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Jain A, Sharma PC. Occurrence and distribution of compound microsatellites in the genomes of three economically important virus families. INFECTION GENETICS AND EVOLUTION 2021; 92:104853. [PMID: 33839312 DOI: 10.1016/j.meegid.2021.104853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 11/15/2022]
Abstract
Microsatellites are nonrandom hypervariable iterations of one to six nucleotides, existing across the coding as well as noncoding regions of virtually all known genomes, arising primarily due to polymerase slippage and unequal crossing over during replication events. Two or more perfect microsatellites located in close proximity form compound microsatellites. We studied the distribution of compound microsatellites in 118 ssDNA virus genomes belonging to three economically important virus families, namely Anelloviridae, Circoviridae, and Parvoviridae, known to predominantly infect livestock and humans. Among these virus families, 0-58.49% of perfect microsatellites were involved in the formation of compound microsatellites, the majority being located in the coding regions. No clear relationship existed between the genomic features (genome size and GC%) and compound microsatellite characteristics (relative abundance and relative density). The majority of the compound microsatellites resulted from di-SSR couples. A strong positive relationship was observed between the maximum distance value and length of compound microsatellite, percentage of microsatellites involved in the compound microsatellite formation, and relative microsatellite density. The degree of variability among microsatellite characteristics studied was largely a species-specific phenomenon. A major proportion of compound microsatellites was represented by similar motif combinations. The findings of the present study will help in better understanding of the structural, functional, and evolutionary role of compound microsatellites prevailing in the smaller genomes.
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Affiliation(s)
- Ankit Jain
- Merck Life Science Pvt. Ltd, Sector-17, Chandigarh, India
| | - Prakash C Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka Sector-16 C, New Delhi 11078, India.
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Genome-wide in silico identification and characterization of Simple Sequence Repeats in diverse completed SARS-CoV-2 genomes. GENE REPORTS 2021; 23:101020. [PMID: 33521382 PMCID: PMC7835092 DOI: 10.1016/j.genrep.2021.101020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/06/2020] [Accepted: 12/29/2020] [Indexed: 12/19/2022]
Abstract
Simple sequence repeats (SSRs) or, Microsatellites are short repeat sequences that have been extensively studied in eukaryotic (plants) and prokaryotic (bacteria) organisms. Compared to other organisms, the presence and incidence of SSR on viral genomes are less studied. With the emergence of novel infectious viruses over the past few decades, it is imperative to study the genetic diversity in such viruses to predict their evolutionary and functional changes over time. Following the emergence of SARS-CoV-2, we have assembled 121 complete genomes reported from 31 countries across the six continents for the identification and characterization of SSR repeats. Using two independent SSR identification tools, we have found remarkable consistency in the diversity of microsatellites pattern (38–42 per genome) found in the 121 analyzed SARS-CoV-2 genomes indication their important role for genome stability. Among the identified motifs, trinucleotide and hexanucleotide repeats were found to be the most abundant form followed by mono- and di-nucleotide. There were no tetra- or penta-nucleotide repeats in the analyzed SARS-CoV-2 genomes. The discovery of microsatellites in SARS-CoV-2 genomes may become useful for the population genetics, evolutionary analysis, strain identification and genetic variation.
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Hassan MM, Hussain MA, Kambal S, Elshikh AA, Gendeel OR, Ahmed SA, Altayeb RA, Muhajir AM, Mohamed SB. NeoCoV Is Closer to MERS-CoV than SARS-CoV. Infect Dis (Lond) 2020; 13:1178633720930711. [PMID: 32595278 PMCID: PMC7298434 DOI: 10.1177/1178633720930711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/07/2020] [Indexed: 01/12/2023] Open
Abstract
Recently, Coronavirus has been given considerable attention from the biomedical
community based on the emergence and isolation of a deadly coronavirus infecting
human. To understand the behavior of the newly emerging MERS-CoV requires
knowledge at different levels (epidemiologic, antigenic, and pathogenic), and
this knowledge can be generated from the most related viruses. In this study, we
aimed to compare between 3 species of Coronavirus, namely Middle East
Respiratory Syndrome (MERS-CoV), Severe Acute Respiratory Syndrome (SARS-CoV),
and NeoCoV regarding whole genomes and 6 similar proteins (E, M, N, S, ORF1a,
and ORF1ab) using different bioinformatics tools to provide a better
understanding of the relationship between the 3 viruses at the nucleotide and
amino acids levels. All sequences have been retrieved from National Center for
Biotechnology Information (NCBI). Regards to target genomes’ phylogenetic
analysis showed that MERS and SARS-CoVs were closer to each other compared with
NeoCoV, and the last has the longest relative time. We found that all
phylogenetic methods in addition to all parameters (physical and chemical
properties of amino acids such as the number of amino acid, molecular weight,
atomic composition, theoretical pI, and structural formula) indicated that
NeoCoV proteins were the most related to MERS-CoV one. All phylogenetic trees
(by both maximum-likelihood and neighbor-joining methods) indicated that NeoCoV
proteins have less evolutionary changes except for ORF1a by just
maximum-likelihood method. Our results indicated high similarity between viral
structural proteins which are responsible for viral infectivity; therefore, we
expect that NeoCoV sooner may appear in human-related infection.
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Affiliation(s)
- Mohamed M Hassan
- Bioinformatics and Biostatistics Department, National University Biomedical Research Institute, National University, Khartoum, Sudan
| | - Mohamed A Hussain
- Department of Pharmaceutical Microbiology, International University of Africa, Khartoum, Sudan
| | - Sumaya Kambal
- Bioinformatics and Biostatistics Department, National University Biomedical Research Institute, National University, Khartoum, Sudan
| | - Ahmed A Elshikh
- Department of Microbiology, Faculty of Pure and Applied Sciences, International University of Africa, Khartoum, Sudan
| | - Osama R Gendeel
- Faculty of Science and Technology, Omdurman Islamic University, Omdurman, Sudan
| | - Siddig A Ahmed
- Faculty of Science and Technology, Omdurman Islamic University, Omdurman, Sudan
| | - Rami A Altayeb
- Faculty of Science and Technology, Omdurman Islamic University, Omdurman, Sudan
| | | | - Sofia B Mohamed
- Bioinformatics and Biostatistics Department, National University Biomedical Research Institute, National University, Khartoum, Sudan
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Comparative analysis on precise distribution-patterns of microsatellites in HIV-1 with differential statistical method. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Genome-wide In Silico Analysis, Characterization and Identification of Microsatellites in Spodoptera littoralis Multiple nucleopolyhedrovirus (SpliMNPV). Sci Rep 2016; 6:33741. [PMID: 27650818 PMCID: PMC5030640 DOI: 10.1038/srep33741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 09/01/2016] [Indexed: 01/10/2023] Open
Abstract
In this study, we undertook a survey to analyze the distribution and frequency of microsatellites or Simple Sequence Repeats (SSRs) in Spodoptera littoralis multiple nucleopolyhedrovirus (SpliMNPV) genome (isolate AN-1956). Out of the 55 microsatellite motifs, identified in the SpliMNPV-AN1956 genome using in silico analysis (inclusive of mono-, di-, tri- and hexa-nucleotide repeats), 39 were found to be distributed within coding regions (cSSRs), whereas 16 were observed to lie within intergenic or noncoding regions. Among the 39 motifs located in coding regions, 21 were located in annotated functional genes whilst 18 were identified in unknown functional genes (hypothetical proteins). Among the identified motifs, trinucleotide (80%) repeats were found to be the most abundant followed by dinucleotide (13%), mononucleotide (5%) and hexanucleotide (2%) repeats. The 39 motifs located within coding regions were further validated in vitro by using PCR analysis, while the 21 motifs located within known functional genes (15 genes) were characterized using nucleotide sequencing. A comparison of the sequence analysis data of the 21 sequenced cSSRs with the published sequences is presented. Finally, the developed SSR markers of the 39 motifs were further mapped/localized onto the SpliMNPV-AN1956 genome. In conclusion, the SSR markers specific to SpliMNPV, developed in this study, could be a useful tool for the identification of isolates and analysis of genetic diversity and viral evolutionary status.
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Uyaguari-Diaz MI, Chan M, Chaban BL, Croxen MA, Finke JF, Hill JE, Peabody MA, Van Rossum T, Suttle CA, Brinkman FSL, Isaac-Renton J, Prystajecky NA, Tang P. A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples. MICROBIOME 2016; 4:20. [PMID: 27391119 PMCID: PMC5011856 DOI: 10.1186/s40168-016-0166-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/04/2016] [Indexed: 05/16/2023]
Abstract
BACKGROUND Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary. RESULTS We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels. CONCLUSION This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.
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Affiliation(s)
- Miguel I. Uyaguari-Diaz
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Michael Chan
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Bonnie L. Chaban
- South Kensington Campus, Imperial College London, Sir Ernst Chain Building, London, SW7 2AZ UK
| | - Matthew A. Croxen
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Jan F. Finke
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4 Canada
| | - Michael A. Peabody
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Thea Van Rossum
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8 Canada
| | - Fiona S. L. Brinkman
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Judith Isaac-Renton
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Natalie A. Prystajecky
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
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Hatcher EL, Wang C, Lefkowitz EJ. Genome variability and gene content in chordopoxviruses: dependence on microsatellites. Viruses 2015; 7:2126-46. [PMID: 25912716 PMCID: PMC4411693 DOI: 10.3390/v7042126] [Citation(s) in RCA: 15] [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: 02/27/2015] [Revised: 03/24/2015] [Accepted: 04/17/2015] [Indexed: 11/20/2022] Open
Abstract
To investigate gene loss in poxviruses belonging to the Chordopoxvirinae subfamily, we assessed the gene content of representative members of the subfamily, and determined whether individual genes present in each genome were intact, truncated, or fragmented. When nonintact genes were identified, the early stop mutations (ESMs) leading to gene truncation or fragmentation were analyzed. Of all the ESMs present in these poxvirus genomes, over 65% co-localized with microsatellites—simple sequence nucleotide repeats. On average, microsatellites comprise 24% of the nucleotide sequence of these poxvirus genomes. These simple repeats have been shown to exhibit high rates of variation, and represent a target for poxvirus protein variation, gene truncation, and reductive evolution.
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Affiliation(s)
- Eneida L Hatcher
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276/11, 845 19th St S, Birmingham, AL 35222, USA.
| | - Chunlin Wang
- Stanford Genome Technology Center, Stanford University, 855 California Ave, Palo Alto, CA 94304, USA.
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276/11, 845 19th St S, Birmingham, AL 35222, USA.
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