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Van Horn KS, Zhao Y, Parvatkar PT, Maier J, Mutka T, Lacrue A, Brockmeier F, Ebert D, Wu W, Casandra DR, Namelikonda N, Yacoub J, Sigal M, Knapp S, Floyd D, Waterson D, Burrows JN, Duffy J, DeRisi JL, Kyle DE, Guy RK, Manetsch R. Optimization of diastereomeric dihydropyridines as antimalarials. Eur J Med Chem 2024; 275:116599. [PMID: 38909569 DOI: 10.1016/j.ejmech.2024.116599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/04/2024] [Accepted: 06/12/2024] [Indexed: 06/25/2024]
Abstract
The increase in research funding for the development of antimalarials since 2000 has led to a surge of new chemotypes with potent antimalarial activity. High-throughput screens have delivered several thousand new active compounds in several hundred series, including the 4,7-diphenyl-1,4,5,6,7,8-hexahydroquinolines, hereafter termed dihydropyridines (DHPs). We optimized the DHPs for antimalarial activity. Structure-activity relationship studies focusing on the 2-, 3-, 4-, 6-, and 7-positions of the DHP core led to the identification of compounds potent (EC50 < 10 nM) against all strains of P. falciparum tested, including the drug-resistant parasite strains K1, W2, and TM90-C2B. Evaluation of efficacy of several compounds in vivo identified two compounds that reduced parasitemia by >75 % in mice 6 days post-exposure following a single 50 mg/kg oral dose. Resistance acquisition experiments with a selected dihydropyridine led to the identification of a single mutation conveying resistance in the gene encoding for Plasmodium falciparum multi-drug resistance protein 1 (PfMDR1). The same dihydropyridine possessed transmission blocking activity. The DHPs have the potential for the development of novel antimalarial drug candidates.
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Affiliation(s)
- Kurt S Van Horn
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL, 33620, United States; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States.
| | - Yingzhao Zhao
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States
| | - Prakash T Parvatkar
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States
| | - Julie Maier
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, United States
| | - Tina Mutka
- Department of Global Health, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, United States
| | - Alexis Lacrue
- Department of Global Health, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, United States
| | - Fabian Brockmeier
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States
| | - Daniel Ebert
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94158, United States
| | - Wesley Wu
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94158, United States
| | - Debora R Casandra
- Department of Global Health, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, United States
| | - Niranjan Namelikonda
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL, 33620, United States
| | - Jeanine Yacoub
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL, 33620, United States
| | - Martina Sigal
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, United States
| | - Spencer Knapp
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, 610 Taylor Road, Piscataway, NJ, 08854, United States
| | - David Floyd
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, 610 Taylor Road, Piscataway, NJ, 08854, United States
| | - David Waterson
- Medicines for Malaria Venture, 20, Route de Pré-Bois, P.O. Box 1826, 1215, Geneva, 15, Switzerland
| | - Jeremy N Burrows
- Medicines for Malaria Venture, 20, Route de Pré-Bois, P.O. Box 1826, 1215, Geneva, 15, Switzerland
| | - James Duffy
- Medicines for Malaria Venture, 20, Route de Pré-Bois, P.O. Box 1826, 1215, Geneva, 15, Switzerland
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94158, United States; Howard Hughes Medical Institute, Chevy Chase, MD, 20815, United States
| | - Dennis E Kyle
- Department of Global Health, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, United States; Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA, 30602, United States
| | - R Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, United States; Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40506, United States
| | - Roman Manetsch
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL, 33620, United States; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States; Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, United States.
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Mejías-Molina C, Estarlich-Landajo I, Martínez-Puchol S, Bofill-Mas S, Rusiñol M. Exploring waterborne viruses in groundwater: Quantification and Virome characterization via passive sampling and targeted enrichment sequencing. WATER RESEARCH 2024; 266:122305. [PMID: 39216128 DOI: 10.1016/j.watres.2024.122305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/07/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Aquifers, which provide drinking water for nearly half the world's population, face significant challenges from microbial contamination, particularly from waterborne viruses such as human adenovirus (HAdV), norovirus (NoV) and enterovirus (EV). This study, conducted as part of the UPWATER project, investigates the sources of urban groundwater contamination using viral passive sampling (VPS) and target enrichment sequencing (TES). We assessed the abundance of eight viral pathogens (HAdV, EV, NoV genogroup I and II, rotavirus, influenza A virus, hepatitis E virus and SARS-CoV-2) and investigated the virome diversity of groundwater in the aquifer of the Besòs River Delta in Catalonia. Over a period of 7 months, we collected 114 samples from the aquifer using nylon and nitrocellulose membranes to adsorb viruses over a 10-day period. Human faecal contamination was detected in nearly 50 % of the groundwater samples, with mean HAdV total counts ranging from 1.23E+02 to 3.66E+03 GC, and occasional detections of EV and NoV GI and GII. In addition, deep sequencing revealed a diverse virome in the aquifer, with detection of human pathogens, including adenovirus, astrovirus, calicivirus, enterovirus, herpesvirus, papillomavirus and rotavirus. Time-integrated sampling using VPS increases the likelihood of virus detection and, when combined with TES, can provide a deeper understanding of virus prevalence in this important water compartment. This approach is expected to streamline long-term monitoring efforts and enable small communities or water managers with limited resources to effectively manage their groundwater reservoirs.
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Affiliation(s)
- Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), 08001 Barcelona, Spain
| | - Ignasi Estarlich-Landajo
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Vicerectorat de Recerca, Universitat de Barcelona (UB), 08007 Barcelona, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), 08001 Barcelona, Spain
| | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), 08001 Barcelona, Spain.
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3
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Sadurski J, Polak-Berecka M, Staniszewski A, Waśko A. Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review. Foods 2024; 13:2216. [PMID: 39063300 PMCID: PMC11276190 DOI: 10.3390/foods13142216] [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: 06/11/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
This review article offers a comprehensive overview of the current understanding of using metagenomic tools in food microbiome research. It covers the scientific foundation and practical application of genetic analysis techniques for microbial material from food, including bioinformatic analysis and data interpretation. The method discussed in the article for analyzing microorganisms in food without traditional culture methods is known as food metagenomics. This approach, along with other omics technologies such as nutrigenomics, proteomics, metabolomics, and transcriptomics, collectively forms the field of foodomics. Food metagenomics allows swift and thorough examination of bacteria and potential metabolic pathways by utilizing foodomic databases. Despite its established scientific basis and available bioinformatics resources, the research approach of food metagenomics outlined in the article is not yet widely implemented in industry. The authors believe that the integration of next-generation sequencing (NGS) with rapidly advancing digital technologies such as artificial intelligence (AI), the Internet of Things (IoT), and big data will facilitate the widespread adoption of this research strategy in microbial analysis for the food industry. This adoption is expected to enhance food safety and product quality in the near future.
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Affiliation(s)
- Jan Sadurski
- Department of Biotechnology, Microbiology and Human Nutrition, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, 20-704 Lublin, Poland; (M.P.-B.); (A.S.); (A.W.)
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Peng C, Fan S. The complete mitochondrial genome of bamboo shrimp Atyopsis moluccensis (Atyidae, Decapoda). Mitochondrial DNA B Resour 2024; 9:808-811. [PMID: 38903542 PMCID: PMC11188945 DOI: 10.1080/23802359.2024.2368206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/10/2024] [Indexed: 06/22/2024] Open
Abstract
Atyopsis moluccensis, belonging to the family Atyidae, is one of the popular species in aquarium industry. Here, we sequenced the mitochondrial genome of A. moluccensis. The mitogenome of A. moluccensis is 15,933 bp in length, consisting 22 transfer RNAs, 13 protein-coding genes (PCGs), and two ribosomal RNAs. The composition of A. moluccensis mitogenome is 33.77% for A, 13.81% for G, 28.74% for T, and 23.68% for C. The A + T content of the heavy-strand was 62.51%. Except ND5, most of the PCGs had ATN as the start codon. Only COX2 and ND4 were stopped by incomplete stop codon. The phylogenetic relationship was reconstructed with 16 shrimp from six genera of family Atyidae, which revealed that A. moluccensis and A. gabonensis clustered together and species of the same genus were grouped together in a clade. The data are beneficial in understanding the evolution and phylogenetic relationships of Atyidae shrimp.
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Affiliation(s)
- Chao Peng
- Hunan Provincial Collaborative Innovation Center for Efficient and Health Production of Fisheries, Hunan University of Arts and Science, Changde, China
| | - Sigang Fan
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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5
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Mwakibete L, Greening SS, Kalantar K, Ahyong V, Anis E, Miller EA, Needle DB, Oglesbee M, Thomas WK, Sevigny JL, Gordon LM, Nemeth NM, Ogbunugafor CB, Ayala AJ, Faith SA, Neff N, Detweiler AM, Baillargeon T, Tanguay S, Simpson SD, Murphy LA, Ellis JC, Tato CM, Gagne RB. Metagenomics for Pathogen Detection During a Mass Mortality Event in Songbirds. J Wildl Dis 2024; 60:362-374. [PMID: 38345467 DOI: 10.7589/jwd-d-23-00109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/02/2024] [Indexed: 04/06/2024]
Abstract
Mass mortality events in wildlife can be indications of an emerging infectious disease. During the spring and summer of 2021, hundreds of dead passerines were reported across the eastern US. Birds exhibited a range of clinical signs including swollen conjunctiva, ocular discharge, ataxia, and nystagmus. As part of the diagnostic investigation, high-throughput metagenomic next-generation sequencing was performed across three molecular laboratories on samples from affected birds. Many potentially pathogenic microbes were detected, with bacteria forming the largest proportion; however, no singular agent was consistently identified, with many of the detected microbes also found in unaffected (control) birds and thus considered to be subclinical infections. Congruent results across laboratories have helped drive further investigation into alternative causes, including environmental contaminants and nutritional deficiencies. This work highlights the utility of metagenomic approaches in investigations of emerging diseases and provides a framework for future wildlife mortality events.
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Affiliation(s)
| | - Sabrina S Greening
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Eman Anis
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
- Department of Pathobiology, PADLS New Bolton Center, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Erica A Miller
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - David B Needle
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Michael Oglesbee
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - W Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Joseph L Sevigny
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Lawrence M Gordon
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Nicole M Nemeth
- Southeastern Cooperative Wildlife Disease Study and Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, USA
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Georgia 30602, USA
| | - C Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Andrea J Ayala
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Seth A Faith
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | | | - Tessa Baillargeon
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Stacy Tanguay
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Stephen D Simpson
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Lisa A Murphy
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
- Department of Pathobiology, PADLS New Bolton Center, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Julie C Ellis
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Cristina M Tato
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Roderick B Gagne
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
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Hirayama H, Takaki Y, Abe M, Miyazaki M, Uematsu K, Matsui Y, Takai K. Methylomarinovum tepidoasis sp. nov., a moderately thermophilic methanotroph of the family Methylothermaceae isolated from a deep-sea hydrothermal field. Int J Syst Evol Microbiol 2024; 74:006288. [PMID: 38478579 PMCID: PMC10950024 DOI: 10.1099/ijsem.0.006288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/24/2024] [Indexed: 03/21/2024] Open
Abstract
A novel aerobic methanotrophic bacterium, designated as strain IN45T, was isolated from in situ colonisation systems deployed at the Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough. IN45T was a moderately thermophilic obligate methanotroph that grew only on methane or methanol at temperatures between 25 and 56 °C (optimum 45-50 °C). It was an oval-shaped, Gram-reaction-negative, motile bacterium with a single polar flagellum and an intracytoplasmic membrane system. It required 1.5-4.0 % (w/v) NaCl (optimum 2-3 %) for growth. The major phospholipid fatty acids were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8. The 16S rRNA gene sequence comparison revealed 99.1 % sequence identity with Methylomarinovum caldicuralii IT-9T, the only species of the genus Methylomarinovum with a validly published name within the family Methylothermaceae. The complete genome sequence of IN45T consisted of a 2.42-Mbp chromosome (DNA G+C content, 64.1 mol%) and a 20.5-kbp plasmid. The genome encodes genes for particulate methane monooxygenase and two types of methanol dehydrogenase (mxaFI and xoxF). Genes involved in the ribulose monophosphate pathway for carbon assimilation are encoded, but the transaldolase gene was not found. The genome indicated that IN45T performs partial denitrification of nitrate to N2O, and its occurrence was indirectly confirmed by N2O production in cultures grown with nitrate. Genomic relatedness indices between the complete genome sequences of IN45T and M. caldicuralii IT-9T, such as digital DNA-DNA hybridisation (51.2 %), average nucleotide identity (92.94 %) and average amino acid identity (93.21 %), indicated that these two methanotrophs should be separated at the species level. On the basis of these results, strain IN45T represents a novel species, for which we propose the name Methylomarinovum tepidoasis sp. nov. with IN45T (=JCM 35101T =DSM 113422T) as the type strain.
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Affiliation(s)
- Hisako Hirayama
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Mariko Abe
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Masayuki Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | | | - Yohei Matsui
- Research Institute for Global Change (RIGC), JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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7
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Kallifidas D, Dhakal D, Chen M, Chen QY, Kokkaliari S, Colon Rosa NA, Ratnayake R, Bruner SD, Paul VJ, Ding Y, Luesch H. Biosynthesis of Dolastatin 10 in Marine Cyanobacteria, a Prototype for Multiple Approved Cancer Drugs. Org Lett 2024; 26:1321-1325. [PMID: 38330916 PMCID: PMC10915760 DOI: 10.1021/acs.orglett.3c04083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Dolastatin 10, a potent tubulin-targeting marine anticancer natural product, provided the basis for the development of six FDA-approved antibody-drug conjugates. Through the screening of cyanobacterial Caldora penicillata environmental DNA libraries and metagenome sequencing, we identified its biosynthetic gene cluster. Functional prediction of 10 enzymes encoded in the 39 kb cluster supports the dolastatin 10 biosynthesis. The nonheme diiron monooxygenase DolJ was biochemically characterized to mediate the terminal thiazole formation in dolastatin 10.
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Affiliation(s)
- Dimitris Kallifidas
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, United States
| | - Dipesh Dhakal
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, United States
| | - Manyun Chen
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, United States
| | - Qi-Yin Chen
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, United States
| | - Sofia Kokkaliari
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, United States
| | - Nicole A. Colon Rosa
- Department of Chemistry, University of Florida, Gainesville, FL 32611, United States
| | - Ranjala Ratnayake
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, United States
| | - Steven D. Bruner
- Department of Chemistry, University of Florida, Gainesville, FL 32611, United States
| | - Valerie J. Paul
- Smithsonian Marine Station, Fort Pierce, FL 34949, United States
| | - Yousong Ding
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, United States
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8
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Mejías-Molina C, Pico-Tomàs A, Martínez-Puchol S, Itarte M, Torrell H, Canela N, Borrego CM, Corominas L, Rusiñol M, Bofill-Mas S. Wastewater-based epidemiology applied at the building-level reveals distinct virome profiles based on the age of the contributing individuals. Hum Genomics 2024; 18:10. [PMID: 38303015 PMCID: PMC10832175 DOI: 10.1186/s40246-024-00580-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/24/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Human viruses released into the environment can be detected and characterized in wastewater. The study of wastewater virome offers a consolidated perspective on the circulation of viruses within a population. Because the occurrence and severity of viral infections can vary across a person's lifetime, studying the virome in wastewater samples contributed by various demographic segments can provide valuable insights into the prevalence of viral infections within these segments. In our study, targeted enrichment sequencing was employed to characterize the human virome in wastewater at a building-level scale. This was accomplished through passive sampling of wastewater in schools, university settings, and nursing homes in two cities in Catalonia. Additionally, sewage from a large urban wastewater treatment plant was analysed to serve as a reference for examining the collective excreted human virome. RESULTS The virome obtained from influent wastewater treatment plant samples showcased the combined viral presence from individuals of varying ages, with astroviruses and human bocaviruses being the most prevalent, followed by human adenoviruses, polyomaviruses, and papillomaviruses. Significant variations in the viral profiles were observed among the different types of buildings studied. Mamastrovirus 1 was predominant in school samples, salivirus and human polyomaviruses JC and BK in the university settings while nursing homes showed a more balanced distribution of viral families presenting papillomavirus and picornaviruses and, interestingly, some viruses linked to immunosuppression. CONCLUSIONS This study shows the utility of building-level wastewater-based epidemiology as an effective tool for monitoring the presence of viruses circulating within specific age groups. It provides valuable insights for public health monitoring and epidemiological studies.
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Affiliation(s)
- Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain.
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | | | - Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Helena Torrell
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira I Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Reus, Catalonia, Spain
| | - Núria Canela
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira I Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Reus, Catalonia, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Catalonia, Spain
| | | | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
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9
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Hopfe C, Ospina-Jara B, Schulze T, Tischer M, Morales D, Reinhartz V, Esfahani RE, Valderrama C, Pérez-Rigueiro J, Bleidorn C, Feldhaar H, Cabra-García J, Scheibel T. Impact of environmental factors on spider silk properties. Curr Biol 2024; 34:56-67.e5. [PMID: 38118450 DOI: 10.1016/j.cub.2023.11.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/11/2023] [Accepted: 11/20/2023] [Indexed: 12/22/2023]
Abstract
Spider orb webs have evolved to stop flying prey, fast and slow alike. One of the main web elements dissipating impact energy is the radial fibers, or major ampullate silks, which possess a toughness surpassing most man-made materials. Orb webs are extended phenotypes, and as such their architectural elements, including major ampullate silks, have been selected to optimize prey capture under the respective environmental conditions. In this study, we investigated the correlation of three landscape scales and three microhabitat characteristics with intrinsic silk properties (elastic modulus, yield stress, tensile strength, extensibility, and toughness) to understand underlying ecological patterns. For this purpose, we collected and mechanically tested major ampullate silks from 50 spider species inhabiting large altitudinal and climatic gradients in Colombia. Using regression analysis and model selection, we investigated the environmental drivers of inter- and intra-specific patterns of major ampullate silk properties, taking into account phylogenetic relatedness based on newly sequenced mitochondrial genomes. We found that the total amount of energy absorbed, i.e., toughness and tensile strength, is higher for fibers from species inhabiting regions where heavy rainfall is common. Interestingly, we observe the same general trend between individuals of the same species, stressing the importance of this environmental driver. We also observe a phylogenetic conservation in the relation of environmental variables with silk tensile strength and yield stress. In conclusion, the increase in major ampullate silk tensile strength and toughness may reflect an adaptation to prevent frequent rain damage to orb webs and the associated energetic loss.
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Affiliation(s)
- Charlotte Hopfe
- Department of Biomaterials, Universität Bayreuth, Prof.-Rüdiger-Bormann-Str. 1, Bayreuth 95447, Germany.
| | - Bryan Ospina-Jara
- Department of Biology, Universidad del Valle, Cl. 13 #100-00, Cali 760042, Colombia
| | - Thilo Schulze
- Department of Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Untere Karspüle 2, Göttingen 37073, Germany
| | - Marta Tischer
- Department of Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Untere Karspüle 2, Göttingen 37073, Germany
| | - Diego Morales
- Department of Biology, Universidad del Valle, Cl. 13 #100-00, Cali 760042, Colombia
| | - Vivien Reinhartz
- Department of Biomaterials, Universität Bayreuth, Prof.-Rüdiger-Bormann-Str. 1, Bayreuth 95447, Germany
| | - Rashin Eshghi Esfahani
- Department of Biomaterials, Universität Bayreuth, Prof.-Rüdiger-Bormann-Str. 1, Bayreuth 95447, Germany
| | - Carlos Valderrama
- Facultad de Ciencias, Universidad del Rosario, Cl. 12c #6-25, Bogotá 111711, Colombia
| | - José Pérez-Rigueiro
- Center for Biomedical Technology, Universidad Politécnica de Madrid, Crta. M40, Madrid 28223, Spain; Departamento de Ciencia de Materiales, ETSI Caminos, Canales y Puertos, Universidad Politécnica de Madrid, C/Prof. Aranguren 3, Madrid 28040, Spain; Biomedical Research Networking Center in Bioengineering Biomaterials and Nanomedicine (CIBER-BBN), Madrid 28029, Spain; Biomaterials and Regenerative Medicine Group, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), C/ Prof. Martín Lagos s/n, Madrid 28040, Spain
| | - Christoph Bleidorn
- Department of Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Untere Karspüle 2, Göttingen 37073, Germany
| | - Heike Feldhaar
- Department of Animal Ecology I, Bayreuth Center of Ecology and Environmental Research (BayCEER), Universität Bayreuth, Universitätsstraße 30, Bayreuth 95440, Germany
| | - Jimmy Cabra-García
- Department of Biology, Universidad del Valle, Cl. 13 #100-00, Cali 760042, Colombia
| | - Thomas Scheibel
- Department of Biomaterials, Universität Bayreuth, Prof.-Rüdiger-Bormann-Str. 1, Bayreuth 95447, Germany; Bayreuther Zentrum für Kolloide und Grenzflächen, Universität Bayreuth, Universitätsstraße 30, Bayreuth 95440, Germany; Bayreuther Materialzentrum, Universität Bayreuth, Universitätsstraße 30, Bayreuth 95440, Germany; Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, Universitätsstraße 30, Bayreuth 95440, Germany; Bayrisches Polymerinstitut, Universität Bayreuth, Universitätsstraße 30, Bayreuth 95440, Germany.
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10
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Rozo-Lopez P, Brewer W, Käfer S, Martin MM, Parker BJ. Untangling an insect's virome from its endogenous viral elements. BMC Genomics 2023; 24:636. [PMID: 37875824 PMCID: PMC10594914 DOI: 10.1186/s12864-023-09737-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Insects are an important reservoir of viral biodiversity, but the vast majority of viruses associated with insects have not been discovered. Recent studies have employed high-throughput RNA sequencing, which has led to rapid advances in our understanding of insect viral diversity. However, insect genomes frequently contain transcribed endogenous viral elements (EVEs) with significant homology to exogenous viruses, complicating the use of RNAseq for viral discovery. METHODS In this study, we used a multi-pronged sequencing approach to study the virome of an important agricultural pest and prolific vector of plant pathogens, the potato aphid Macrosiphum euphorbiae. We first used rRNA-depleted RNAseq to characterize the microbes found in individual insects. We then used PCR screening to measure the frequency of two heritable viruses in a local aphid population. Lastly, we generated a quality draft genome assembly for M. euphorbiae using Illumina-corrected Nanopore sequencing to identify transcriptionally active EVEs in the host genome. RESULTS We found reads from two insect-specific viruses (a Flavivirus and an Ambidensovirus) in our RNAseq data, as well as a parasitoid virus (Bracovirus), a plant pathogenic virus (Tombusvirus), and two phages (Acinetobacter and APSE). However, our genome assembly showed that part of the 'virome' of this insect can be attributed to EVEs in the host genome. CONCLUSION Our work shows that EVEs have led to the misidentification of aphid viruses from RNAseq data, and we argue that this is a widespread challenge for the study of viral diversity in insects.
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Affiliation(s)
- Paula Rozo-Lopez
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA.
| | - William Brewer
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA
| | - Simon Käfer
- Institut Für Biologie Und Umweltwissenschaften, Carl Von Ossietzky Universität Oldenburg, 26129, Oldenburg, Germany
| | - McKayla M Martin
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA
| | - Benjamin J Parker
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA.
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11
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Mwakibete L, Takahashi S, Ahyong V, Black A, Rek J, Ssewanyana I, Kamya M, Dorsey G, Jagannathan P, Rodríguez-Barraquer I, Tato CM, Greenhouse B. Metagenomic next-generation sequencing to characterize potential etiologies of non-malarial fever in a cohort living in a high malaria burden area of Uganda. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001675. [PMID: 37134083 PMCID: PMC10156012 DOI: 10.1371/journal.pgph.0001675] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/12/2023] [Indexed: 05/04/2023]
Abstract
Causes of non-malarial fevers in sub-Saharan Africa remain understudied. We hypothesized that metagenomic next-generation sequencing (mNGS), which allows for broad genomic-level detection of infectious agents in a biological sample, can systematically identify potential causes of non-malarial fevers. The 212 participants in this study were of all ages and were enrolled in a longitudinal malaria cohort in eastern Uganda. Between December 2020 and August 2021, respiratory swabs and plasma samples were collected at 313 study visits where participants presented with fever and were negative for malaria by microscopy. Samples were analyzed using CZ ID, a web-based platform for microbial detection in mNGS data. Overall, viral pathogens were detected at 123 of 313 visits (39%). SARS-CoV-2 was detected at 11 visits, from which full viral genomes were recovered from nine. Other prevalent viruses included Influenza A (14 visits), RSV (12 visits), and three of the four strains of seasonal coronaviruses (6 visits). Notably, 11 influenza cases occurred between May and July 2021, coinciding with when the Delta variant of SARS-CoV-2 was circulating in this population. The primary limitation of this study is that we were unable to estimate the contribution of bacterial microbes to non-malarial fevers, due to the difficulty of distinguishing bacterial microbes that were pathogenic from those that were commensal or contaminants. These results revealed the co-circulation of multiple viral pathogens likely associated with fever in the cohort during this time period. This study illustrates the utility of mNGS in elucidating the multiple potential causes of non-malarial febrile illness. A better understanding of the pathogen landscape in different settings and age groups could aid in informing diagnostics, case management, and public health surveillance systems.
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Affiliation(s)
- Lusajo Mwakibete
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Saki Takahashi
- Department of Medicine, Division of HIV, ID, and Global Medicine, EPPIcenter Research Program, University of California San Francisco, San Francisco, CA, United States of America
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Allison Black
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - John Rek
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Moses Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Medicine, Makerere University, Kampala, Uganda
| | - Grant Dorsey
- Department of Medicine, Division of HIV, ID, and Global Medicine, University of California San Francisco, San Francisco, CA, United States of America
| | - Prasanna Jagannathan
- Department of Medicine, Stanford University, Palo Alto, CA, United States of America
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA, United States of America
| | - Isabel Rodríguez-Barraquer
- Department of Medicine, Division of HIV, ID, and Global Medicine, EPPIcenter Research Program, University of California San Francisco, San Francisco, CA, United States of America
| | - Cristina M. Tato
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Bryan Greenhouse
- Department of Medicine, Division of HIV, ID, and Global Medicine, EPPIcenter Research Program, University of California San Francisco, San Francisco, CA, United States of America
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12
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Guo W, Comai L, Henry IM. Chromoanagenesis in the asy1 meiotic mutant of Arabidopsis. G3 (BETHESDA, MD.) 2023; 13:jkac185. [PMID: 35920777 PMCID: PMC9911071 DOI: 10.1093/g3journal/jkac185] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023]
Abstract
Chromoanagenesis is a catastrophic event that involves localized chromosomal shattering and reorganization. In this study, we report a case of chromoanagenesis resulting from defective meiosis in the MEIOTIC ASYNAPTIC MUTANT 1 (asy1) background in Arabidopsis thaliana. We provide a detailed characterization of the genomic structure of this individual with a severely shattered segment of chromosome 1. We identified 260 novel DNA junctions in the affected region, most of which affect gene sequence on 1 or both sides of the junction. Our results confirm that asy1-related defective meiosis is a potential trigger for chromoanagenesis. This is the first example of chromoanagenesis associated with female meiosis and indicates the potential for genome evolution during oogenesis. PLAIN LANGUAGE SUMMARY Chromoanagenesis is a complex and catastrophic event that results in severely restructured chromosomes. It has been identified in cancer cells and in some plant samples, after specific triggering events. Here, we identified this kind of genome restructuring in a mutant that exhibits defective meiosis in the model plant system Arabidopsis thaliana.
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Affiliation(s)
- Weier Guo
- Genome Center and Dept. Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Luca Comai
- Genome Center and Dept. Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Isabelle M Henry
- Genome Center and Dept. Plant Biology, University of California, Davis, Davis, CA 95616, USA
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13
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Zuckerman NS, Shulman LM. Next-Generation Sequencing in the Study of Infectious Diseases. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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14
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Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
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15
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Zhang N, Li Y, Halanych KM, Kong L, Li Q. A comparative analysis of mitochondrial ORFs provides new insights on expansion of mitochondrial genome size in Arcidae. BMC Genomics 2022; 23:809. [PMID: 36474182 PMCID: PMC9727918 DOI: 10.1186/s12864-022-09040-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Arcidae, comprising about 260 species of ark shells, is an ecologically and economically important lineage of bivalve mollusks. Interestingly, mitochondrial genomes of several Arcidae species are 2-3 times larger than those of most bilaterians, and are among the largest bilaterian mitochondrial genomes reported to date. The large mitochondrial genome size is mainly due to expansion of unassigned regions (regions that are functionally unassigned). Previous work on unassigned regions of Arcidae mtDNA genomes has focused on nucleotide-level analyses to observe sequence characteristics, however the origin of expansion remains unclear. RESULTS We assembled six new mitogenomes and sequenced six transcriptomes of Scapharca broughtonii to identify conserved functional ORFs that are transcribed in unassigned regions. Sixteen lineage-specific ORFs with different copy numbers were identified from seven Arcidae species, and 11 of 16 ORFs were expressed and likely biologically active. Unassigned regions of 32 Arcidae mitogenomes were compared to verify the presence of these novel mitochondrial ORFs and their distribution. Strikingly, multiple structural analyses and functional prediction suggested that these additional mtDNA-encoded proteins have potential functional significance. In addition, our results also revealed that the ORFs have a strong connection to the expansion of Arcidae mitochondrial genomes and their large-scale duplication play an important role in multiple expansion events. We discussed the possible origin of ORFs and hypothesized that these ORFs may originate from duplication of mitochondrial genes. CONCLUSIONS The presence of lineage-specific mitochondrial ORFs with transcriptional activity and potential functional significance supports novel features for Arcidae mitochondrial genomes. Given our observation and analyses, these ORFs may be products of mitochondrial gene duplication. These findings shed light on the origin and function of novel mitochondrial genes in bivalves and provide new insights into evolution of mitochondrial genome size in metazoans.
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Affiliation(s)
- Ning Zhang
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yuanning Li
- grid.27255.370000 0004 1761 1174Shandong University, Qingdao, China
| | - Kenneth M. Halanych
- grid.217197.b0000 0000 9813 0452Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC 28409 USA
| | - Lingfeng Kong
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qi Li
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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16
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Wei L, Liu TJ, Hao G, Ge XJ, Yan HF. Comparative analyses of three complete Primula mitogenomes with insights into mitogenome size variation in Ericales. BMC Genomics 2022; 23:770. [PMID: 36424546 PMCID: PMC9686101 DOI: 10.1186/s12864-022-08983-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/01/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Although knowledge of the sizes, contents, and forms of plant mitochondrial genomes (mitogenomes) is increasing, little is known about the mechanisms underlying their structural diversity. Evolutionary information on the mitogenomes of Primula, an important ornamental taxon, is more limited than the information on their nuclear and plastid counterparts, which has hindered the comprehensive understanding of Primula mitogenomic diversity and evolution. The present study reported and compared three Primula mitogenomes and discussed the size expansion of mitogenomes in Ericales. RESULTS Mitogenome master circles were sequenced and successfully assembled for three Primula taxa and were compared with publicly available Ericales mitogenomes. The three mitogenomes contained similar gene contents and varied primarily in their structures. The Primula mitogenomes possessed relatively high nucleotide diversity among all examined plant lineages. In addition, high nucleotide diversity was found among Primula species between the Mediterranean and Himalaya-Hengduan Mountains. Most predicted RNA editing sites appeared in the second amino acid codon, increasing the hydrophobic character of the protein. An early stop in atp6 caused by RNA editing was conserved across all examined Ericales species. The interfamilial relationships within Ericales and interspecific relationships within Primula could be well resolved based on mitochondrial data. Transfer of the two longest mitochondrial plastid sequences (MTPTs) occurred before the divergence of Primula and its close relatives, and multiple independent transfers could also occur in a single MTPT sequence. Foreign sequence [MTPTs and mitochondrial nuclear DNA sequences (NUMTs)] uptake and repeats were to some extent associated with changes in Ericales mitogenome size, although none of these relationships were significant overall. CONCLUSIONS The present study revealed relatively conserved gene contents, gene clusters, RNA editing, and MTPTs but considerable structural variation in Primula mitogenomes. Relatively high nucleotide diversity was found in the Primula mitogenomes. In addition, mitogenomic genes, collinear gene clusters, and locally collinear blocks (LCBs) all showed phylogenetic signals. The evolutionary history of MTPTs in Primula was complicated, even in a single MTPT sequence. Various reasons for the size variation observed in Ericales mitogenomes were found.
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Affiliation(s)
- Lei Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tong-Jian Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
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17
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The Genome of the Mitochondrion-Related Organelle in Cepedea longa, a Large Endosymbiotic Opalinid Inhabiting the Recta of Frogs. Int J Mol Sci 2022; 23:ijms232113472. [DOI: 10.3390/ijms232113472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/13/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Mitochondrion-related organelles (MROs) are loosely defined as degenerated mitochondria in anaerobic and microaerophilic lineages. Opalinids are commonly regarded as commensals in the guts of cold-blooded amphibians. It may represent an intermediate adaptation stage between the conventional aerobic mitochondria and derived anaerobic MROs. In the present study, we sequenced and analyzed the MRO genome of Cepedea longa. It has a linear MRO genome with large inverted repeat gene regions at both ends. Compared to Blastocystis and Proteromonas lacertae, the MRO genome of C. longa has a higher G + C content and repeat sequences near the central region. Although three Opalinata species have different morphological characteristics, phylogenetic analyses based on eight concatenated nad genes indicate that they are close relatives. The phylogenetic analysis showed that C. longa clustered with P. lacertae with strong support. The 18S rRNA gene-based phylogeny resolved the Opalinea clade as a sister clade to Karotomorpha, which then further grouped with Proteromonas. The paraphyly of Proteromonadea needs to be verified due to the lack of MRO genomes for key species, such as Karotomorpha, Opalina and Protoopalina. Besides, our dataset and analyses offered slight support for the paraphyly of Bigyra.
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18
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Garand M, Huang SSY, Goessling LS, Santillan DA, Santillan MK, Brar A, Wylie TN, Wylie KM, Eghtesady P. A Case of Persistent Human Pegivirus Infection in Two Separate Pregnancies of a Woman. Microorganisms 2022; 10:1925. [PMID: 36296201 PMCID: PMC9610878 DOI: 10.3390/microorganisms10101925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 05/26/2024] Open
Abstract
Human pegivirus (HPgV) is best known for persistent, presumably non-pathogenic, infection and a propensity to co-infect with human immunodeficiency virus or hepatitis C virus. However, unique attributes, such as the increased risk of malignancy or immune modulation, have been recently recognized for HPgV. We have identified a unique case of a woman with high levels HPgV infection in two pregnancies, which occurred 4 years apart and without evidence of human immunodeficiency virus or hepatitis C virus infection. The second pregnancy was complicated by congenital heart disease. A high level of HPgV infection was detected in the maternal blood from different trimesters by RT-PCR and identified as HPgV type 1 genotype 2 in both pregnancies. In the second pregnancy, the decidua and intervillous tissue of the placenta were positive for HPgV by PCR but not the chorion or cord blood (from both pregnancies), suggesting no vertical transmission despite high levels of viremia. The HPgV genome sequence was remarkably conserved over the 4 years. Using VirScan, sera antibodies for HPgV were detected in the first trimester of both pregnancies. We observed the same anti-HPgV antibodies against the non-structural NS5 protein in both pregnancies, suggesting a similar non-E2 protein humoral immune response over time. To the best of our knowledge, this is the first report of persistent HPgV infection involving placental tissues with no clear indication of vertical transmission. Our results reveal a more elaborate viral-host interaction than previously reported, expand our knowledge about tropism, and opens avenues for exploring the replication sites of this virus.
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Affiliation(s)
- Mathieu Garand
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susie S. Y. Huang
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lisa S. Goessling
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Donna A. Santillan
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA 52242, USA
| | - Mark K. Santillan
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA 52242, USA
| | - Anoop Brar
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Todd N. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kristine M. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Pirooz Eghtesady
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
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Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022; 23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.,Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
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20
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Serpa PH, Deng X, Abdelghany M, Crawford E, Malcolm K, Caldera S, Fung M, McGeever A, Kalantar KL, Lyden A, Ghale R, Deiss T, Neff N, Miller SA, Doernberg SB, Chiu CY, DeRisi JL, Calfee CS, Langelier CR. Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections. Genome Med 2022; 14:74. [PMID: 35818068 PMCID: PMC9275031 DOI: 10.1186/s13073-022-01072-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 06/15/2022] [Indexed: 12/14/2022] Open
Abstract
Background Antimicrobial resistance (AMR) is rising at an alarming rate and complicating the management of infectious diseases including lower respiratory tract infections (LRTI). Metagenomic next-generation sequencing (mNGS) is a recently established method for culture-independent LRTI diagnosis, but its utility for predicting AMR has remained unclear. We aimed to assess the performance of mNGS for AMR prediction in bacterial LRTI and demonstrate proof of concept for epidemiological AMR surveillance and rapid AMR gene detection using Cas9 enrichment and nanopore sequencing. Methods We studied 88 patients with acute respiratory failure between 07/2013 and 9/2018, enrolled through a previous observational study of LRTI. Inclusion criteria were age ≥ 18, need for mechanical ventilation, and respiratory specimen collection within 72 h of intubation. Exclusion criteria were decline of study participation, unclear LRTI status, or no matched RNA and DNA mNGS data from a respiratory specimen. Patients with LRTI were identified by clinical adjudication. mNGS was performed on lower respiratory tract specimens. The primary outcome was mNGS performance for predicting phenotypic antimicrobial susceptibility and was assessed in patients with LRTI from culture-confirmed bacterial pathogens with clinical antimicrobial susceptibility testing (n = 27 patients, n = 32 pathogens). Secondary outcomes included the association between hospital exposure and AMR gene burden in the respiratory microbiome (n = 88 patients), and AMR gene detection using Cas9 targeted enrichment and nanopore sequencing (n = 10 patients). Results Compared to clinical antimicrobial susceptibility testing, the performance of respiratory mNGS for predicting AMR varied by pathogen, antimicrobial, and nucleic acid type sequenced. For gram-positive bacteria, a combination of RNA + DNA mNGS achieved a sensitivity of 70% (95% confidence interval (CI) 47–87%) and specificity of 95% (CI 85–99%). For gram-negative bacteria, sensitivity was 100% (CI 87–100%) and specificity 64% (CI 48–78%). Patients with hospital-onset LRTI had a greater AMR gene burden in their respiratory microbiome versus those with community-onset LRTI (p = 0.00030), or those without LRTI (p = 0.0024). We found that Cas9 targeted sequencing could enrich for low abundance AMR genes by > 2500-fold and enabled their rapid detection using a nanopore platform. Conclusions mNGS has utility for the detection and surveillance of resistant bacterial LRTI pathogens. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01072-4.
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Affiliation(s)
- Paula Hayakawa Serpa
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Xianding Deng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Mazin Abdelghany
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Emily Crawford
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Katherine Malcolm
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Saharai Caldera
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Monica Fung
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Amy Lyden
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Rajani Ghale
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Thomas Deiss
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Steven A Miller
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Sarah B Doernberg
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Carolyn S Calfee
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Charles R Langelier
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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21
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Bautista MAC, Zheng Y, Boufford DE, Hu Z, Deng Y, Chen T. Phylogeny and Taxonomic Synopsis of the Genus Bougainvillea (Nyctaginaceae). PLANTS 2022; 11:plants11131700. [PMID: 35807654 PMCID: PMC9269543 DOI: 10.3390/plants11131700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022]
Abstract
Bougainvillea Comm. ex Juss. is one of the renowned genera in the Nyctaginaceae, but despite its recognized horticultural value, the taxonomy and phylogeny of the genus is not well-studied. Phylogenetic reconstructions based on plastid genomes showed that B. pachyphylla and B. peruviana are basal taxa, while B. spinosa is sister to two distinct clades: the predominantly cultivated Bougainvillea clade (B. spectabilis, B. glabra, B. arborea, B. cultivar, B. praecox) and the clade containing wild species of Bougainvillea (B. berberidifolia, B. campanulata, B. infesta, B. modesta, B. luteoalba, B. stipitata, and B. stipitata var. grisebachiana). Early divergence of B. peruviana, B. pachyphylla and B. spinosa is highly supported, thus the previously proposed division of Bougainvillea into two subgenera (Bougainvillea and Tricycla) was not reflected in this study. Morphological analysis also revealed that leaf arrangement, size, and indumentum together with the perianth tube and anthocarp shape and indumentum are important characteristics in differentiating the species of Bougainvillea. In the present study, 11 species and one variety are recognized in Bougainvillea. Six names are newly reduced to synonymy, and lectotypes are designated for 27 names. In addition, a revised identification key and illustrations of the distinguishing parts are also provided in the paper.
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Affiliation(s)
- Mary Ann C. Bautista
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
- Key Laboratory of South Subtropical Plant Diversity, Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen 518004, China
- International School, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Conservation Innovations Ph, Inc., Alabang, Muntinlupa City 1770, Philippines
| | - Yan Zheng
- Guangdong Institute of Traditional Chinese Medicine, Guangzhou 510520, China;
| | - David E. Boufford
- Harvard University Herbaria, 22 Divinity Ave., Cambridge, MA 02138, USA;
| | - Zhangli Hu
- School of Life Sciences and Oceanology, Shenzhen University, Shenzhen 518055, China;
| | - Yunfei Deng
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
- International School, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Y.D.); (T.C.); Tel.: +86-20-2725-2677 (Y.D.); +86-755-2582-5277 (T.C.)
| | - Tao Chen
- Key Laboratory of South Subtropical Plant Diversity, Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen 518004, China
- International School, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Y.D.); (T.C.); Tel.: +86-20-2725-2677 (Y.D.); +86-755-2582-5277 (T.C.)
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22
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Finger AJ, Benjamin A, Crookshanks C, Campbell MA, Sağlam İK. Broad‐ and fine‐scale structure across the distribution of the relict dace (
Relictus solitarius
) in the Great Basin desert,
USA. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Amanda J. Finger
- Department of Animal Science University of California Davis California USA
| | - Alyssa Benjamin
- Department of Animal Science University of California Davis California USA
| | | | | | - İsmail K. Sağlam
- Department of Molecular Biology and Genetics Koç University Istanbul Turkey
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23
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Duarte MA, Campos FS, Araújo Neto OF, Silva LA, Silva AB, Aguiar TC, Santos RN, Souza UJB, Alves GB, Melo FL, Ardisson-Araujo DMP, Aguiar RWS, Ribeiro BM. Identification of potential new mosquito-associated viruses of adult Aedes aegypti mosquitoes from Tocantins state, Brazil. Braz J Microbiol 2021; 53:51-62. [PMID: 34727360 DOI: 10.1007/s42770-021-00632-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/07/2021] [Indexed: 11/29/2022] Open
Abstract
Medically important arboviruses such as dengue virus (DENV), Zika virus (ZIKV), and chikungunya virus (CHIKV) are primarily transmitted by the globally distributed mosquito Aedes aegypti. Increasing evidence suggests that the transmission of some viruses can be influenced by mosquito-specific and mosquito-borne viruses. Advancements in high-throughput sequencing (HTS) and bioinformatics have expanded our knowledge on the richness of viruses harbored by mosquitoes. HTS was used to characterize the presence of virus sequences in wild-caught adult Ae. aegypti from Tocantins (TO) state, Brazil. Samples of mosquitoes were collected in four cities of Tocantins state and submitted to RNA isolation, followed by sequencing at an Illumina HiSeq platform. Our results showed initially by Krona the presence of 3% of the sequenced reads belonging to the viral database. After further analysis, the virus sequences were found to have homology to two viral families found in insects Phenuiviridae and Metaviridae. Three possible viral strains including putative new viruses were detected and named Phasi Charoen-like phasivirus isolate To-1 (PCLV To-1), Aedes aegypti To virus 1 (AAToV1), and Aedes aegypti To virus 2 (AAToV2). The results presented in this work contribute to the growing knowledge about the diversity of viruses in mosquitoes and might be useful for future studies on the interaction between insect-specific viruses and arboviruses.
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Affiliation(s)
- Matheus A Duarte
- Faculdade de Agronomia E Veterinária, Universidade de Brasília, Brasília, DF, 70.910-900, Brazil
| | - Fabrício S Campos
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil.
| | - Osvaldo F Araújo Neto
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Leonardo A Silva
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, DF, 70.910-900, Brazil
| | - Arthur B Silva
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Thalita C Aguiar
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Raissa N Santos
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Ueric J B Souza
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Giselly B Alves
- Laboratório de Biologia Molecular, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Fernando L Melo
- Departamento de Fitopatologia, Instituto de Biologia, Universidade de Brasília, Brasília, DF, 70.910-900, Brazil
| | - Daniel M P Ardisson-Araujo
- Laboratório de Virologia de Insetos, Universidade Federal de Santa Maria, Santa Maria, RS, 97.105-900, Brazil
| | - Raimundo W S Aguiar
- Laboratório de Biologia Molecular, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Bergmann M Ribeiro
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, DF, 70.910-900, Brazil
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24
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Abuduaini A, Wang YB, Zhou HY, Kang RP, Ding ML, Jiang Y, Suo FY, Huang LD. The complete mitochondrial genome of Ophiocordyceps gracilis and its comparison with related species. IMA Fungus 2021; 12:31. [PMID: 34670626 PMCID: PMC8527695 DOI: 10.1186/s43008-021-00081-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/10/2021] [Indexed: 01/06/2023] Open
Abstract
In this study, the complete mitochondrial genome of O. gracilis was sequenced and assembled before being compared with related species. As the second largest mitogenome reported in the family Ophiocordycipitaceae, the mitogenome of O. gracilis (voucher OG201301) is a circular DNA molecule of 134,288 bp that contains numerous introns and longer intergenomic regions. UCA was detected as anticodon in tRNA-Sec of O. gracilis, while comparative mitogenome analysis of nine Ophiocordycipitaceae fungi indicated that the order and contents of PCGs and rRNA genes were considerably conserved and could descend from a common ancestor in Ophiocordycipitaceae. In addition, the expansion of mitochondrial organization, introns, gene length, and order of O. gracilis were determined to be similar to those of O. sinensis, which indicated common mechanisms underlying adaptive evolution in O. gracilis and O. sinensis. Based on the mitochondrial gene dataset (15 PCGs and 2 RNA genes), a close genetic relationship between O. gracilis and O. sinensis was revealed through phylogenetic analysis. This study is the first to investigate the molecular evolution, phylogenetic pattern, and genetic structure characteristics of mitogenome in O. gracilis. Based on the obtained results, the mitogenome of O. gracilis can increase understanding of the genetic diversity and evolution of cordycipitoid fungi.
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Affiliation(s)
- Aifeire Abuduaini
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Yuan-Bing Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Hui-Ying Zhou
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Rui-Ping Kang
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Ming-Liang Ding
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Yu Jiang
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Fei-Ya Suo
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Luo-Dong Huang
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China. .,Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, Nanning, 530004, China.
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25
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Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. Funct Integr Genomics 2021; 22:3-26. [PMID: 34657989 DOI: 10.1007/s10142-021-00810-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/25/2021] [Accepted: 10/03/2021] [Indexed: 10/20/2022]
Abstract
This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the research area, provides details about major analytical methods, examines the taxonomy and assembly of genomes, emphasizes some tools, and concludes by celebrating the richness of the ecosystem populated by the "metagenome."
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26
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Lin M, Li Y, Luo Y, Chen J, Qin X. Characterization of complete mitochondrial genome of rice flower carp Cyprinus carpio rubrofuscus (Cypriniformes: Cyprinidae). Mitochondrial DNA B Resour 2021; 6:2913-2914. [PMID: 34532585 PMCID: PMC8439227 DOI: 10.1080/23802359.2021.1970642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Rice flower carp (Cyprinus carpio rubrofuscus) is a subspecies of Cyprinus carpio distributed in South China. In this study, we sequenced the mitochondrial genome of C. carpio rubrofuscus using Illumina HiSeq. The complete mitochondrial genome of C. carpio rubrofuscus was 16,582 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. The contents of the four bases in the mitochondrial DNA were A (31.89%), T (24.82%), C (27.53%), and G (15.76%). Phylogenetic analysis showed that C. carpio rubrofuscus was clustered with Cyprinus carpio and its varieties.
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Affiliation(s)
| | - Yao Li
- Guangdong Polytechnic of Science and Trade, Guangzhou, China
| | | | - Jinhui Chen
- Qingyuan Polytechnic, Qingyuan, China
- Guangdong Polytechnic of Science and Trade, Guangzhou, China
| | - Xiaoling Qin
- Guangdong Polytechnic of Science and Trade, Guangzhou, China
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27
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Abderemane-Ali F, Rossen ND, Kobiela ME, Craig RA, Garrison CE, Chen Z, Colleran CM, O’Connell LA, Du Bois J, Dumbacher JP, Minor DL. Evidence that toxin resistance in poison birds and frogs is not rooted in sodium channel mutations and may rely on "toxin sponge" proteins. J Gen Physiol 2021; 153:e202112872. [PMID: 34351379 PMCID: PMC8348241 DOI: 10.1085/jgp.202112872] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/30/2021] [Accepted: 07/01/2021] [Indexed: 12/18/2022] Open
Abstract
Many poisonous organisms carry small-molecule toxins that alter voltage-gated sodium channel (NaV) function. Among these, batrachotoxin (BTX) from Pitohui poison birds and Phyllobates poison frogs stands out because of its lethality and unusual effects on NaV function. How these toxin-bearing organisms avoid autointoxication remains poorly understood. In poison frogs, a NaV DIVS6 pore-forming helix N-to-T mutation has been proposed as the BTX resistance mechanism. Here, we show that this variant is absent from Pitohui and poison frog NaVs, incurs a strong cost compromising channel function, and fails to produce BTX-resistant channels in poison frog NaVs. We also show that captivity-raised poison frogs are resistant to two NaV-directed toxins, BTX and saxitoxin (STX), even though they bear NaVs sensitive to both. Moreover, we demonstrate that the amphibian STX "toxin sponge" protein saxiphilin is able to protect and rescue NaVs from block by STX. Taken together, our data contradict the hypothesis that BTX autoresistance is rooted in the DIVS6 N→T mutation, challenge the idea that ion channel mutations are a primary driver of toxin resistance, and suggest the possibility that toxin sequestration mechanisms may be key for protecting poisonous species from the action of small-molecule toxins.
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Affiliation(s)
- Fayal Abderemane-Ali
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
| | - Nathan D. Rossen
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
| | - Megan E. Kobiela
- School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, NE
| | | | | | - Zhou Chen
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
| | - Claire M. Colleran
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
| | | | - J. Du Bois
- Department of Chemistry, Stanford University, Stanford, CA
| | - John P. Dumbacher
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA
- Department of Biology, San Francisco State University, San Francisco, CA
| | - Daniel L. Minor
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA
- Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA
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28
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Guo W, Comai L, Henry IM. Chromoanagenesis from radiation-induced genome damage in Populus. PLoS Genet 2021; 17:e1009735. [PMID: 34432802 PMCID: PMC8423247 DOI: 10.1371/journal.pgen.1009735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/07/2021] [Accepted: 07/22/2021] [Indexed: 11/18/2022] Open
Abstract
Chromoanagenesis is a genomic catastrophe that results in chromosomal shattering and reassembly. These extreme single chromosome events were first identified in cancer, and have since been observed in other systems, but have so far only been formally documented in plants in the context of haploid induction crosses. The frequency, origins, consequences, and evolutionary impact of such major chromosomal remodeling in other situations remain obscure. Here, we demonstrate the occurrence of chromoanagenesis in poplar (Populus sp.) trees produced from gamma-irradiated pollen. Specifically, in this population of siblings carrying indel mutations, two individuals exhibited highly frequent copy number variation (CNV) clustered on a single chromosome, one of the hallmarks of chromoanagenesis. Using short-read sequencing, we confirmed the presence of clustered segmental rearrangement. Independently, we identified and validated novel DNA junctions and confirmed that they were clustered and corresponded to these rearrangements. Our reconstruction of the novel sequences suggests that the chromosomal segments have reorganized randomly to produce a novel rearranged chromosome but that two different mechanisms might be at play. Our results indicate that gamma irradiation can trigger chromoanagenesis, suggesting that this may also occur when natural or induced mutagens cause DNA breaks. We further demonstrate that such events can be tolerated in poplar, and even replicated clonally, providing an attractive system for more in-depth investigations of their consequences. Plant breeders often use radiation treatment to produce variation, with the goal of identifying new varieties with superior traits. We studied a population of poplar trees produced by gamma irradiation of pollen, and asked what kind of DNA changes were associated with this variation. We found many changes, most often in the form of added (insertions) or removed (deletions) pieces of DNA. We also found two lines with much more drastic changes. In those lines, we observed massive reorganization. We characterized these two lines in detail and found that catastrophic pulverization and random reassembly only occurred on a single chromosome. Looking closely at how the pieces were put back together suggest that the rearrangements in these two lines may have resulted from two slightly different mechanisms. This type of rearrangement is commonly observed in human cancer cells, but has rarely been observed in plants. We demonstrated here that they can be induced by gamma irradiation, indicating this type of event might be more widespread than we expected. Characterizing such genome restructuring instances helps to understand how genome instability can remodel chromosomes and affect genome function.
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Affiliation(s)
- Weier Guo
- Genome Center and Dept. Plant Biology, University of California Davis, Davis, California, United States of America
| | - Luca Comai
- Genome Center and Dept. Plant Biology, University of California Davis, Davis, California, United States of America
| | - Isabelle M. Henry
- Genome Center and Dept. Plant Biology, University of California Davis, Davis, California, United States of America
- * E-mail:
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Ayling M, Clark MD, Leggett RM. New approaches for metagenome assembly with short reads. Brief Bioinform 2021; 21:584-594. [PMID: 30815668 PMCID: PMC7299287 DOI: 10.1093/bib/bbz020] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 02/07/2023] Open
Abstract
In recent years, the use of longer range read data combined with advances in assembly algorithms has stimulated big improvements in the contiguity and quality of genome assemblies. However, these advances have not directly transferred to metagenomic data sets, as assumptions made by the single genome assembly algorithms do not apply when assembling multiple genomes at varying levels of abundance. The development of dedicated assemblers for metagenomic data was a relatively late innovation and for many years, researchers had to make do using tools designed for single genomes. This has changed in the last few years and we have seen the emergence of a new type of tool built using different principles. In this review, we describe the challenges inherent in metagenomic assemblies and compare the different approaches taken by these novel assembly tools.
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Affiliation(s)
- Martin Ayling
- Earlham Institute, Norwich Research Park, Norwich, UK
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Ge ML, Shi WG, Li YX, Li Z, Zhang XL, Xu QZ. Complete mitochondrial genome of Dibranchus japonicus (Actinopterygii, Lophiiformes, Ogcocephalidae), from the West Pacific Ocean. Mitochondrial DNA B Resour 2021; 6:2214-2215. [PMID: 34286083 PMCID: PMC8266229 DOI: 10.1080/23802359.2021.1915203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Dibranchus japonicus is a benthic fish living in the deep Pacific Ocean. Here, we described the complete mitochondrial genome of this species, with the sequences about 17,233 bp in length, containing 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. The gene arrangement of this species was identical with others from family Ogcocephalidae. The content of GC and AT for D. japonicus was 45.41% and 54.59%, respectively. Phylogenetic analysis, based on 13 PCGs and two rRNA genes, revealed the close relationship between D. japonicus and other species of Ogcocephalidae, which was consistent with the morphology.
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Affiliation(s)
- Mei-Ling Ge
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Wen-Ge Shi
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Yi-Xuan Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Zhong Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Xue-Lei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Qin-Zeng Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
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Beric A, Mabry ME, Harkess AE, Brose J, Schranz ME, Conant GC, Edger PP, Meyers BC, Pires JC. Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales). G3 (BETHESDA, MD.) 2021; 11:jkab140. [PMID: 33993297 PMCID: PMC8495927 DOI: 10.1093/g3journal/jkab140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/10/2021] [Indexed: 11/14/2022]
Abstract
Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to further test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana-chosen as the model plant system for this reason-as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we confirm the correlation between genome size and TE content, however, we are unable to reconstruct phylogenetic relationships and do not detect any shift in TE abundance associated with WGD.
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Affiliation(s)
- Aleksandra Beric
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Makenzie E Mabry
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Alex E Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Julia Brose
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen 6700 AA, The Netherlands
| | - Gavin C Conant
- Bioinformatics Research Center, Program in Genetics and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Department of Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI 48824, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - J Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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Kupritz J, Martin J, Fischer K, Curtis KC, Fauver JR, Huang Y, Choi YJ, Beatty WL, Mitreva M, Fischer PU. Isolation and characterization of a novel bacteriophage WO from Allonemobius socius crickets in Missouri. PLoS One 2021; 16:e0250051. [PMID: 34197460 PMCID: PMC8248633 DOI: 10.1371/journal.pone.0250051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/15/2021] [Indexed: 11/19/2022] Open
Abstract
Wolbachia are endosymbionts of numerous arthropod and some nematode species, are important for their development and if present can cause distinct phenotypes of their hosts. Prophage DNA has been frequently detected in Wolbachia, but particles of Wolbachia bacteriophages (phage WO) have been only occasionally isolated. Here, we report the characterization and isolation of a phage WO of the southern ground cricket, Allonemobius socius, and provided the first whole-genome sequence of phage WO from this arthropod family outside of Asia. We screened A. socius abdomen DNA extracts from a cricket population in eastern Missouri by quantitative PCR for Wolbachia surface protein and phage WO capsid protein and found a prevalence of 55% and 50%, respectively, with many crickets positive for both. Immunohistochemistry using antibodies against Wolbachia surface protein showed many Wolbachia clusters in the reproductive system of female crickets. Whole-genome sequencing using Oxford Nanopore MinION and Illumina technology allowed for the assembly of a high-quality, 55 kb phage genome containing 63 open reading frames (ORF) encoding for phage WO structural proteins and host lysis and transcriptional manipulation. Taxonomically important regions of the assembled phage genome were validated by Sanger sequencing of PCR amplicons. Analysis of the nucleotides sequences of the ORFs encoding the large terminase subunit (ORF2) and minor capsid (ORF7) frequently used for phage WO phylogenetics showed highest homology to phage WOAu of Drosophila simulans (94.46% identity) and WOCin2USA1 of the cherry fruit fly, Rhagoletis cingulata (99.33% identity), respectively. Transmission electron microscopy examination of cricket ovaries showed a high density of phage particles within Wolbachia cells. Isolation of phage WO revealed particles characterized by 40–62 nm diameter heads and up to 190 nm long tails. This study provides the first detailed description and genomic characterization of phage WO from North America that is easily accessible in a widely distributed cricket species.
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Affiliation(s)
- Jonah Kupritz
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - John Martin
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kerstin Fischer
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kurt C. Curtis
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Joseph R. Fauver
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yuefang Huang
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Young-Jun Choi
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Wandy L. Beatty
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Makedonka Mitreva
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Peter U. Fischer
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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POECIVIRUS IS PRESENT IN INDIVIDUALS WITH BEAK DEFORMITIES IN SEVEN SPECIES OF NORTH AMERICAN BIRDS. J Wildl Dis 2021; 57:273-281. [PMID: 33822149 DOI: 10.7589/jwd-d-20-00017] [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: 01/29/2020] [Accepted: 08/08/2020] [Indexed: 11/20/2022]
Abstract
Avian keratin disorder (AKD), a disease of unknown etiology characterized by debilitating beak overgrowth, has increasingly affected wild bird populations since the 1990s. A novel picornavirus, poecivirus, is closely correlated with disease status in Black-capped Chickadees (Poecile atricapillus) in Alaska, US. However, our knowledge of the relationship between poecivirus and beak deformities in other species and other geographic areas remains limited. The growing geographic scope and number of species affected by AKD-like beak deformities require a better understanding of the causative agent to evaluate the population-level impacts of this epizootic. Here, we tested eight individuals from six avian species with AKD-consistent deformities for the presence of poecivirus: Mew Gull (Larus canus), Hairy Woodpecker (Picoides villosus), Black-billed Magpie (Pica hudsonia), American Crow (Corvus brachyrhynchos), Red-breasted Nuthatch (Sitta canadensis), and Blackpoll Warbler (Setophaga striata). The birds were sampled in Alaska and Maine (1999-2016). We used targeted PCR followed by Sanger sequencing to test for the presence of poecivirus in each specimen and to obtain viral genome sequence from virus-positive host individuals. We detected poecivirus in all individuals tested, but not in negative controls (water and tissue samples). Furthermore, we used unbiased metagenomic sequencing to test for the presence of other pathogens in six of these specimens (Hairy Woodpecker, two American Crows, two Red-breasted Nuthatches, Blackpoll Warbler). This analysis yielded additional viral sequences from several specimens, including the complete coding region of poecivirus from one Red-breasted Nuthatch, which we confirmed via targeted PCR followed by Sanger sequencing. This study demonstrates that poecivirus is present in individuals with AKD-consistent deformities from six avian species other than Black-capped Chickadee. While further investigation will be required to explore whether there exists a causal link between this virus and AKD, this study demonstrates that poecivirus is not geographically restricted to Alaska, but rather occurs elsewhere in North America.
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Abstract
Narnaviruses are RNA viruses detected in diverse fungi, plants, protists, arthropods, and nematodes. Though initially described as simple single-gene nonsegmented viruses encoding RNA-dependent RNA polymerase (RdRp), a subset of narnaviruses referred to as "ambigrammatic" harbor a unique genomic configuration consisting of overlapping open reading frames (ORFs) encoded on opposite strands. Phylogenetic analysis supports selection to maintain this unusual genome organization, but functional investigations are lacking. Here, we establish the mosquito-infecting Culex narnavirus 1 (CxNV1) as a model to investigate the functional role of overlapping ORFs in narnavirus replication. In CxNV1, a reverse ORF without homology to known proteins covers nearly the entire 3.2-kb segment encoding the RdRp. Additionally, two opposing and nearly completely overlapping novel ORFs are found on the second putative CxNV1 segment, the 0.8-kb "Robin" RNA. We developed a system to launch CxNV1 in a naive mosquito cell line and then showed that functional RdRp is required for persistence of both segments, and an intact reverse ORF is required on the RdRp segment for persistence. Mass spectrometry of persistently CxNV1-infected cells provided evidence for translation of this reverse ORF. Finally, ribosome profiling yielded a striking pattern of footprints for all four CxNV1 RNA strands that was distinct from actively translating ribosomes on host mRNA or coinfecting RNA viruses. Taken together, these data raise the possibility that the process of translation itself is important for persistence of ambigrammatic narnaviruses, potentially by protecting viral RNA with ribosomes, thus suggesting a heretofore undescribed viral tactic for replication and transmission. IMPORTANCE Fundamental to our understanding of RNA viruses is a description of which strand(s) of RNA are transmitted as the viral genome relative to which encode the viral proteins. Ambigrammatic narnaviruses break the mold. These viruses, found broadly in fungi, plants, and insects, have the unique feature of two overlapping genes encoded on opposite strands, comprising nearly the full length of the viral genome. Such extensive overlap is not seen in other RNA viruses and comes at the cost of reduced evolutionary flexibility in the sequence. The present study is motivated by investigating the benefits which balance that cost. We show for the first time a functional requirement for the ambigrammatic genome configuration in Culex narnavirus 1, which suggests a model for how translation of both strands might benefit this virus. Our work highlights a new blueprint for viral persistence, distinct from strategies defined by canonical definitions of the coding strand.
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Abstract
By evolving strains of E. coli that hyper-resist sedimentation, we discovered an uncharacterized mechanism that bacteria can use to remain in suspension indefinitely without expending energy. This unusual phenotype was traced to the anchoring of long colanic acid polymers (CAP) that project from the cell surface. Although each characterized mutant activated this same mechanism, the genes responsible and the strengths of the phenotypes varied. Mutations in rcsC, lpp, igaA, or the yjbEFGH operon were sufficient to stimulate sedimentation resistance, while mutations altering the cps promoter, cdgI, or yjbF provided phenotypic enhancements. The sedimentation resistances changed in response to temperature, growth phase, and carbon source and each mutant exhibited significantly reduced biofilm formation. We discovered that the degree of colony mucoidy exhibited by these mutants was not related to the degree of Rcs pathways activation or to the amount of CAP that was produced; rather, it was related to the fraction of CAP that was shed as a true exopolysaccharide. Therefore, these and other mutations that activate this phenotype are likely to be absent from genetic screens that relied on centrifugation to harvest bacteria. We also found that this anchored CAP form is not linked to LPS cores and may not be attached to the outer membrane.IMPORTANCEBacteria can partition in aqueous environments between surface-dwelling, planktonic, sedimentary, and biofilm forms. Residence in each location provides an advantage depending on nutritional and environmental stresses and a community of a single species is often observed to be distributed throughout two or more of these niches. Another adaptive strategy is to produce an extracellular capsule, which provides an environmental shield for the microbe and can allow escape from predators and immune systems. We discovered that bacteria can either shed or stably anchor capsules to dramatically alter their propensity to sediment. The degree to which the bacteria anchor their capsule is controlled by a stress sensing system, suggesting that anchoring may be used as an adaptive response to severe environmental challenges.
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Yang H, Gu W, Li Z, Zhang L, Liao D, Song J, Shi B, Hasimu J, Li Z, Yang Z, Zhong Q, Li H. Novel putative bluetongue virus serotype 29 isolated from inapparently infected goat in Xinjiang of China. Transbound Emerg Dis 2021; 68:2543-2555. [PMID: 33190404 DOI: 10.1111/tbed.13927] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/29/2020] [Accepted: 11/10/2020] [Indexed: 02/04/2023]
Abstract
Bluetongue virus (BTV) is the 'type' species of the genus Orbivirus causing bluetongue (BT) in sheep, bovine and other ruminants. Twenty-four serotypes and several atypical serotypes of BTV were identified worldwide. In present study, a novel strain of BTV (V196/XJ/2014) was isolated from an asymptomatic sentinel goat in Yuli County, Xinjiang of China. Serotype identification of this isolate exhibited uniform negative results by serotype-specific conventional RT-PCR and real-time RT-PCR for BTV-1 to BTV-27, and virus neutralization tests using reference sera of BTV-1 to BTV-24. Genomic analysis showed V196/XJ/2014 grouped with atypical serotypes of BTV-25 to BTV-28, BTV-X/XJ1407, BTV-X/ITL2015 and BTV-Y/TUN2017, while segment 2 and VP2 protein of V196/XJ/2014 shared <63.4%/61.4% nucleic acids and amino acids sequence identities with other recognized BTV serotypes and its segment 2 formed a separate 'nucleotype' in phylogenetic tree. These results indicated V196/XJ/2014 does not belong to any reported serotypes of BTV. Further studies of infectivity and pathogenicity showed that goats infected with V196/XJ/2014 did not exhibit observed clinical symptoms, but high level of virus amplification and homologous neutralization antibodies were detected post-infection. Our studies suggested a novel putative serotype of BTV-29 was isolated in Xinjiang of China, which expands our knowledge about the diversity of BTV.
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Affiliation(s)
- Heng Yang
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
| | - Wenxi Gu
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Autonomous Region, China
| | - Zhanhong Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
| | - Ling Zhang
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Autonomous Region, China
| | - Defang Liao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
| | - Jianling Song
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
| | - Baoxin Shi
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Autonomous Region, China
| | - Jiapaer Hasimu
- Yuli Animal Husbandry and Veterinary Station, Yuli, Xinjiang Autonomous Region, China
| | - Zhuoran Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
| | - Zhenxing Yang
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
| | - Qi Zhong
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, Xinjiang Autonomous Region, China
| | - Huachun Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan Province, China
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Peek RA, O'Rourke SM, Miller MR. Flow modification associated with reduced genetic health of a river‐breeding frog,
Rana boylii. Ecosphere 2021. [DOI: 10.1002/ecs2.3496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Ryan A. Peek
- Center for Watershed Sciences University of California Davis California95616USA
| | - Sean M. O'Rourke
- Department of Animal Science University of California Davis California95616USA
| | - Michael R. Miller
- Department of Animal Science University of California Davis California95616USA
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Lapidus AL, Korobeynikov AI. Metagenomic Data Assembly - The Way of Decoding Unknown Microorganisms. Front Microbiol 2021; 12:613791. [PMID: 33833738 PMCID: PMC8021871 DOI: 10.3389/fmicb.2021.613791] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 03/03/2021] [Indexed: 01/08/2023] Open
Abstract
Metagenomics is a segment of conventional microbial genomics dedicated to the sequencing and analysis of combined genomic DNA of entire environmental samples. The most critical step of the metagenomic data analysis is the reconstruction of individual genes and genomes of the microorganisms in the communities using metagenomic assemblers - computational programs that put together small fragments of sequenced DNA generated by sequencing instruments. Here, we describe the challenges of metagenomic assembly, a wide spectrum of applications in which metagenomic assemblies were used to better understand the ecology and evolution of microbial ecosystems, and present one of the most efficient microbial assemblers, SPAdes that was upgraded to become applicable for metagenomics.
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Affiliation(s)
- Alla L. Lapidus
- Center for Algorithmic Biotechnology, St. Petersburg State University, Saint Petersburg, Russia
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Deng Z, Delwart E. ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data. BMC Bioinformatics 2021; 22:119. [PMID: 33706720 PMCID: PMC7953547 DOI: 10.1186/s12859-021-04038-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Metagenomics is the study of microbial genomes for pathogen detection and discovery in human clinical, animal, and environmental samples via Next-Generation Sequencing (NGS). Metagenome de novo sequence assembly is a crucial analytical step in which longer contigs, ideally whole chromosomes/genomes, are formed from shorter NGS reads. However, the contigs generated from the de novo assembly are often very fragmented and rarely longer than a few kilo base pairs (kb). Therefore, a time-consuming extension process is routinely performed on the de novo assembled contigs. RESULTS To facilitate this process, we propose a new tool for metagenome contig extension after de novo assembly. ContigExtender employs a novel recursive extending strategy that explores multiple extending paths to achieve highly accurate longer contigs. We demonstrate that ContigExtender outperforms existing tools in synthetic, animal, and human metagenomics datasets. CONCLUSIONS A novel software tool ContigExtender has been developed to assist and enhance the performance of metagenome de novo assembly. ContigExtender effectively extends contigs from a variety of sources and can be incorporated in most viral metagenomics analysis pipelines for a wide variety of applications, including pathogen detection and viral discovery.
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Affiliation(s)
- Zachary Deng
- Vitalant Research Institute, San Francisco, CA, 94118, USA.
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94107, USA.
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94118, USA.
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94107, USA.
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Podlevsky JD, Hudson CM, Timlin JA, Williams KP. CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data. NAR Genom Bioinform 2021; 2:lqaa063. [PMID: 33575613 PMCID: PMC7671303 DOI: 10.1093/nargab/lqaa063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/20/2020] [Accepted: 09/01/2020] [Indexed: 12/25/2022] Open
Abstract
CRISPR arrays and CRISPR-associated (Cas) proteins comprise a widespread adaptive immune system in bacteria and archaea. These systems function as a defense against exogenous parasitic mobile genetic elements that include bacteriophages, plasmids and foreign nucleic acids. With the continuous spread of antibiotic resistance, knowledge of pathogen susceptibility to bacteriophage therapy is becoming more critical. Additionally, gene-editing applications would benefit from the discovery of new cas genes with favorable properties. While next-generation sequencing has produced staggering quantities of data, transitioning from raw sequencing reads to the identification of CRISPR/Cas systems has remained challenging. This is especially true for metagenomic data, which has the highest potential for identifying novel cas genes. We report a comprehensive computational pipeline, CasCollect, for the targeted assembly and annotation of cas genes and CRISPR arrays—even isolated arrays—from raw sequencing reads. Benchmarking our targeted assembly pipeline demonstrates significantly improved timing by almost two orders of magnitude compared with conventional assembly and annotation, while retaining the ability to detect CRISPR arrays and cas genes. CasCollect is a highly versatile pipeline and can be used for targeted assembly of any specialty gene set, reconfigurable for user provided Hidden Markov Models and/or reference nucleotide sequences.
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Affiliation(s)
- Joshua D Podlevsky
- Molecular and Microbiology, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Corey M Hudson
- Computational Biology and Biophysics, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Jerilyn A Timlin
- Computational Biology and Biophysics, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Kelly P Williams
- Systems Biology, Sandia National Laboratories, Livermore, CA 94550, USA
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Mycoviral diversity and characteristics of a negative-stranded RNA virus LeNSRV1 in the edible mushroom Lentinula edodes. Virology 2020; 555:89-101. [PMID: 33308828 DOI: 10.1016/j.virol.2020.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/04/2020] [Accepted: 11/12/2020] [Indexed: 11/23/2022]
Abstract
Bioinformatics and RT-PCR analysis of RNA from four Lentinula edodes samples identified 22 different virus-like contigs comprising 15 novel and 3 previously reported viruses. We further investigated the Lentinula edodes negative-stranded RNA virus 1 (LeNSRV1) isolated from a symptomatic sample, whose virion is a filamentous particle with a diameter of ~15 nm and a length of ~1200 nm. RT-PCR analysis detected LeNSRV1 in 10 of the 56 Chinese L. edodes core collection strains and 6 of the 22 monokaryotic strains from the L. edodes strain HNZMD. Genetic variation analysis showed that the sequences encoding the nucleocapsid protein (ORF2) from all the aforementioned LeNSRV1 positive strains are very conservative. The results presented here may enrich our understanding of L. edodes virus diversity and the characteristics of LeNSRV1, and will promote further research on virus-host interaction in L. edodes.
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Kalantar KL, Carvalho T, de Bourcy CFA, Dimitrov B, Dingle G, Egger R, Han J, Holmes OB, Juan YF, King R, Kislyuk A, Lin MF, Mariano M, Morse T, Reynoso LV, Cruz DR, Sheu J, Tang J, Wang J, Zhang MA, Zhong E, Ahyong V, Lay S, Chea S, Bohl JA, Manning JE, Tato CM, DeRisi JL. IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. Gigascience 2020; 9:giaa111. [PMID: 33057676 PMCID: PMC7566497 DOI: 10.1093/gigascience/giaa111] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 08/28/2020] [Accepted: 09/22/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) has enabled the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Existing mNGS data analysis tools typically require bioinformatics expertise and access to local server-class hardware resources. For many research laboratories, this presents an obstacle, especially in resource-limited environments. FINDINGS We present IDseq, an open source cloud-based metagenomics pipeline and service for global pathogen detection and monitoring (https://idseq.net). The IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes an assembly-based alignment pipeline, which results in the assignment of reads and contigs to taxonomic categories. The taxonomic relative abundances are reported and visualized in an easy-to-use web application to facilitate data interpretation and hypothesis generation. Furthermore, IDseq supports environmental background model generation and automatic internal spike-in control recognition, providing statistics that are critical for data interpretation. IDseq was designed with the specific intent of detecting novel pathogens. Here, we benchmark novel virus detection capability using both synthetically evolved viral sequences and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist from Wuhan, China, infected with the recently emergent SARS-CoV-2. CONCLUSION The IDseq Portal reduces the barrier to entry for mNGS data analysis and enables bench scientists, clinicians, and bioinformaticians to gain insight from mNGS datasets for both known and novel pathogens.
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Affiliation(s)
- Katrina L Kalantar
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Tiago Carvalho
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | | | - Boris Dimitrov
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Greg Dingle
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Rebecca Egger
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Julie Han
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Olivia B Holmes
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Yun-Fang Juan
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Ryan King
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Andrey Kislyuk
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Michael F Lin
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Maria Mariano
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Todd Morse
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Lucia V Reynoso
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - David Rissato Cruz
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Jonathan Sheu
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Jennifer Tang
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - James Wang
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Mark A Zhang
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Emily Zhong
- Chan Zuckerberg Initiative, Science, PO Box 8040 Redwood City, CA 94063, USA
| | - Vida Ahyong
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - Sreyngim Lay
- Malaria and Vector Research Laboratory, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Sophana Chea
- Malaria and Vector Research Laboratory, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Jennifer A Bohl
- Malaria and Vector Research Laboratory, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Jessica E Manning
- Malaria and Vector Research Laboratory, National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | - Cristina M Tato
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
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Abstract
Viruses are key drivers of evolution and ecosystem function and are increasingly recognized as symbionts of fungi. Fungi in early-diverging lineages are widespread, ecologically important, and comprise the majority of the phylogenetic diversity of the kingdom. Viruses infecting early-diverging lineages of fungi have been almost entirely unstudied. In this study, we screened fungi for viruses by two alternative approaches: a classic culture-based method and by transcriptome-mining. The results of our large-scale survey demonstrate that early-diverging lineages have higher infection rates than have been previously reported in other fungal taxa and that laboratory strains worldwide are host to infections, the implications of which are unknown. The function and diversity of mycoviruses found in these basal fungal lineages will help guide future studies into mycovirus origins and their evolutionary ramifications and ecological impacts. Mycoviruses are widespread and purportedly common throughout the fungal kingdom, although most are known from hosts in the two most recently diverged phyla, Ascomycota and Basidiomycota, together called Dikarya. To augment our knowledge of mycovirus prevalence and diversity in underexplored fungi, we conducted a large-scale survey of fungi in the earlier-diverging lineages, using both culture-based and transcriptome-mining approaches to search for RNA viruses. In total, 21.6% of 333 isolates were positive for RNA mycoviruses. This is a greater proportion than expected based on previous taxonomically broad mycovirus surveys and is suggestive of a strong phylogenetic component to mycoviral infection. Our newly found viral sequences are diverse, composed of double-stranded RNA, positive-sense single-stranded RNA (ssRNA), and negative-sense ssRNA genomes and include novel lineages lacking representation in the public databases. These identified viruses could be classified into 2 orders, 5 families, and 5 genera; however, half of the viruses remain taxonomically unassigned. Further, we identified a lineage of virus-like sequences in the genomes of members of Phycomycetaceae and Mortierellales that appear to be novel genes derived from integration of a viral RNA-dependent RNA polymerase gene. The two screening methods largely agreed in their detection of viruses; thus, we suggest that the culture-based assay is a cost-effective means to quickly assess whether a laboratory culture is virally infected. This study used culture collections and publicly available transcriptomes to demonstrate that mycoviruses are abundant in laboratory cultures of early-diverging fungal lineages. The function and diversity of mycoviruses found here will help guide future studies into mycovirus origins and ecological functions.
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Abstract
B cells serve as a key weapon against infectious diseases. They also contribute to multiple autoimmune diseases, including multiple sclerosis (MS) where depletion of B cells is a highly effective therapy. We describe a comprehensive profile of central nervous system (CNS)-specific transcriptional B cell phenotypes in MS at single-cell resolution with paired immune repertoires. We reveal a polyclonal immunoglobulin M (IgM) and IgG1 cerebrospinal fluid B cell expansion polarized toward an inflammatory, memory and plasmablast/plasma cell phenotype, with differential up-regulation of specific proinflammatory pathways. We did not find evidence that CNS B cells harbor a neurotropic virus. These data support the targeting of activated resident B cells in the CNS as a potentially effective strategy for control of treatment-resistant chronic disease. Central nervous system B cells have several potential roles in multiple sclerosis (MS): secretors of proinflammatory cytokines and chemokines, presenters of autoantigens to T cells, producers of pathogenic antibodies, and reservoirs for viruses that trigger demyelination. To interrogate these roles, single-cell RNA sequencing (scRNA-Seq) was performed on paired cerebrospinal fluid (CSF) and blood from subjects with relapsing-remitting MS (RRMS; n = 12), other neurologic diseases (ONDs; n = 1), and healthy controls (HCs; n = 3). Single-cell immunoglobulin sequencing (scIg-Seq) was performed on a subset of these subjects and additional RRMS (n = 4), clinically isolated syndrome (n = 2), and OND (n = 2) subjects. Further, paired CSF and blood B cell subsets (RRMS; n = 7) were isolated using fluorescence activated cell sorting for bulk RNA sequencing (RNA-Seq). Independent analyses across technologies demonstrated that nuclear factor kappa B (NF-κB) and cholesterol biosynthesis pathways were activated, and specific cytokine and chemokine receptors were up-regulated in CSF memory B cells. Further, SMAD/TGF-β1 signaling was down-regulated in CSF plasmablasts/plasma cells. Clonally expanded, somatically hypermutated IgM+ and IgG1+ CSF B cells were associated with inflammation, blood–brain barrier breakdown, and intrathecal Ig synthesis. While we identified memory B cells and plasmablast/plasma cells with highly similar Ig heavy-chain sequences across MS subjects, similarities were also identified with ONDs and HCs. No viral transcripts, including from Epstein–Barr virus, were detected. Our findings support the hypothesis that in MS, CSF B cells are driven to an inflammatory and clonally expanded memory and plasmablast/plasma cell phenotype.
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Viral diversity in oral cavity from Sapajus nigritus by metagenomic analyses. Braz J Microbiol 2020; 51:1941-1951. [PMID: 32780265 DOI: 10.1007/s42770-020-00350-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/25/2020] [Indexed: 01/14/2023] Open
Abstract
Sapajus nigritus are non-human primates which are widespread in South America. They are omnivores and live in troops of up to 40 individuals. The oral cavity is one of the main entry routes for microorganisms, including viruses. Our study proposed the identification of viral sequences from oral swabs collected in a group of capuchin monkeys (n = 5) living in a public park in a fragment of Mata Atlantica in South Brazil. Samples were submitted to nucleic acid extraction and enrichment, which was followed by the construction of libraries. After high-throughput sequencing and contig assembly, we used a pipeline to identify 11 viral families, which are Herpesviridae, Parvoviridae, Papillomaviridae, Polyomaviridae, Caulimoviridae, Iridoviridae, Astroviridae, Poxviridae, and Baculoviridae, in addition to two complete viral genomes of Anelloviridae and Genomoviridae. Some of these viruses were closely related to known viruses, while other fragments are more distantly related, with 50% of identity or less to the currently available virus sequences in databases. In addition to host-related viruses, insect and small vertebrate-related viruses were also found, as well as plant-related viruses, bringing insights about their diet. In conclusion, this viral metagenomic analysis reveals, for the first time, the profile of viruses in the oral cavity of wild, free ranging capuchin monkeys.
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Prayogo FA, Budiharjo A, Kusumaningrum HP, Wijanarka W, Suprihadi A, Nurhayati N. Metagenomic applications in exploration and development of novel enzymes from nature: a review. J Genet Eng Biotechnol 2020; 18:39. [PMID: 32749574 PMCID: PMC7403272 DOI: 10.1186/s43141-020-00043-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Microbial community has an essential role in various fields, especially the industrial sector. Microbes produce metabolites in the form of enzymes, which are one of the essential compounds for industrial processes. Unfortunately, there are still numerous microbes that cannot be identified and cultivated because of the limitations of the culture-based method. The metagenomic approach is a solution for researchers to overcome these problems. Metagenomics is a strategy used to analyze the genomes of microbial communities in the environment directly. Metagenomics application used to explore novel enzymes is essential because it allows researchers to obtain data on microbial diversity, reaching of 99% and various types of genes encoding an enzyme that has not yet been identified. Basic methods in metagenomics have been developed and are commonly used in various studies. A basic understanding of metagenomics for researchers is needed, especially young researchers to support the success of the research. SHORT CONCLUSION Therefore, this review was done in order to provide a deep understanding of metagenomics. It also discussed the application and basic methods of metagenomics in the exploration of novel enzymes, especially in the latest research. Several types of enzymes, such as cellulases, proteases, and lipases, which have been explored using metagenomics, were reviewed in this article.
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Affiliation(s)
- Fitra Adi Prayogo
- Department of Biology, Faculty of Science and Mathematics, Diponegoro University, Semarang City, 50275 Indonesia
| | - Anto Budiharjo
- Biotechnology Study Program, Faculty of Science and Mathematics, Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
- Molecular and Applied Microbiology Laboratory, Center Central Laboratory of Research and Service - Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
| | | | - Wijanarka Wijanarka
- Biotechnology Study Program, Faculty of Science and Mathematics, Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
| | - Agung Suprihadi
- Biotechnology Study Program, Faculty of Science and Mathematics, Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
| | - Nurhayati Nurhayati
- Biotechnology Study Program, Faculty of Science and Mathematics, Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
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47
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Zinter MS, Dvorak CC, Mayday MY, Iwanaga K, Ly NP, McGarry ME, Church GD, Faricy LE, Rowan CM, Hume JR, Steiner ME, Crawford ED, Langelier C, Kalantar K, Chow ED, Miller S, Shimano K, Melton A, Yanik GA, Sapru A, DeRisi JL. Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children. Clin Infect Dis 2020; 68:1847-1855. [PMID: 30239621 PMCID: PMC6784263 DOI: 10.1093/cid/ciy802] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/13/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. Therefore, we aimed to develop a highly sensitive metagenomic next-generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children. METHODS We collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children's hospitals from 2014-2016. Samples underwent mechanical homogenization, parallel RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the National Center for Biotechnology Information nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort. RESULTS We identified a rich cross-domain pulmonary microbiome that contained bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median, 0.61; interquartile range [IQR], 0.33-0.72 vs median, 0.96; IQR, 0.94-0.96; P < .001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (P < .001). CONCLUSIONS An optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.
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Affiliation(s)
- Matt S Zinter
- Division of Critical Care, University of California, San Francisco School of Medicine
| | - Christopher C Dvorak
- Division of Allergy, Immunology, and Blood & Marrow Transplantation, University of California, San Francisco School of Medicine
| | - Madeline Y Mayday
- Division of Critical Care, University of California, San Francisco School of Medicine
| | - Kensho Iwanaga
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Ngoc P Ly
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Meghan E McGarry
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Gwynne D Church
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Lauren E Faricy
- Division of Pulmonology, Department of Pediatrics, University of Vermont School of Medicine, Burlington
| | - Courtney M Rowan
- Division of Critical Care, Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis
| | - Janet R Hume
- Division of Critical Care, University of Minnesota School of Medicine, Minneapolis
| | - Marie E Steiner
- Division of Critical Care, University of Minnesota School of Medicine, Minneapolis.,Hematology/Oncology, Department of Pediatrics, Masonic Children's Hospital, University of Minnesota School of Medicine, Minneapolis
| | - Emily D Crawford
- Chan Zuckerberg Biohub, University of California-San Francisco School of Medicine.,Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
| | - Charles Langelier
- Division of Infectious Diseases, Department of Internal Medicine, University of California-San Francisco School of Medicine
| | - Katrina Kalantar
- Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
| | - Eric D Chow
- Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
| | - Steve Miller
- Department of Laboratory Medicine, University of California-San Francisco School of Medicine
| | - Kristen Shimano
- Division of Allergy, Immunology, and Blood & Marrow Transplantation, University of California, San Francisco School of Medicine
| | - Alexis Melton
- Division of Allergy, Immunology, and Blood & Marrow Transplantation, University of California, San Francisco School of Medicine
| | - Gregory A Yanik
- Division of Oncology, Department of Pediatrics, Motts Children's Hospital, University of Michigan School of Medicine, Ann Arbor
| | - Anil Sapru
- Division of Critical Care, University of California, San Francisco School of Medicine.,Division of Critical Care, Department of Pediatrics, Mattel Children's Hospital, University of California-Los Angeles, Geffen School of Medicine
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, University of California-San Francisco School of Medicine.,Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
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Mitogenomics reveals phylogenetic relationships of Arcoida (Mollusca, Bivalvia) and multiple independent expansions and contractions in mitochondrial genome size. Mol Phylogenet Evol 2020; 150:106857. [PMID: 32473333 DOI: 10.1016/j.ympev.2020.106857] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 04/09/2020] [Accepted: 05/21/2020] [Indexed: 11/24/2022]
Abstract
Arcoida, comprising about 570 species of blood cockles, is an ecologically and economically important lineage of bivalve molluscs. Current classification of arcoids is largely based on morphology, which shows widespread homoplasy. Despite two recent studies employing multi-locus analyses with broad sampling of Arcoida, evolutionary relationships among major lineages remain controversial. Interestingly, mitochondrial genomes of several ark shell species are 2-3 times larger than those found in most bilaterians, and are among the largest bilaterian mitochondrial genomes reported to date. These results highlight the need of detailed phylogenetic study to explore evolutionary relationships within Arcoida so that the evolution of mitochondrial genome size can be understood. To this end, we sequenced 17 mitochondrial genomes and compared them with publicly available data, including those from other lineages of Arcoida with emphasis on the subclade Arcoidea species. Our phylogenetic analyses indicate that Noetiidae, Cucullaeidae and Glycymerididae are nested within a polyphyletic Arcidae. Moreover, we find multiple independent expansions and potential contractions of mitochondrial genome size, suggesting that the large mitochondrial genome is not a shared ancestral feature in Arcoida. We also examined tandem repeats and inverted repeats in non-coding regions and investigated the presence of such repeats with relation to genome size variation. Our results suggest that tandem repeats might facilitate intraspecific mitochondrial genome size variation, and that inverted repeats, which could be derived from transposons, might be responsible for mitochondrial genome expansions and contractions. We show that mitochondrial genome size in Arcoida is more dynamic than previously understood and provide insights into evolution of mitochondrial genome size variation in metazoans.
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Dovrolis N, Kolios G, Spyrou GM, Maroulakou I. Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders. Brief Bioinform 2020; 20:825-841. [PMID: 29186317 DOI: 10.1093/bib/bbx154] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/17/2017] [Indexed: 12/14/2022] Open
Abstract
Almost 2500 years after Hippocrates' observations on health and its direct association to the gastrointestinal tract, a paradigm shift has recently occurred, making the gut and its symbionts (bacteria, fungi, archaea and viruses) a point of convergence for studies. It is nowadays well established that the gut microflora's compositional diversity regulates via its genes (the microbiome) the host's health and provides preliminary insights into disease progression and regulation. The microbiome's involvement is evident in immunological and physiological studies that link changes in its biodiversity to its contributions to the host's phenotype but also in neurological investigations, substantiating the aptly named gut-brain axis. The definitive mechanisms of this last bidirectional interaction will be our main focus because it presents researchers with a new conundrum. In this review, we prospect current literature for computational analysis methodologies that accommodate the need for better understanding of the microbiome-gut-brain interactions and neurological disorder onset and progression, through cross-disciplinary systems biology applications. We will present bioinformatics tools used in exploring these synergies that help build and interpret microbial 16S ribosomal RNA data sets, produced by shotgun and high-throughput sequencing of healthy and neurological disorder samples stored in biological databases. These approaches provide alternative means for researchers to form hypotheses to their inquests faster, cheaper and swith precision. The goal of these studies relies on the integration of combined metagenomics and metabolomics assessments. An accurate characterization of the microbiome and its functionality can support new diagnostic, prognostic and therapeutic strategies for neurological disorders, customized for each individual host.
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50
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Alves PR, Halanych KM, Santos CSG. The phylogeny of Nereididae (Annelida) based on mitochondrial genomes. ZOOL SCR 2020. [DOI: 10.1111/zsc.12413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paulo Ricardo Alves
- Programa de Pós‐Graduação em Biologia Marinha e Ambientes Costeiros Laboratório de Sistemática e Ecologia de Polychaeta Departamento de Biologia Marinha Universidade Federal Fluminense Niterói Brasil
| | - Kenneth M. Halanych
- Molette Laboratory for Environmental and Climate Change Studies Department of Biological Sciences Auburn University Auburn AL USA
| | - Cinthya Simone Gomes Santos
- Programa de Pós‐Graduação em Biologia Marinha e Ambientes Costeiros Laboratório de Sistemática e Ecologia de Polychaeta Departamento de Biologia Marinha Universidade Federal Fluminense Niterói Brasil
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