can be transmitted from animals to human and from human to human. Diabetes mellitus may represent a potential risk factor for the development of COVID-19, possibly due to the relative state of immunosuppression frequently encountered in diabetic patients. This review sheds light on COVID-19 based on the currently available data with reference to the role of the primary care in diabetic patients.
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Affiliation(s)
| | | | | | | | | | - Ahmed M Kabel
- Department of Clinical Pharmacy, College of Pharmacy, Taif University, Taif, KSA.,Department of Pharmacology, Faculty of Medicine, Tanta University, Tanta, Egypt
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Parmin NA, Hashim U, Hamidah A Halim N, Uda M, Afnan Uda M. Characterization of Genome Sequence 2019 Novel Coronavirus (2019-nCoV) by using BioinformaticTool. ACTA ACUST UNITED AC 2020. [DOI: 10.1088/1757-899x/864/1/012168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Near-Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Peru. Microbiol Resour Announc 2020; 9:9/19/e00303-20. [PMID: 32381617 PMCID: PMC7206495 DOI: 10.1128/mra.00303-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A near-complete genome sequence was obtained for a novel coronavirus (SARS-CoV-2) strain obtained from an oropharyngeal swab from a Peruvian patient with coronavirus syndrome (COVID-19) who had contact with an individual who had returned to Peru from travel to Italy.
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Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal. Microbiol Resour Announc 2020; 9:9/11/e00169-20. [PMID: 32165386 PMCID: PMC7067954 DOI: 10.1128/mra.00169-20] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A complete genome sequence was obtained for a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an oropharyngeal swab specimen of a Nepalese patient with coronavirus disease 2019 (COVID-19), who had returned to Nepal after traveling to Wuhan, China.
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DeBlasio DF, Wisecaver JH. SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees. PeerJ 2016; 4:e2359. [PMID: 27635331 PMCID: PMC5012314 DOI: 10.7717/peerj.2359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/23/2016] [Indexed: 11/25/2022] Open
Abstract
We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4,589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/.
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Affiliation(s)
- Dan F DeBlasio
- Department of Computer Science, University of Arizona , Tucson , AZ , United States
| | - Jennifer H Wisecaver
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
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Murray SA, Diwan R, Orr RJS, Kohli GS, John U. Gene duplication, loss and selection in the evolution of saxitoxin biosynthesis in alveolates. Mol Phylogenet Evol 2015; 92:165-80. [PMID: 26140862 DOI: 10.1016/j.ympev.2015.06.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/01/2015] [Accepted: 06/25/2015] [Indexed: 11/29/2022]
Abstract
A group of marine dinoflagellates (Alveolata, Eukaryota), consisting of ∼10 species of the genus Alexandrium, Gymnodinium catenatum and Pyrodinium bahamense, produce the toxin saxitoxin and its analogues (STX), which can accumulate in shellfish, leading to ecosystem and human health impacts. The genes, sxt, putatively involved in STX biosynthesis, have recently been identified, however, the evolution of these genes within dinoflagellates is not clear. There are two reasons for this: uncertainty over the phylogeny of dinoflagellates; and that the sxt genes of many species of Alexandrium and other dinoflagellate genera are not known. Here, we determined the phylogeny of STX-producing and other dinoflagellates based on a concatenated eight-gene alignment. We determined the presence, diversity and phylogeny of sxtA, domains A1 and A4 and sxtG in 52 strains of Alexandrium, and a further 43 species of dinoflagellates and thirteen other alveolates. We confirmed the presence and high sequence conservation of sxtA, domain A4, in 40 strains (35 Alexandrium, 1 Pyrodinium, 4 Gymnodinium) of 8 species of STX-producing dinoflagellates, and absence from non-producing species. We found three paralogs of sxtA, domain A1, and a widespread distribution of sxtA1 in non-STX producing dinoflagellates, indicating duplication events in the evolution of this gene. One paralog, clade 2, of sxtA1 may be particularly related to STX biosynthesis. Similarly, sxtG appears to be generally restricted to STX-producing species, while three amidinotransferase gene paralogs were found in dinoflagellates. We investigated the role of positive (diversifying) selection following duplication in sxtA1 and sxtG, and found negative selection in clades of sxtG and sxtA1, clade 2, suggesting they were functionally constrained. Significant episodic diversifying selection was found in some strains in clade 3 of sxtA1, a clade that may not be involved in STX biosynthesis, indicating pressure for diversification of function.
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Affiliation(s)
- Shauna A Murray
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia; Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW, Australia.
| | - Rutuja Diwan
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia; Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW, Australia
| | - Russell J S Orr
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Norway
| | - Gurjeet S Kohli
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia
| | - Uwe John
- Section Ecological Chemistry, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
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Caballero ZC, Costa-Martins AG, Ferreira RC, P Alves JM, Serrano MG, Camargo EP, Buck GA, Minoprio P, G Teixeira MM. Phylogenetic and syntenic data support a single horizontal transference to a Trypanosoma ancestor of a prokaryotic proline racemase implicated in parasite evasion from host defences. Parasit Vectors 2015; 8:222. [PMID: 25890302 PMCID: PMC4417235 DOI: 10.1186/s13071-015-0829-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 03/25/2015] [Indexed: 02/02/2023] Open
Abstract
Background Proline racemase (PRAC) enzymes of Trypanosoma cruzi (TcPRAC), the agent of Chagas disease, and Trypanosoma vivax (TvPRAC), the agent of livestock trypanosomosis, have been implicated in the B-cells polyclonal activation contributing to immunosuppression and the evasion of host defences. The similarity to prokaryotic PRAC and the absence in Trypanosoma brucei and Trypanosoma congolense have raised many questions about the origin, evolution, and functions of trypanosome PRAC (TryPRAC) enzymes. Findings We identified TryPRAC homologs as single copy genes per haploid genome in 12 of 15 Trypanosoma species, including T. cruzi and T. cruzi marinkellei, T. dionisii, T. erneyi, T. rangeli, T. conorhini and T. lewisi, all parasites of mammals. Polymorphisms in TcPRAC genes matched T. cruzi genotypes: TcI-TcIV and Tcbat have unique genes, while the hybrids TcV and TcVI contain TcPRACA and TcPRACB from parental TcII and TcIII, respectively. PRAC homologs were identified in trypanosomes from anurans, snakes, crocodiles, lizards, and birds. Most trypanosomes have intact PRAC genes. T. rangeli possesses only pseudogenes, maybe in the process of being lost. T. brucei, T. congolense and their allied species, except the more distantly related T. vivax, have completely lost PRAC genes. Conclusions The genealogy of TryPRAC homologs supports an evolutionary history congruent with the Trypanosoma phylogeny. This finding, together with the synteny of PRAC loci, the relationships with prokaryotic PRAC inferred by taxon-rich phylogenetic analysis, and the absence in trypanosomatids of any other genera or in bodonids or euglenids suggest that a common ancestor of Trypanosoma gained PRAC gene by a single and ancient horizontal gene transfer (HGT) from a Firmicutes bacterium more closely related to Gemella and other species of Bacilli than to Clostridium as previously suggested. Our broad phylogenetic study allowed investigation of TryPRAC evolution over long and short timescales. TryPRAC genes diverged to become species-specific and genotype-specific for T. cruzi and T. rangeli, with resulting genealogies congruent with those obtained using vertically inherited genes. The inventory of TryPRAC genes described here is the first step toward the understanding of the roles of PRAC enzymes in trypanosomes differing in life cycles, virulence, and infection and immune evasion strategies. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-0829-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zuleima C Caballero
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil. .,Instituto de Investigaciones Científicas y Servicios de Alta Tecnología-AIP (INDICASAT-AIP), Ciudad del Saber, Clayon, Panamá.
| | - Andre G Costa-Martins
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil.
| | - Robson C Ferreira
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil.
| | - João M P Alves
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil.
| | - Myrna G Serrano
- Department of Microbiology and Immunology, Virginia Commonwealth University, Virginia, USA.
| | - Erney P Camargo
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil.
| | - Gregory A Buck
- Department of Microbiology and Immunology, Virginia Commonwealth University, Virginia, USA.
| | - Paola Minoprio
- Département Infection et Epidemiologie, Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Paris, France.
| | - Marta M G Teixeira
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil.
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