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Han S, Li S, Li L, Li S. Genetic characterization of four bacteriophages of Salmonella enterica derived from different geographic regions in China via genomic comparison. Res Vet Sci 2025; 189:105608. [PMID: 40199046 DOI: 10.1016/j.rvsc.2025.105608] [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: 07/06/2024] [Revised: 09/27/2024] [Accepted: 03/07/2025] [Indexed: 04/10/2025]
Abstract
Based on the AT content > GC content in four Salmonella enterica lytic bacteriophage genomes, information entropy analysis revealed that overall nucleotide usage bias is shaped in the gene population. This genetic feature directly contributes to synonymous codons tending toward the A/T end rather than the C/G end. Furthermore, the interplay between the nucleotide composition constraint from the bacteriophage itself and the natural selection caused by outside environments forces our bacteriophages into similar evolutionary trends in terms of overall codon usage patterns. We identified the nucleotide composition constraint which plays an important role in shaping synonymous codon usage patterns including the keto skew at the first codon position, the pyrimidine skew at the second position and the AT skew at the third position. Although the four bacteriophages were isolated from different geographical regions in China, they display similar evolutionary trends in terms of genomic organization and synonymous codon usage, which are strongly influenced by the nucleotide composition constraint of the bacteriophage. The findings of the present study reveal important details of the evolutionary and host-pathogen interactions of Salmonella enterica, which will benefit the efficient utilization of phages for therapeutic and other applications.
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Affiliation(s)
- Shengyi Han
- Qinghai University, Xining 810016, China; College of Animal Science and Veterinary Science, Xining 810016, China
| | - Shuping Li
- Qinghai University, Xining 810016, China; College of Animal Science and Veterinary Science, Xining 810016, China
| | - Lingxia Li
- Qinghai University, Xining 810016, China; College of Animal Science and Veterinary Science, Xining 810016, China; College of Agriculture and Animal Husbandry, Xining 810016, China.
| | - Shengqing Li
- Qinghai University, Xining 810016, China; College of Animal Science and Veterinary Science, Xining 810016, China.
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2
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Oyeniran KA, Tenibiaje MO. Detectable episodic positive selection in the virion strand a-strain Maize streak virus genes may have a role in its host adaptation. Virus Genes 2025:10.1007/s11262-025-02157-z. [PMID: 40237943 DOI: 10.1007/s11262-025-02157-z] [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: 11/06/2024] [Accepted: 04/06/2025] [Indexed: 04/18/2025]
Abstract
Maize streak virus (MSV) has four genes: cp, encoding the coat protein; mp, the movement protein; and repA and rep, encoding two distinct replication-associated proteins from an alternatively spliced transcript. These genes play roles in encapsidation, movement, replication, and interactions with the external environment, making them prone to stimuli-driven molecular adaptation. We accomplished selection studies on publicly available curated, recombination-free, complete coding sequences for representative A-strain maize streak virus (MSV-A) cp and mp genes. We found evidence of gene-wide selection in these two MSV genes at specific sites within the genes (cp 1.23% and mp 0.99%). Positively selected sites have amino acids that are 60% hydrophilic and 40% hydrophobic in nature. We found significant evidence of positive selection at branches (cp: 0.76 and mp:1.66%) representing the diversity of MSV-A-strain in South Africa, which is related to the MSV-A-matA isolate (GenBank accession number: AF329881), well disseminated and adapted to the maize plant in sub-Saharan Africa. In the mp gene, selection significantly intensified for the overall diversities of the MSV-A sequences and those more related to the MSV-Mat-A isolate. These findings reveal that despite predominantly undergoing non-diversifying selection, the detectable diversifying positive selection observed in these genes may play a major role in MSV-A host adaptive evolution, ensuring sufficient pathogenicity for onward transmission without killing the host.
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Affiliation(s)
- Kehinde A Oyeniran
- Department of Biological Sciences, Bamidele Olumilua University of Education Science and Technology, P.M.B. 250, Ikere-Ekiti, Ekiti, Nigeria.
- Plant Systems Biology, International Centre for Genetic Engineering and Biotechnology, Cape Town, 7925, South Africa.
| | - Mobolaji O Tenibiaje
- Department of Computing and Information Science, Bamidele Olumilua University of Education Science and Technology, P.M.B. 250, Ikere-Ekiti, Ekiti, Nigeria
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3
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Feng X, Liu Z, Mo Y, Zhang S, Ma XX. Role of nucleotide pair frequency and synonymous codon usage in the evolution of bovine viral diarrhea virus. Arch Virol 2025; 170:64. [PMID: 40011265 DOI: 10.1007/s00705-025-06250-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Accepted: 11/26/2024] [Indexed: 02/28/2025]
Abstract
Synonymous codon usage plays an important role in the adaptation of viruses to their hosts. Bovine viral diarrhea virus (BVDV) relies on a high mutation rate in its genome to achieve the necessary fitness in a particular host. However, the question of which selective forces influence nucleotide pair and synonymous codon usage patterns in different BVDV genotypes remains unresolved. Here, 169 BVDV strains isolated at different times in various countries were analyzed to compare their dinucleotide frequency and synonymous codon usage. Examination of the nucleotide usage pattern in the open reading frame (ORF) of BVDV revealed a significantly higher frequency of purine than pyrimidine, with the highest extent of nucleotide usage bias observed in the first codon position. Moreover, a nucleotide pair bias, especially favoring CpG dinucleotides, was observed in all of the genotypes. Together, the nucleotide composition constraints and nucleotide pair bias appear to have influenced the overall codon usage pattern. Nucleotide pair and synonymous codon usage biases were associated with individual genotypes to different degrees. Of particular note, BVDV-1 exhibited more variation in its nucleotide pair and synonymous codon usage than BVDV-2 and BVDV-3, suggesting that these patterns are shaped both by selection of mutations in the viral genome and translational selection in the host.
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Affiliation(s)
- Xili Feng
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Zeyu Liu
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China
| | - Yongli Mo
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China
| | - Shubin Zhang
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China
| | - Xiao-Xia Ma
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China.
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Mohan G, Choudhury A, Bhat J, Phartyal R, Lal R, Verma M. Human Riboviruses: A Comprehensive Study. J Mol Evol 2025; 93:11-37. [PMID: 39739017 DOI: 10.1007/s00239-024-10221-9] [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: 06/03/2024] [Accepted: 11/20/2024] [Indexed: 01/02/2025]
Abstract
The urgency to understand the complex interactions between viruses, their animal reservoirs, and human populations has been necessitated by the continuous spread of zoonotic viral diseases as evidenced in epidemics and pandemics throughout human history. Riboviruses are involved in some of the most prevalent human diseases, responsible for causing epidemics and pandemics. These viruses have an animal origin and have been known to cross the inter-species barrier time and time again, eventually infecting human beings. Their evolution has been a long road to harbour important adaptations for increasing fitness, mutability and virulence; a result of natural selection and mutation pressure, making these viruses highly infectious and difficult to counter. Accumulating favourable mutations in the course, they imitate the GC content and codon usage patterns of the host for maximising the chances of infection. A myriad of viral and host factors determine the fate of specific viral infections, which may include virus protein and host receptor compatibility, host restriction factors and others. Thus, understanding the biology, transmission and molecular mechanisms of Riboviruses is essential for the development of effective antiviral treatments, vaccine development and strategies to prevent and control viral infections. Keeping these aspects in mind, this review aims to provide a holistic approach towards understanding Riboviruses.
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Affiliation(s)
- Gauravya Mohan
- Department of Biological Sciences, Sri Venkateswara College, University of Delhi (South Campus), New Delhi, 110021, India
| | - Akangkha Choudhury
- Department of Biological Sciences, Sri Venkateswara College, University of Delhi (South Campus), New Delhi, 110021, India
| | - Jeevika Bhat
- Department of Biological Sciences, Sri Venkateswara College, University of Delhi (South Campus), New Delhi, 110021, India
| | - Rajendra Phartyal
- Department of Zoology, Sri Venkateswara College, University of Delhi (South Campus), New Delhi, 110021, India
| | - Rup Lal
- PhiXGen Private Limited, Gurugram, Haryana, 122001, India
| | - Mansi Verma
- Department of Zoology, Hansraj College, University of Delhi, Mahatma Hansraj Marg, Malkaganj, Delhi, 110007, India.
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Thomas PD, Ferrer MF, Lozano MJ, Gómez RM. A study on the codon usage bias of arenavirus common genes. Front Microbiol 2025; 15:1490076. [PMID: 39917269 PMCID: PMC11799557 DOI: 10.3389/fmicb.2024.1490076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Accepted: 12/30/2024] [Indexed: 02/09/2025] Open
Abstract
Introduction The Arenaviridae family consists of the genera Mammarenavirus, Reptarenavirus, Hartmanivirus, Antennavirus and Innmovirus. The codon usage bias between the different genera has not yet been studied comparatively. Methods We retrieved the arenavirus genome sequences from public databases and used bioinformatics tools to compare the codon usage bias between the different genera for the GPC, NP and L proteins, common to all arenaviruses. Results and discussion Hartmaniviruses show a larger codon usage bias, which can be partially explained by mutational bias. Patterns of relative use of synonymous codons were maintained within genera, with individual genera differing in their preference for the third nucleotide position in synonymous codons. Of the three proteins examined, the ARN polymerase L protein exhibited a slightly stronger codon usage bias, but overall, the patterns were repeated between genera for the three proteins examined. Our results suggest that codon usage pattern bias in arenaviruses is influenced by selection pressure and to a lesser extent by mutational selection.
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Affiliation(s)
- Pablo Daniel Thomas
- Laboratorio de Patogénesis Viral, Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, La Plata, Argentina
| | - María Florencia Ferrer
- Laboratorio de Patogénesis Viral, Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, La Plata, Argentina
| | - Mauricio J. Lozano
- Laboratorio de Genómica y Ecología Molecular de Microorganismos del Suelo Asociados con Plantas, Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, La Plata, Argentina
| | - Ricardo Martín Gómez
- Laboratorio de Patogénesis Viral, Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, La Plata, Argentina
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Guo F, Tan H, Yang J, Jia R, Wang R, Wu L, Pan F, Kang K, Xie W, Li Y, Fan K. Insight into the codon usage patterns and adaptation of Tembusu Virus. Poult Sci 2025; 104:104651. [PMID: 39667183 PMCID: PMC11699206 DOI: 10.1016/j.psj.2024.104651] [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: 07/29/2024] [Revised: 12/05/2024] [Accepted: 12/06/2024] [Indexed: 12/14/2024] Open
Abstract
Since its emergence in 2010, Tembusu virus (TMUV) has rapidly spread across poultry populations in Asia, leading to substantial economic losses in these areas. Here, we investigate the codon usage patterns (CUPs) underlying TMUV's adaptation and evolutionary dynamics within host environments. Phylogenetic and compositional analyses consistently classify TMUV into four evolutionary lineages-Clusters 1, 2, 3, and ancestral TMUV-with Cluster 2 emerging as the dominant lineage. Codon adaptation index (CAI) analysis reveals that this lineage of TMUV show best adapted to the CUPs of duck than other lineages, underscoring the role of natural selection in shaping viral evolution, a finding in line with evidence that CUPs in the TMUV genome is predominantly shaped by natural selection. Furthermore, TMUV exhibits markedly higher adaptation to the CUPs of poultry hosts (duck, goose, and chicken) compared to potential host humans or vector mosquito. Thus, species-specific adaptability to the host environment may be a reason account for the distinct infectivity and clinic outcome of TMUV acted on hosts. Analysis of dinucleotide distribution reveals significant suppression of CpG and UpA dinucleotides in the TMUV genome, reflecting adaptive pressures to evade vertebrate immune responses. During transmission, TMUV shows increasing alignment with host CUPs and a continuous reduction in CpG dinucleotides, potentially enhancing its fitness within host microenvironments. This work advances our understanding of the basic biology underlying TMUV epidemiology, pathogenicity, and species-specific adaptation.
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Affiliation(s)
- Fucheng Guo
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China; Fujian Provincial Key Laboratory for Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan, 364012, Fujian, China
| | - Huiming Tan
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jinjin Yang
- Technology Center of Zhanjiang Customs District, Zhanjiang, 524000, Guangdong, China
| | - Rumin Jia
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Ruichen Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lie Wu
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Fengzhi Pan
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Kai Kang
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Weitian Xie
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Youquan Li
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Kewei Fan
- Fujian Provincial Key Laboratory for Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan, 364012, Fujian, China.
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Sun M, Wang J, Smagghe G, Dai R, Wang X, Yang Y, Li M, You S. Description of mitochondrial genomes and phylogenetic analysis of Megophthalminae (Hemiptera: Cicadellidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2024; 24:9. [PMID: 39657582 PMCID: PMC11631095 DOI: 10.1093/jisesa/ieae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 09/20/2024] [Accepted: 10/30/2024] [Indexed: 12/12/2024]
Abstract
To elucidate phylogenetic relationships within the leafhopper's subfamily Megophthalminae (Hemiptera: Cicadellidae), mitogenomes of 12 species of the subfamily were sequenced and assembled. These were added to the mitogenomes of the eight other species that are currently available. Mitogenome size ranged from 15,193 bp in Onukigallia onukii (Matsumura, 1912) to 15,986 bp in Multinervis guangxiensis (Li and Li, 2013), they all contained 37 genes, and gene order was similar to that in other leafhoppers. Nucleotide composition analysis showed that the AT content was higher than that of GC, and the protein-coding genes usually ended with A/T at the 3rd codon position. The Ka/Ks ratio showed that the CYTB gene has the slowest evolutionary rate, while ND4 is the gene with the fastest evolutionary rate. Relative synonymous codon usage analysis revealed the most frequently used codon was UUA (L), followed by CGA (R), and the least frequently used codon was CCG (P). Parity plot and neutrality plot analyses showed that the codon usage bias of mitochondrial genes was influenced by natural selection and mutation pressure. However, natural selection plays a major role, while the effect of mutation pressure was small. Effective number of codons values were 40.15-49.17, which represented relatively low codon bias. Phylogenetic analyses based on three datasets (AA, 13PCG, 13PCG_2rRNA) using two methods (maximum likelihood and Bayesian inference). In the obtained topology, the Megophthalminae species were clustered into a monophyletic group. In conclusion, our results clarify structural modules of the mitochondrial genes and confirm the monophyly of Megophthalminae within Cicadellidae.
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Affiliation(s)
- Mingming Sun
- Department of Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Guiyang, Guizhou, China
| | - Jiajia Wang
- Department of Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Guiyang, Guizhou, China
- Department of College of Biology and Food Engineering, Chuzhou University, Chuzhou, Anhui, China
| | - Guy Smagghe
- Department of Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Guiyang, Guizhou, China
- Department of Plants and Crops, Ghent University, Ghent, Belgium
- Department of Biology, Vrije Universiteit Brussels (VUB), Brussels, Belgium
| | - RenHuai Dai
- Department of Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Guiyang, Guizhou, China
| | - Xianyi Wang
- Department of Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Guiyang, Guizhou, China
- Department of Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yanqiong Yang
- Department of Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Guiyang, Guizhou, China
| | - Min Li
- Department of Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Guiyang, Guizhou, China
| | - Siying You
- Department of Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Guiyang, Guizhou, China
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Zhao Y, Su X, He D. Codon Usage Analysis Reveals Distinct Evolutionary Patterns and Host Adaptation Strategies in Duck Hepatitis Virus 1 (DHV-1) Phylogroups. Viruses 2024; 16:1380. [PMID: 39339856 PMCID: PMC11437458 DOI: 10.3390/v16091380] [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: 06/22/2024] [Revised: 08/18/2024] [Accepted: 08/28/2024] [Indexed: 09/30/2024] Open
Abstract
Duck hepatitis virus 1 (DHV-1) is a major threat to the global poultry industry, causing significant economic losses due to high mortality rates in young ducklings. To better understand the evolution and host adaptation strategies of DHV-1, we conducted a comprehensive codon usage analysis of DHV-1 genomes. Our phylogenetic analysis revealed three well-supported DHV-1 phylogroups (Ia, Ib, and II) with distinct genetic diversity patterns. Comparative analyses of the codon usage bias and dinucleotide abundance uncovered a strong preference for A/U-ended codons and a biased pattern of dinucleotide usage in the DHV-1 genome, with CG dinucleotides being extremely underrepresented. Effective number of codons (ENC) analysis indicated a low codon usage bias in the DHV-1 ORF sequences, suggesting adaptation to host codon usage preferences. PR2 bias, ENC plot, and neutrality analyses revealed that both mutation pressure and natural selection influence the codon usage patterns of DHV-1. Notably, the three DHV-1 phylogroups exhibited distinct evolutionary trends, with phylogroups Ia and Ib showing evidence of neutral evolution accompanied by selective pressure, while the phylogroup II evolution was primarily driven by random genetic drift. Comparative analysis of the codon usage indices (CAI, RCDI, and SiD) among the phylogroups highlighted significant differences between subgroups Ia and Ib, suggesting distinct evolutionary pressures or adaptations influencing their codon usage. These findings contribute to our understanding of DHV-1 evolution and host adaptation, with potential implications for the development of effective control measures and vaccines.
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Affiliation(s)
| | | | - Dongchang He
- Department of Veterinary Medicine, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China
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Shan KJ, Wu C, Tang X, Lu R, Hu Y, Tan W, Lu J. Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad003. [PMID: 38862422 PMCID: PMC11425058 DOI: 10.1093/gpbjnl/qzad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 06/13/2024]
Abstract
The monkeypox virus (mpox virus, MPXV) epidemic in 2022 has posed a significant public health risk. Yet, the evolutionary principles of MPXV remain largely unknown. Here, we examined the evolutionary patterns of protein sequences and codon usage in MPXV. We first demonstrated the signal of positive selection in OPG027, specifically in the Clade I lineage of MPXV. Subsequently, we discovered accelerated protein sequence evolution over time in the variants responsible for the 2022 outbreak. Furthermore, we showed strong epistasis between amino acid substitutions located in different genes. The codon adaptation index (CAI) analysis revealed that MPXV genes tended to use more non-preferred codons compared to human genes, and the CAI decreased over time and diverged between clades, with Clade I > IIa and IIb-A > IIb-B. While the decrease in fatality rate among the three groups aligned with the CAI pattern, it remains unclear whether this correlation was coincidental or if the deoptimization of codon usage in MPXV led to a reduction in fatality rates. This study sheds new light on the mechanisms that govern the evolution of MPXV in human populations.
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Affiliation(s)
- Ke-Jia Shan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
- Sinovac Biotech Ltd., Beijing 100085, China
| | - Changcheng Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Roujian Lu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Yaling Hu
- Sinovac Biotech Ltd., Beijing 100085, China
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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10
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Kaushik R, Kumar N, Yadav P, Sircar S, Shete-Aich A, Singh A, Tomar S, Launey T, Malik YS. Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity. Microorganisms 2024; 12:696. [PMID: 38674640 PMCID: PMC11052288 DOI: 10.3390/microorganisms12040696] [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: 03/06/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Neboviruses (NeVs) from the Caliciviridae family have been linked to enteric diseases in bovines and have been detected worldwide. As viruses rely entirely on the cellular machinery of the host for replication, their ability to thrive in a specific host is greatly impacted by the specific codon usage preferences. Here, we systematically analyzed the codon usage bias in NeVs to explore the genetic and evolutionary patterns. Relative Synonymous Codon Usage and Effective Number of Codon analyses indicated a marginally lower codon usage bias in NeVs, predominantly influenced by the nucleotide compositional constraints. Nonetheless, NeVs showed a higher codon usage bias for codons containing G/C at the third codon position. The neutrality plot analysis revealed natural selection as the primary factor that shaped the codon usage bias in both the VP1 (82%) and VP2 (57%) genes of NeVs. Furthermore, the NeVs showed a highly comparable codon usage pattern to bovines, as reflected through Codon Adaptation Index and Relative Codon Deoptimization Index analyses. Notably, yak NeVs showed considerably different nucleotide compositional constraints and mutational pressure compared to bovine NeVs, which appear to be predominantly host-driven. This study sheds light on the genetic mechanism driving NeVs' adaptability, evolution, and fitness to their host species.
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Affiliation(s)
- Rahul Kaushik
- Biotechnology Research Center, Technology Innovation Institute, Masdar City, Abu Dhabi P.O. Box 9639, United Arab Emirates;
| | - Naveen Kumar
- Diagnostics and Vaccines Group, ICAR—National Institute of High Security Animal Diseases, Bhopal 462021, Madhya Pradesh, India;
| | - Pragya Yadav
- Maximum Containment Facility, ICMR—National Institute of Virology, Pune 411001, Maharashtra, India; (P.Y.); (A.S.-A.)
| | - Shubhankar Sircar
- Department of Animal Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Anita Shete-Aich
- Maximum Containment Facility, ICMR—National Institute of Virology, Pune 411001, Maharashtra, India; (P.Y.); (A.S.-A.)
| | - Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; (A.S.); (S.T.)
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; (A.S.); (S.T.)
| | - Thomas Launey
- Biotechnology Research Center, Technology Innovation Institute, Masdar City, Abu Dhabi P.O. Box 9639, United Arab Emirates;
| | - Yashpal Singh Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana 141004, Punjab, India
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Yang Q, Xin C, Xiao QS, Lin YT, Li L, Zhao JL. Codon usage bias in chloroplast genes implicate adaptive evolution of four ginger species. FRONTIERS IN PLANT SCIENCE 2023; 14:1304264. [PMID: 38169692 PMCID: PMC10758403 DOI: 10.3389/fpls.2023.1304264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
Abstract
Codon usage bias (CUB) refers to different codons exhibiting varying frequencies of usage in the genome. Studying CUB is crucial for understanding genome structure, function, and evolutionary processes. Herein, we investigated the codon usage patterns and influencing factors of protein-coding genes in the chloroplast genomes of four sister genera (monophyletic Roscoea and Cautleya, and monophyletic Pommereschea and Rhynchanthus) from the Zingiberaceae family with contrasting habitats in southwestern China. These genera exhibit distinct habitats, providing a unique opportunity to explore the adaptive evolution of codon usage. We conducted a comprehensive analysis of nucleotide composition and codon usage on protein-coding genes in the chloroplast genomes. The study focused on understanding the relationship between codon usage and environmental adaptation, with a particular emphasis on genes associated with photosynthesis. Nucleotide composition analysis revealed that the overall G/C content of the coding genes was ˂ 48%, indicating an enrichment of A/T bases. Additionally, synonymous and optimal codons were biased toward ending with A/U bases. Natural selection is the primary factor influencing CUB characteristics, particularly photosynthesis-associated genes. We observed differential gene expressions related to light adaptation among sister genera inhabiting different environments. Certain codons were favored under specific conditions, possibly contributing to gene expression regulation in particular environments. This study provides insights into the adaptive evolution of these sister genera by analyzing CUB and offers theoretical assistance for understanding gene expression and regulation. In addition, the data support the relationship between RNA editing and CUB, and the findings shed light on potential research directions for investigating adaptive evolution.
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Affiliation(s)
- Qian Yang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Cheng Xin
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Qing-Song Xiao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Ya-Ting Lin
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Li Li
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Jian-Li Zhao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
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12
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Guo F, Yang J, Abd El-Aty AM, Wang R, Ju X. Base composition, adaptation, and evolution of goose astroviruses: codon-based investigation. Poult Sci 2023; 102:103029. [PMID: 37713803 PMCID: PMC10511809 DOI: 10.1016/j.psj.2023.103029] [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: 03/24/2023] [Revised: 07/24/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023] Open
Abstract
Goose astroviruses (GoAstVs) are causative agents that account for fatal infection of goslings characterized by visceral urate deposition, resulting in severe economic losses in major goose-producing regions in China since 2017. In this study, we sought to unravel the intrinsic properties associated with adaptation and evolution in the host environment of GoAstVs. Consistent results from phylogenetic analysis and correspondence analysis performed on the codon usage patterns (CUPs) reveal 2 clusters of GoAstVs, namely, GoAstV-1 and GoAstV-2. However, multiple similar compositional characteristics were found, despite the high divergence between GoAstV-1 and GoAstV-2. Studies on the base composition of GoAstVs reveal an A/U bias, indicating a compositional constraint, while natural selection prevailed in determining the CUPs in the virus genome based on our neutrality plot analysis, reflecting high adaptive pressure to fit the host environment. Codon adaptation index (CAI) analysis revealed a higher degree of fitness to the CUPs of the corresponding host for GoAstVs than avian influenza virus and betacoronaviruses, which may be a favorable factor contributing to the high pathogenicity and wide distribution of GoAstVs in goslings. In addition, GoAstVs were less adapted to ducks and chickens, with significantly lower CAI values than to geese, which may be a reason for the different prevalence of GoAstVs among these species. Extensive investigations on dinucleotide distribution revealed a significant suppression of the CpG and UpA motifs in the virus genome, which may facilitate adaptation to the host's innate immune system by evading surveillance. In addition, our study reported the trends of increasing fitness to the host's microenvironment for GoAstVs through increasing adaptation to host CUPs and ongoing reduction of CpG motifs in the virus genome. The present analysis deepens our understanding of the basic biology, pathogenesis, adaptation and evolutionary pattern of GoAstVs, and contributes to the development of novel antiviral strategies.
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Affiliation(s)
- Fucheng Guo
- Department of Veterinary Medicine, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jinjin Yang
- Technology Center of Zhanjiang Customs District, Zhanjiang, 524000, Guangdong, China
| | - A M Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt; Department of Medical Pharmacology, Medical Faculty, Ataturk University, Erzurum 25240, Turkey
| | - Ruichen Wang
- Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing 102206, China
| | - Xianghong Ju
- Department of Veterinary Medicine, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China; Marine Medical Research and Development Centre, Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China.
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13
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Li G, Chen X, Li X, Liang Y, Li X, Liang W, Yan Z, Wang Y, Wang Y, Luo J, Guo XF, Zhu XT. Analyzing the Evolution and Host Adaptation of the Rabies Virus from the Perspective of Codon Usage Bias. Transbound Emerg Dis 2023; 2023:4667253. [PMID: 40303686 PMCID: PMC12016951 DOI: 10.1155/2023/4667253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/02/2023] [Accepted: 09/12/2023] [Indexed: 05/02/2025]
Abstract
Rabies virus (RABV) is a highly pathogenic virus that causes a fatal disease in humans and other mammals, but the mechanism of its evolution, spread, and spillover remains unknown. In this study, we analyzed the codon usage pattern of 2,018 RABV full-length genome sequences from 79 countries collected between 1931 and 2021 to provide an insight into its molecular evolution and unravel its unknown host-adapted pattern. We found that RABV exhibited a weak codon usage bias, with a preference for the codons ending in A (28.10 ± 0.01) or U (26.43 ± 0.02). Moreover, natural selection plays a major role in shaping the codon usage bias of the RABV. Notably, nearly half of the 18 codons in the virus were best matched to the hosts' most abundant isoacceptor tRNAs, which might account for the wide range of RABV hosts. Furthermore, significant differences were observed in the codon usage patterns of RABV for different host species, suggesting that codon usage bias may be influenced by host-specific factors. In conclusion, our study reveals codon usage patterns of RABV that may help in the development of control strategies and effective vaccines and therapies against this deadly virus.
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Affiliation(s)
- Gen Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xuhong Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xin Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yinyi Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiaolong Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Weiheng Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zhibin Yan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yueming Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yang Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jun Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Feng Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- South China Biological Medicine, Guangzhou 511300, China
| | - Xiu-Tong Zhu
- South China Biological Medicine, Guangzhou 511300, China
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14
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Aktürk Dizman Y. Codon usage bias analysis of the gene encoding NAD +-dependent DNA ligase protein of Invertebrate iridescent virus 6. Arch Microbiol 2023; 205:352. [PMID: 37812231 DOI: 10.1007/s00203-023-03688-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023]
Abstract
The genome of Invertebrate iridescent virus 6 (IIV6) contains a sequence that shows similarity to eubacterial NAD+-dependent DNA ligases. The 615-amino acid open reading frame (ORF 205R) consists of several domains, including an N-terminal domain Ia, followed by an adenylation domain, an OB-fold domain, a helix-hairpin-helix (HhH) domain, and a BRCT domain. Notably, the zinc finger domain, typically present in NAD+-dependent DNA ligases, is absent in ORF 205R. Since the protein encoded by ORF 205R (IIV6 DNA ligase gene) is involved in critical functions such as DNA replication, modification, and repair, it is crucial to comprehend the codon usage associated with this gene. In this paper, the codon usage bias (CUB) in DNA ligase gene of IIV6 and 11 reference iridoviruses was analyzed by comparing the nucleotide contents, relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), relative abundance of dinucleotides and other indices. Both the base content and the RCSU analysis indicated that the A- and T-ending codons were mostly favored in the DNA ligase gene of IIV6. The ENC value of 35.64 implied a high CUB in the IIV6 DNA ligase gene. The ENC plot, neutrality plot, parity rule 2 plot, correspondence analysis revealed that mutation pressure and natural selection had an impact on the CUB of the IIVs DNA ligase genes. Additionally, the analysis of codon adaptation index demonstrated that the IIV6 DNA ligase gene is strongly adapted to its host. These findings will improve our comprehension of the CUB of IIV6 DNA ligase and reference genes, which may provide the required information for a fundamental evolutionary analysis of these genes.
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Affiliation(s)
- Yeşim Aktürk Dizman
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, 53100, Rize, Turkey.
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15
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Rani S, Mamathashree MN, Bharthi I U, Patil SS, Krishnamoorthy P, Shueb M, Pandey RK, Suresh KP. Comprehensive examination on codon usage bias pattern of the Bovine Ephemeral fever virus. J Biomol Struct Dyn 2023; 42:10593-10603. [PMID: 37705249 DOI: 10.1080/07391102.2023.2258220] [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: 05/30/2023] [Accepted: 09/02/2023] [Indexed: 09/15/2023]
Abstract
Bovine Ephemeral Fever Virus (BEFV) is a non-contagious virus that commonly infects cattle and water buffalo, reduces milk productivity, decreases the quality of beef, and causes an adverse economic impact on the global livestock industry. However, the evolution of BEFV is unclear, and uncertainty exists regarding its global geodynamics. Consequently, this study aims to comprehend the pattern of viral evolution and gene expression in the BEFV genes G, M, N, and P, including synonymous codons. Additionally, we performed recombination analyses, which exclusively detected recombination signals in the G- and P-genes. Subsequently, a phylogenetic tree was constructed to validate and support these findings. The codon usage bias results showed that the BEFV-selected genes were influenced by both natural and mutation pressure. Furthermore, nucleotide A is more abundant in all the selected genes. The eNC values, ranging from 42.99 to 47.10, revealed the presence of moderate codon usage bias, where gene P exhibited the highest and gene G had the lowest codon usage bias. The neutrality and PR-2 plots, specified codon usage patterns of the genes, are also being shaped by strong selectional pressure. This comprehensive analysis of BEFV genes (G, M, N, and P) sheds light on the molecular evolutionary patterns, co-adaptation, and different genes expression in diverse regions, facilitating the development of preventative programs and insights into viral pathogenesis and vaccine design.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Swati Rani
- Disease Informatics, Spatial Epidemiology Lab, ICAR - National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
| | - M N Mamathashree
- Disease Informatics, Spatial Epidemiology Lab, ICAR - National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
| | - Uma Bharthi I
- Disease Informatics, Spatial Epidemiology Lab, ICAR - National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
| | - S S Patil
- Disease Informatics, Spatial Epidemiology Lab, ICAR - National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
| | - P Krishnamoorthy
- Disease Informatics, Spatial Epidemiology Lab, ICAR - National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
| | - Mohammad Shueb
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, India
| | - Rajan Kumar Pandey
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - K P Suresh
- Disease Informatics, Spatial Epidemiology Lab, ICAR - National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
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16
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Wang L, Zhao H, Wang Z, Ding S, Qin L, Jiang R, Deng X, He Z, Li L. An Evolutionary Perspective of Codon Usage Pattern, Dinucleotide Composition and Codon Pair Bias in Prunus Necrotic Ringspot Virus. Genes (Basel) 2023; 14:1712. [PMID: 37761852 PMCID: PMC10530913 DOI: 10.3390/genes14091712] [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: 07/31/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Prunus necrotic ringspot virus (PNRSV) is a significant virus of ornamental plants and fruit trees. It is essential to study this virus due to its impact on the horticultural industry. Several studies on PNRSV diversity and phytosanitary detection technology were reported, but the content on the codon usage bias (CUB), dinucleotide preference and codon pair bias (CPB) of PNRSV is still uncertain. We performed comprehensive analyses on a dataset consisting of 359 coat protein (CP) gene sequences in PNRSV to examine the characteristics of CUB, dinucleotide composition, and CPB. The CUB analysis of PNRSV CP sequences showed that it was not only affected by natural selection, but also affected by mutations, and natural selection played a more significant role compared to mutations as the driving force. The dinucleotide composition analysis showed an over-expression of the CpC/GpA dinucleotides and an under-expression of the UpA/GpC dinucleotides. The dinucleotide composition of the PNRSV CP gene showed a weak association with the viral lineages and hosts, but a strong association with viral codon positions. Furthermore, the CPB of PNRSV CP gene is low and is related to dinucleotide preference and codon usage patterns. This research provides reference for future research on PNRSV genetic diversity and gene evolution mechanism.
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Affiliation(s)
- Lingqi Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China;
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Haiting Zhao
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Zhilei Wang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Shiwen Ding
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Lang Qin
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Runzhou Jiang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Xiaolong Deng
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Zhen He
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Liangjun Li
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China;
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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17
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Wu X, Shan K, Zan F, Tang X, Qian Z, Lu J. Optimization and Deoptimization of Codons in SARS-CoV-2 and Related Implications for Vaccine Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205445. [PMID: 37267926 PMCID: PMC10427376 DOI: 10.1002/advs.202205445] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/08/2023] [Indexed: 06/04/2023]
Abstract
The spread of coronavirus disease 2019 (COVID-19), caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2), has progressed into a global pandemic. To date, thousands of genetic variants have been identified among SARS-CoV-2 isolates collected from patients. Sequence analysis reveals that the codon adaptation index (CAI) values of viral sequences have decreased over time but with occasional fluctuations. Through evolution modeling, it is found that this phenomenon may result from the virus's mutation preference during transmission. Using dual-luciferase assays, it is further discovered that the deoptimization of codons in the viral sequence may weaken protein expression during virus evolution, indicating that codon usage may play an important role in virus fitness. Finally, given the importance of codon usage in protein expression and particularly for mRNA vaccines, it is designed several codon-optimized Omicron BA.2.12.1, BA.4/5, and XBB.1.5 spike mRNA vaccine candidates and experimentally validated their high levels of expression. This study highlights the importance of codon usage in virus evolution and provides guidelines for codon optimization in mRNA and DNA vaccine development.
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Affiliation(s)
- Xinkai Wu
- State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China
| | - Ke‐jia Shan
- State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China
| | - Fuwen Zan
- NHC Key Laboratory of Systems Biology of PathogensInstitute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100176China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China
| | - Zhaohui Qian
- NHC Key Laboratory of Systems Biology of PathogensInstitute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100176China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China
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18
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Zhou J, Wang X, Zhou Z, Wang S. Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak. Int J Mol Sci 2023; 24:11524. [PMID: 37511283 PMCID: PMC10380431 DOI: 10.3390/ijms241411524] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The exceptionally widespread outbreak of human monkeypox, an emerging zoonosis caused by the monkeypox virus (MPXV), with more than 69,000 confirmed cases in 100 non-endemic countries since 2022, is a major public health concern. Codon usage patterns reflect genetic variation and adaptation to new hosts and ecological niches. However, detailed analyses of codon usage bias in MPXV based on large-scale genomic data, especially for strains responsible for the 2022 outbreak, are lacking. In this study, we analyzed codon usage in MPXV and its relationship with host adaptation. We confirmed the ongoing outbreak of MPXVs belonging to the West Africa (WA) lineage by principal component analysis based on their codon usage patterns. The 2022 outbreak strains had a relatively low codon usage bias. Codon usage of MPXVs was shaped by mutation and natural selection; however, different from past strains, codon usage in the 2022 outbreak strains was predominantly determined by mutation pressure. Additionally, as revealed by the codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses, the codon usage patterns of MPXVs were also affected by their hosts. In particular, the 2022 outbreak strains showed slightly but significantly greater adaptation to many primates, including humans, and were subjected to stronger selection pressure induced by hosts. Our results suggest that MPXVs contributing to the 2022 outbreak have unique evolutionary features, emphasizing the importance of sustained monitoring of their transmission and evolution.
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Affiliation(s)
| | | | - Zhe Zhou
- Bioinformatics Center of AMMS, Beijing 100850, China; (J.Z.); (X.W.)
| | - Shengqi Wang
- Bioinformatics Center of AMMS, Beijing 100850, China; (J.Z.); (X.W.)
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19
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Noor F, Ashfaq UA, Bakar A, Qasim M, Masoud MS, Alshammari A, Alharbi M, Riaz MS. Identification and characterization of codon usage pattern and influencing factors in HFRS-causing hantaviruses. Front Immunol 2023; 14:1131647. [PMID: 37492567 PMCID: PMC10364125 DOI: 10.3389/fimmu.2023.1131647] [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: 12/25/2022] [Accepted: 06/22/2023] [Indexed: 07/27/2023] Open
Abstract
Hemorrhagic fever with renal syndrome (HFRS) is an acute viral zoonosis carried and transmitted by infected rodents through urine, droppings, or saliva. The etiology of HFRS is complex due to the involvement of viral factors and host immune and genetic factors which hinder the development of potential therapeutic solutions for HFRS. Hantaan virus (HTNV), Dobrava-Belgrade virus (DOBV), Seoul virus (SEOV), and Puumala virus (PUUV) are predominantly found in hantaviral species that cause HFRS in patients. Despite ongoing prevention and control efforts, HFRS remains a serious economic burden worldwide. Furthermore, recent studies reported that the hantavirus nucleocapsid protein is a multi-functional protein and plays a major role in the replication cycle of the hantavirus. However, the precise mechanism of the nucleoproteins in viral pathogenesis is not completely understood. In the framework of the current study, various in silico approaches were employed to identify the factors influencing the codon usage pattern of hantaviral nucleoproteins. Based on the relative synonymous codon usage (RSCU) values, a comparative analysis was performed between HFRS-causing hantavirus and their hosts, suggesting that HTNV, DOBV, SEOV, and PUUV, were inclined to evolve their codon usage patterns that were comparable to those of their hosts. The results indicated that most of the overrepresented codons had AU-endings, which revealed that mutational pressure is the major force shaping codon usage patterns. However, the influence of natural selection and geographical factors cannot be ignored on viral codon usage bias. Further analysis also demonstrated that HFRS causing hantaviruses adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts. To our knowledge, no study to date reported the factors influencing the codon usage pattern within hantaviral nucleoproteins. Thus, the proposed computational scheme can help in understanding the underlying mechanism of codon usage patterns in HFRS-causing hantaviruses which lend a helping hand in designing effective anti-HFRS treatments in future. This study, although comprehensive, relies on in silico methods and thus necessitates experimental validation for more solid outcomes. Beyond the identified factors influencing viral behavior, there could be other yet undiscovered influences. These potential factors should be targets for further research to improve HFRS therapeutic strategies.
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Affiliation(s)
- Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Abu Bakar
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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20
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Xin W, Guo Z, Wang L, Li Y, Shangguan H, Xue K, Chen H, Yang H, Zhao L, Ge J. Multiple genotypes infection and molecular characterization of Torque teno neovison virus: A novel Anelloviridae of mink in China. Res Vet Sci 2023; 161:145-155. [PMID: 37384973 DOI: 10.1016/j.rvsc.2023.06.021] [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: 04/11/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/01/2023]
Abstract
A novel Torque teno neovison virus (TTVs) was identified in specimens collected from dead mink during an outbreak of the Aleutian mink disease virus. Eighteen complete genomic sequences were obtained, ranging from 2109 to 2158 nucleotides in length and consisting of an untranslated region and three open reading frames. The genomic organization of mink TTVs is similar to previously reported anelloviruses. However, the deduced amino acid sequence of its ORF1 protein shows genetic diversity compared to related anelloviruses, suggesting that it represents a putative new species within the Anelloviridae family. This study provides a detailed molecular characterization of the novel mink anelloviruses, including its codon usage pattern, origin, and evolution. Analysis of the viral genomic sequences reveals the existence of multiple genotypes of co-infection. Principal component analysis and phylogenetic trees confirm the coexistence of multiple genotypes. Furthermore, the codon usage analyses indicate that mink TTVs have a genotype-specific codon usage pattern and show a low codon usage bias. Host-specific adaptation analysis suggests that TTVs are less adapted to mink. The possible origin and evolutionary history of mink TTVs were elucidated. Mink TTVs was genetically closely related to giant panda anellovirus, representing a new species. The observed incongruence between the phylogenetic history of TTVs and that of their hosts suggests that the evolution of anellovirus is largely determined by cross-species transmission. The study provides insights into the co-infection and genetic evolution of anellovirus in China.
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Affiliation(s)
- Weizhi Xin
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Zhiyuan Guo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Lin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Yifan Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Haikun Shangguan
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Kun Xue
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, PR China
| | - Hongliang Yang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Lili Zhao
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, PR China; College of Veterinary Medicine, Jilin University, 5333 Xian Road, Changchun 130062, China.
| | - Junwei Ge
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal, Pathogen Biology, Harbin 150030, China.
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21
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Chen L, Jiang W, Wu W, Zhang S, Cai J, Lv T, Xiang B, Lin Q, Liao M, Ding C, Ren T. Insights into the Epidemiology, Phylodynamics, and Evolutionary Changes of Lineage GI-7 Infectious Bronchitis Virus. Transbound Emerg Dis 2023; 2023:9520616. [PMID: 40303710 PMCID: PMC12016960 DOI: 10.1155/2023/9520616] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/10/2023] [Accepted: 05/11/2023] [Indexed: 05/02/2025]
Abstract
Infectious bronchitis virus (IBV) is distributed worldwide and causes significant losses in the poultry industry. In recent decades, lineages GI-19 and GI-7 have become the most prevalent IBV strains in China. However, the molecular evolution and phylodynamics of the lineage GI-7 IBV strains remain largely unknown. In this study, we identified 19 IBV strains from clinical samples from January 2021 to June 2022 in China, including 12 strains of GI-19, 3 strains of GI-7, and 1 strain each of GI-1, GI-9, GI-13, and GI-28. These results indicated that lineages GI-19 and GI-7 IBVs are still the most prevalent IBVs in China. Here, we investigated the evolution and transmission dynamics of lineage GI-7 IBVs. Our results revealed that the Taiwan province might be the origin of lineage GI-7 IBVs and that South China plays an important role in the spread of IBV. Furthermore, we found low codon usage bias of the S1 gene in lineage GI-7 IBVs. This allowed IBV to replicate in the host during evolution as a result of reduced competition, mainly driven by natural selection and mutational pressure, where the role of natural selection is more prominent. Collectively, our results reveal the genetic diversity and evolutionary dynamics of lineage GI-7 IBVs, which could assist in the prevention and control of viral infection.
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Affiliation(s)
- Libin Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Weiwei Jiang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Wanyan Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Siyuan Zhang
- Guangzhou South China Biological Medicine Co., Ltd., Guangzhou 510642, China
| | - Juncheng Cai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Ting Lv
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Bin Xiang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Qiuyan Lin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Ming Liao
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Chan Ding
- Shanghai Veterinary Research Institute (SHVRI), Chinese Academy of Agricultural Sciences (CAAS), Shanghai 200241, China
| | - Tao Ren
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
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22
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Khandia R, Khan AA, Karuvantevida N, Gurjar P, Rzhepakovsky IV, Legaz I. Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts. Pathogens 2023; 12:pathogens12020325. [PMID: 36839597 PMCID: PMC9961758 DOI: 10.3390/pathogens12020325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Hepatitis C virus (HCV) is enveloped RNA virus, encoding for a polyprotein that is processed by cellular proteases. The virus is responsible for liver cirrhosis, allograft rejection, and human hepatocellular carcinoma. Based on studies including compositional analysis, odds ratio analysis, parity analysis, skew analysis, relative synonymous codon usage, codon bias, and protein properties, it was evident that codon usage bias in HCV is dependent upon the nucleotide composition. Codon context analysis revealed CTC-CTG as a preferred codon pair. While CGA and CGT codons were rare, none of the codons were rare in HCV-like viruses envisaged in the present study. Many of the preferred codon pairs were valine amino acid-initiated, which possibly infers viral infectivity; hence the role of selection forces appears to act on the HCV genome, which was further validated by neutrality analysis where selection accounted for 87.28%, while mutation accounted for 12.72% force shaping codon usage. Furthermore, codon usage was correlated with the length of the genome. HCV viruses prefer valine-initiated codon pairs, while HCV-like viruses prefer alanine-initiated codon pairs. The HCV host range is very narrow and is confined to only humans and chimpanzees. Based on indices including codon usage correlation analysis, similarity index, and relative codon deoptimization index, it is evident in the study that the chimpanzee is the primary host of the virus. The present study helped elucidate the preferred host for HCV. The information presented in the study paved the way for generating an attenuated vaccine candidate through viral recoding, with finely tuned nucleotide composition and a perfect balance of preferred and rare codons.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal 462026, India
- Correspondence: (R.K.); (I.L.)
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O. Box 505055, United Arab Emirates
| | - Pankaj Gurjar
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
| | | | - Isabel Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, 30120 Murcia, Spain
- Correspondence: (R.K.); (I.L.)
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23
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Pu F, Wang R, Yang X, Hu X, Wang J, Zhang L, Zhao Y, Zhang D, Liu Z, Liu J. Nucleotide and codon usage biases involved in the evolution of African swine fever virus: A comparative genomics analysis. J Basic Microbiol 2023; 63:499-518. [PMID: 36782108 DOI: 10.1002/jobm.202200624] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/05/2023] [Accepted: 01/21/2023] [Indexed: 02/15/2023]
Abstract
Since African swine fever virus (ASFV) replication is closely related to its host's machinery, codon usage of viral genome can be subject to selection pressures. A better understanding of codon usage can give new insights into viral evolution. We implemented information entropy and revealed that the nucleotide usage pattern of ASFV is significantly associated with viral isolation factors (region and time), especially the usages of thymine and cytosine. Despite the domination of adenine and thymine in the viral genome, we found that mutation pressure alters the overall codon usage pattern of ASFV, followed by selective forces from natural selection. Moreover, the nucleotide skew index at the gene level indicates that nucleotide usages influencing synonymous codon bias of ASFV are significantly correlated with viral protein hydropathy. Finally, evolutionary plasticity is proved to contribute to the weakness in synonymous codons with A- or T-end serving as optimal codons of ASFV, suggesting that fine-tuning translation selection plays a role in synonymous codon usages of ASFV for adapting host. Taken together, ASFV is subject to evolutionary dynamics on nucleotide selections and synonymous codon usage, and our detailed analysis offers deeper insights into the genetic characteristics of this newly emerging virus around the world.
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Affiliation(s)
- Feiyang Pu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Rui Wang
- Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - Xuanye Yang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Xinyan Hu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Jinqian Wang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Lijuan Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Yongqing Zhao
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Derong Zhang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Zewen Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Junlin Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
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24
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Zhou J, Xing Y, Zhou Z, Wang S. A comprehensive analysis of Usutu virus (USUV) genomes revealed lineage-specific codon usage patterns and host adaptations. Front Microbiol 2023; 13:967999. [PMID: 36713228 PMCID: PMC9878346 DOI: 10.3389/fmicb.2022.967999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/19/2022] [Indexed: 01/15/2023] Open
Abstract
The Usutu virus (USUV) is an emerging arbovirus virus maintained in the environment of Afro-Eurasia via a bird-mosquito-bird enzootic cycle and sporadically infected other vertebrates. Despite primarily asymptomatic or mild symptoms, humans infected by USUV can develop severe neurological diseases such as meningoencephalitis. However, no detailed study has yet been conducted to investigate its evolution from the perspective of codon usage patterns. Codon usage choice of viruses reflects the genetic variations that enable them to reconcile their viability and fitness toward the external environment and new hosts. This study performed a comprehensive evolution and codon usage analysis of USUVs. Our reconstructed phylogenetic tree confirmed that the circulation viruses belong to eight distinct lineages, reaffirmed by principal component analysis based on codon usage patterns. We also found a relatively small codon usage bias and that natural selection, mutation pressure, dinucleotide abundance, and evolutionary processes collectively shaped the codon usage of the USUV, with natural selection predominating over the others. Additionally, a complex interaction of codon usage between the USUV and its host was observed. This process could have enabled USUV to adapt to various hosts and vectors, including humans. Therefore, the USUV may possess a potential risk of cross-species transmission and subsequent outbreaks. In this respect, further epidemiologic surveys, diversity monitoring, and pathogenetic research are warranted.
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25
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Rahman SU, Rehman HU, Rahman IU, Khan MA, Rahim F, Ali H, Chen D, Ma W. Evolution of codon usage in Taenia saginata genomes and its impact on the host. Front Vet Sci 2023; 9:1021440. [PMID: 36713873 PMCID: PMC9875090 DOI: 10.3389/fvets.2022.1021440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/03/2022] [Indexed: 01/13/2023] Open
Abstract
The beef tapeworm, also known as Taenia saginata, is a zoonotic tapeworm from the genus Taenia in the order Cyclophyllidea. Taenia saginata is a food-borne zoonotic parasite with a worldwide distribution. It poses serious health risks to the host and has a considerable negative socioeconomic impact. Previous studies have explained the population structure of T. saginata within the evolutionary time scale and adaptive evolution. However, it is still unknown how synonymous codons are used by T. saginata. In this study, we used 90 T. saginata strains, applying the codon usage bias (CUB). Both base content and relative synonymous codon usage (RSCU) analysis revealed that AT-ended codons were more frequently used in the genome of T. saginata. Further low CUB was observed from the effective number of codons (ENC) value. The neutrality plot analysis suggested that the dominant factor of natural selection was involved in the structuring of CUB in T. saginata. Further analysis showed that T. saginata has adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts (Bos taurus and Homo sapiens). Generally, both natural selection and mutational pressure have an impact on the codon usage patterns of the protein-coding genes in T. saginata. This study is important because it characterized the codon usage pattern in the T. saginata genomes and provided the necessary data for a basic evolutionary study on them.
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Affiliation(s)
- Siddiq Ur Rahman
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan
| | - Hassan Ur Rehman
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan
| | - Inayat Ur Rahman
- Department of Botany, Khushal Khan Khattak University, Karak, Pakistan
| | - Muazzam Ali Khan
- Department of Botany, Bacha Khan University, Charsadda, KP, Pakistan
| | - Fazli Rahim
- Department of Botany, Bacha Khan University, Charsadda, KP, Pakistan
| | - Hamid Ali
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Dekun Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Wentao Ma
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China,*Correspondence: Wentao Ma ✉
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26
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Rahman SU, Rehman HU, Rahman IU, Rauf A, Alshammari A, Alharbi M, Haq NU, Suleria HAR, Raza SHA. Analysis of codon usage bias of lumpy skin disease virus causing livestock infection. Front Vet Sci 2022; 9:1071097. [PMID: 36544551 PMCID: PMC9762553 DOI: 10.3389/fvets.2022.1071097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/10/2022] [Indexed: 12/07/2022] Open
Abstract
Lumpy skin disease virus (LSDV) causes lumpy skin disease (LSD) in livestock, which is a double-stranded DNA virus that belongs to the genus Capripoxvirus of the family Poxviridae. LSDV is an important poxvirus that has spread out far and wide to become distributed worldwide. It poses serious health risks to the host and causes considerable negative socioeconomic impact on farmers financially and on cattle by causing ruminant-related diseases. Previous studies explained the population structure of the LSDV within the evolutionary time scale and adaptive evolution. However, it is still unknown and remains enigmatic as to how synonymous codons are used by the LSDV. Here, we used 53 LSDV strains and applied the codon usage bias (CUB) analysis to them. Both the base content and the relative synonymous codon usage (RSCU) analysis revealed that the AT-ended codons were more frequently used in the genome of LSDV. Further low codon usage bias was calculated from the effective number of codons (ENC) value. The neutrality plot analysis suggested that the dominant factor of natural selection played a role in the structuring of CUB in LSDV. Additionally, the results from a comparative analysis suggested that the LSDV has adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts (Bos taurus and Homo sapiens). Both natural selection and mutational pressure have an impact on the codon usage patterns of the protein-coding genes in LSDV. This study is important because it has characterized the codon usage pattern in the LSDV genomes and has provided the necessary data for a basic evolutionary study on them.
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Affiliation(s)
- Siddiq Ur Rahman
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan
| | - Hassan Ur Rehman
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan
| | - Inayat Ur Rahman
- Department of Botany, Khushal Khan Khattak University, Karak, Pakistan
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Swabi, Pakistan
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Noor ul Haq
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan
| | - Hafiz Ansar Rasul Suleria
- Faculty of Veterinary and Agricultural Sciences, School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, Australia
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
- Safety of Livestock and Poultry Products, College of Food Science, South China Agricultural University, Guangzhou, China
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27
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Gao Y, Lu Y, Song Y, Jing L. Analysis of codon usage bias of WRKY transcription factors in Helianthus annuus. BMC Genom Data 2022; 23:46. [PMID: 35725374 PMCID: PMC9210703 DOI: 10.1186/s12863-022-01064-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 06/13/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The phenomenon of codon usage bias is known to exist in many genomes and is mainly determined by mutation and selection. Codon usage bias analysis is a suitable strategy for identifying the principal evolutionary driving forces in different organisms. Sunflower (Helianthus annuus L.) is an annual crop that is cultivated worldwide as ornamentals, food plants and for their valuable oil. The WRKY family genes in plants play a central role in diverse regulation and multiple stress responses. Evolutionary analysis of WRKY family genes of H. annuus can provide rich genetic information for developing hybridization resources of the genus Helianthus.
Results
Bases composition analysis showed the average GC content of WRKY genes of H. annuus was 43.42%, and the average GC3 content was 39.60%, suggesting that WRKY gene family prefers A/T(U) ending codons. There were 29 codons with relative synonymous codon usage (RSCU) greater than 1 and 22 codons ending with A and U base. The effective number of codons (ENC) and codon adaptation index (CAI) in WRKY genes ranged from 43.47–61.00 and 0.14–0.26, suggesting that the codon bias was weak and WRKY genes expression level was low. Neutrality analysis found a significant correlation between GC12 and GC3. ENC-plot showed most genes on or close to the expected curve, suggesting that mutational bias played a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that the usage of AT and GC was disproportionate. A total of three codons were identified as the optimal codons.
Conclusion
Apart from natural selection effects, most of the genetic evolution in the H. annuus WRKY genome might be driven by mutation pressure. Our results provide a theoretical foundation for elaborating the genetic architecture and mechanisms of H. annuus and contributing to enrich H. annuus genetic resources.
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28
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Bansal S, Mallikarjuna MG, Balamurugan A, Nayaka SC, Prakash G. Composition and Codon Usage Pattern Results in Divergence of the Zinc Binuclear Cluster ( Zn(II)2Cys6) Sequences among Ascomycetes Plant Pathogenic Fungi. J Fungi (Basel) 2022; 8:1134. [PMID: 36354901 PMCID: PMC9694491 DOI: 10.3390/jof8111134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 07/29/2023] Open
Abstract
Zinc binuclear cluster proteins (ZBC; Zn(II)2Cys6) are unique to the fungi kingdom and associated with a series of functions, viz., the utilization of macromolecules, stress tolerance, and most importantly, host-pathogen interactions by imparting virulence to the pathogen. Codon usage bias (CUB) is the phenomenon of using synonymous codons in a non-uniform fashion during the translation event, which has arisen because of interactions among evolutionary forces. The Zn(II)2Cys6 coding sequences from nine Ascomycetes plant pathogenic species and model system yeast were analysed for compositional and codon usage bias patterns. The clustering analysis diverged the Ascomycetes fungi into two clusters. The nucleotide compositional and relative synonymous codon usage (RSCU) analysis indicated GC biasness toward Ascomycetes fungi compared with the model system S. cerevisiae, which tends to be AT-rich. Further, plant pathogenic Ascomycetes fungi belonging to cluster-2 showed a higher number of GC-rich high-frequency codons than cluster-1 and was exclusively AT-rich in S. cerevisiae. The current investigation also showed the mutual effect of the two evolutionary forces, viz. natural selection and compositional constraints, on the CUB of Zn(II)2Cys6 genes. The perseverance of GC-rich codons of Zn(II)2Cys6 in Ascomycetes could facilitate the invasion process. The findings of the current investigation show the role of CUB and nucleotide composition in the evolutionary divergence of Ascomycetes plant pathogens and paves the way to target specific codons and sequences to modulate host-pathogen interactions through genome editing and functional genomics tools.
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Affiliation(s)
- Shilpi Bansal
- Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India
| | | | - Alexander Balamurugan
- Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India
| | - S. Chandra Nayaka
- Department of Studies in Applied Botany and Biotechnology, University of Mysore, Mysore 570005, India
| | - Ganesan Prakash
- Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India
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29
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Qin L, Ding S, Wang Z, Jiang R, He Z. Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus. Viruses 2022; 14:v14102267. [PMID: 36298822 PMCID: PMC9607058 DOI: 10.3390/v14102267] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 01/25/2023] Open
Abstract
Turnip mosaic virus (TuMV), an important pathogen that causes mosaic diseases in vegetable crops worldwide, belongs to the genus Potyvirus of the family Potyviridae. Previously, the areas of genetic variation, population structure, timescale, and migration of TuMV have been well studied. However, the codon usage pattern and host adaptation analysis of TuMV is unclear. Here, compositional bias and codon usage of TuMV were performed using 184 non-recombinant sequences. We found a relatively stable change existed in genomic composition and a slightly lower codon usage choice displayed in TuMV protein-coding sequences. Statistical analysis presented that the codon usage patterns of TuMV protein-coding sequences were mainly affected by natural selection and mutation pressure, and natural selection was the key influencing factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) revealed that TuMV genes were strongly adapted to Brassica oleracea from the present data. Similarity index (SiD) analysis also indicated that B. oleracea is potentially the preferred host of TuMV. Our study provides the first insights for assessing the codon usage bias of TuMV based on complete genomes and will provide better advice for future research on TuMV origins and evolution patterns.
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Affiliation(s)
- Lang Qin
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
| | - Shiwen Ding
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
| | - Zhilei Wang
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
| | - Runzhou Jiang
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
| | - Zhen He
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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30
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Sophiarani Y, Chakraborty S. Comparison of compositional constraints: Nuclear genome vs plasmid genome of Pseudomonas syringae pv. tomato DC3000. J Biosci 2022. [DOI: 10.1007/s12038-022-00296-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Fan Y, Guo D, Zhao S, Wei Q, Li Y, Lin T. Human genes with relative synonymous codon usage analogous to that of polyomaviruses are involved in the mechanism of polyomavirus nephropathy. Front Cell Infect Microbiol 2022; 12:992201. [PMID: 36159639 PMCID: PMC9492876 DOI: 10.3389/fcimb.2022.992201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/12/2022] [Indexed: 11/28/2022] Open
Abstract
Human polyomaviruses (HPyVs) can cause serious and deleterious infections in human. Yet, the molecular mechanism underlying these infections, particularly in polyomavirus nephropathy (PVAN), is not well-defined. In the present study, we aimed to identify human genes with codon usage bias (CUB) similar to that of HPyV genes and explore their potential involvement in the pathogenesis of PVAN. The relative synonymous codon usage (RSCU) values of genes of HPyVs and those of human genes were computed and used for Pearson correlation analysis. The involvement of the identified correlation genes in PVAN was analyzed by validating their differential expression in publicly available transcriptomics data. Functional enrichment was performed to uncover the role of sets of genes. The RSCU analysis indicated that the A- and T-ending codons are preferentially used in HPyV genes. In total, 5400 human genes were correlated to the HPyV genes. The protein-protein interaction (PPI) network indicated strong interactions between these proteins. Gene expression analysis indicated that 229 of these genes were consistently and differentially expressed between normal kidney tissues and kidney tissues from PVAN patients. Functional enrichment analysis indicated that these genes were involved in biological processes related to transcription and in pathways related to protein ubiquitination pathway, apoptosis, cellular response to stress, inflammation and immune system. The identified genes may serve as diagnostic biomarkers and potential therapeutic targets for HPyV associated diseases, especially PVAN.
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Affiliation(s)
- Yu Fan
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Duan Guo
- Department of Palliative Medicine, West China School of Public Health and West China fourth Hospital, Sichuan University, Chengdu, China
- Palliative Medicine Research Center, West China−Peking Union Medical College, Chen Zhiqian (PUMC C.C). Chen Institute of Health, Sichuan University, Chengdu, China
| | - Shangping Zhao
- Department of Urology, West China School of Nursing and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Qiang Wei
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Yi Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Tao Lin, ; ; Yi Li,
| | - Tao Lin
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Tao Lin, ; ; Yi Li,
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Wang X, Sun J, Lu L, Pu FY, Zhang DR, Xie FQ. Evolutionary dynamics of codon usages for peste des petits ruminants virus. Front Vet Sci 2022; 9:968034. [PMID: 36032280 PMCID: PMC9412750 DOI: 10.3389/fvets.2022.968034] [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] [Received: 06/14/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Peste des petits ruminants virus (PPRV) is an important agent of contagious, acute and febrile viral diseases in small ruminants, while its evolutionary dynamics related to codon usage are still lacking. Herein, we adopted information entropy, the relative synonymous codon usage values and similarity indexes and codon adaptation index to analyze the viral genetic features for 45 available whole genomes of PPRV. Some universal, lineage-specific, and gene-specific genetic features presented by synonymous codon usages of the six genes of PPRV that encode N, P, M, F, H and L proteins reflected evolutionary plasticity and independence. The high adaptation of PPRV to hosts at codon usages reflected high viral gene expression, but some synonymous codons that are rare in the hosts were selected in high frequencies in the viral genes. Another obvious genetic feature was that the synonymous codons containing CpG dinucleotides had weak tendencies to be selected in viral genes. The synonymous codon usage patterns of PPRV isolated during 2007–2008 and 2013–2014 in China displayed independent evolutionary pathway, although the overall codon usage patterns of these PPRV strains matched the universal codon usage patterns of lineage IV. According to the interplay between nucleotide and synonymous codon usages of the six genes of PPRV, the evolutionary dynamics including mutation pressure and natural selection determined the viral survival and fitness to its host.
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Affiliation(s)
- Xin Wang
- School of Stomatology, Lanzhou University, Lanzhou, China
| | - Jing Sun
- Geriatrics Department, The Second Hospital of Lanzhou University, Lanzhou, China
| | - Lei Lu
- School of Stomatology, Lanzhou University, Lanzhou, China
| | - Fei-yang Pu
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - De-rong Zhang
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Fu-qiang Xie
- Maxillofacial Surgery Department, The Second Hospital of Lanzhou University, Lanzhou, China
- *Correspondence: Fu-qiang Xie
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Feng JL, Wu LW, Wang Q, Pan YJ, Li BL, Lin YL, Yao H. Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2194021. [PMID: 35937412 PMCID: PMC9348943 DOI: 10.1155/2022/2194021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/06/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022]
Abstract
Iris species, commonly known as rainbow flowers because of their attractive flowers, are extensively grown in landscape gardens. A few species, including Belamcanda chinensis, the synonym of I. domestica and I. tectorum, are known for their medicinal properties. However, research on the genomes and evolutionary relationships of Iris species is scarce. In the current study, the complete chloroplast (CP) genomes of I. tectorum, I. dichotoma, I. japonica, and I. domestica were sequenced and compared for their identification and relationship. The CP genomes of the four Iris species were circular quadripartite with similar lengths, GC contents, and codon usages. A total of 113 specific genes were annotated, including the ycf1 pseudogene in all species and rps19 in I. japonica alone. All the species had mononucleotide (A/T) simple sequence repeats (SSRs) and long forward and palindromic repeats in their genomes. A comparison of the CP genomes based on mVISTA and nucleotide diversity (Pi) identified three highly variable regions (ndhF-rpl32, rps15-ycf1, and rpl16). Phylogenetic analysis based on the complete CP genomes concluded that I. tectorum is a sister of I. japonica, and the subgenus Pardanthopsis with several I. domestica clustered into one branch is a sister of I. dichotoma. These findings confirm the feasibility of superbarcodes (complete CP genomes) for Iris species authentication and could serve as a resource for further research on Iris phylogeny.
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Affiliation(s)
- Jing-lu Feng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Li-wei Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Qing Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Yun-jia Pan
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Bao-li Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Yu-lin Lin
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
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Wang Q, Lyu X, Cheng J, Fu Y, Lin Y, Abdoulaye AH, Jiang D, Xie J. Codon Usage Provides Insights into the Adaptive Evolution of Mycoviruses in Their Associated Fungi Host. Int J Mol Sci 2022; 23:7441. [PMID: 35806445 PMCID: PMC9267111 DOI: 10.3390/ijms23137441] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Codon usage bias (CUB) could reflect co-evolutionary changes between viruses and hosts in contrast to plant and animal viruses, and the systematic analysis of codon usage among the mycoviruses that infect plant pathogenic fungi is limited. We performed an extensive analysis of codon usage patterns among 98 characterized RNA mycoviruses from eight phytopathogenic fungi. The GC and GC3s contents of mycoviruses have a wide variation from 29.35% to 64.62% and 24.32% to 97.13%, respectively. Mycoviral CUB is weak, and natural selection plays a major role in the formation of mycoviral codon usage pattern. In this study, we demonstrated that the codon usage of mycoviruses is similar to that of some host genes, especially those involved in RNA biosynthetic process and transcription, suggesting that CUB is a potential evolutionary mechanism that mycoviruses adapt to in their hosts.
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Affiliation(s)
- Qianqian Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Yanping Fu
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Yang Lin
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Assane Hamidou Abdoulaye
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Wang X, Sun J, Zheng Y, Xie F. Dispersion of synonymous codon usage patterns in hepatitis E virus genomes derived from various hosts. J Basic Microbiol 2022; 62:975-983. [PMID: 35778820 DOI: 10.1002/jobm.202200072] [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: 02/13/2022] [Revised: 05/01/2022] [Accepted: 06/11/2022] [Indexed: 11/09/2022]
Abstract
Hepatitis E virus (HEV) is an important zoonotic pathogen infecting a wide range of host species. It has a positive-sense, single-stranded RNA genome encoding three open reading frames (ORFs). Synonymous codon usages of viruses essentially determine their survival and adaptation to susceptible hosts. To better understand the interplay between the ever-expanding host range and synonymous codon usages of HEV, we quantified the dispersion of synonymous codon usages of HEV genomes isolated from different hosts via Vs calculation and information entropy. HEV ORFs show species-specific synonymous codon usage patterns. Ruminant-derived HEV ORFs own the most synonymous codons with stable usage patterns (Vs value <0.1) which leads to the stable overall codon usage patterns (R value being close to zero). Swine-derived HEV ORFs own more concentrated synonymous codons than those from wild boar. Compared with HEV strains isolated from other hosts, the human-derived HEV exhibits a distinct pattern at the overall codon usage (R < 0). Generally, ORF1 contains more synonymous codons with stable usage patterns (Vs < 0.1) than those of ORFs 2 and 3. Moreover, ORF3 contains more synonymous codons with varied patterns (Vs > 1.0) than ORFs 1 and 2. The host factor serving as one of the evolutionary dynamics probably influences synonymous codon usage patterns of the HEV genome. Taken together, synonymous codons with stable usage patterns in ORF1 might help to sustain the infection, while that with varied usage patterns in ORF3 may facilitate cross-species infection and expand the host range.
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Affiliation(s)
- Xin Wang
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, China
| | - Jing Sun
- Department of Endocrine, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yueyan Zheng
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, China
| | - Fuqiang Xie
- Department of Stomatology, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
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Sarkar I, Dey P, Rathore SS, Singh GD, Singh RP. Global genomic and proteomic analysis indicates co-evolution of Neisseria species and with their human host. World J Microbiol Biotechnol 2022; 38:149. [PMID: 35773545 DOI: 10.1007/s11274-022-03338-w] [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: 11/24/2021] [Accepted: 06/11/2022] [Indexed: 11/30/2022]
Abstract
Neisseria, a genus from the beta-proteobacteria class, is of potential clinical importance. This genus contains both pathogenic and commensal strains. Gonorrhea and meningitis are two major diseases caused by pathogens belonging to this genus. With the increased use of antimicrobial agents against these pathogens they have evolved the antimicrobial resistance capacity making these diseases nearly untreatable. The set of anti-bacterial resistance genes (resistome) and genes associated with signal processing (secretomes) are crucial for the host-microbial interaction. With the virtue of whole-genome sequences and computational biology, it is now possible to study the genomic and proteomic riddles of Neisseria along with their comprehensive evolutionary and metabolic profiling. We have studied relative synonymous codon usage, amino acid usage, reverse ecology, comparative genomics, evolutionary analysis and pathogen-host (Neisseria-human) interaction through bioinformatics analysis. Our analysis revealed the co-evolution of Neisseria genomes with the human host. Moreover, the co-occurrence of Neisseria and humans has been supported through reverse ecology analysis. A differential pattern of the evolutionary rate of resistomes and secretomes was evident among the pathogenic and commensal strains. Comparative genomics supported the presence of virulent genes in both pathogenic and commensal strains of the select genus. Our analysis also indicated a transition from commensal to pathogenic Neisseria strains through the long run of evolution.
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Affiliation(s)
- Indrani Sarkar
- Salim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641 108, India
| | - Prateek Dey
- Salim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641 108, India
| | | | | | - Ram Pratap Singh
- Department of Life Science, Central University of South Bihar, Gaya, Bihar, 824236, India.
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Tyagi N, Sardar R, Gupta D. Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC). PeerJ 2022; 10:e13562. [PMID: 35765592 PMCID: PMC9233899 DOI: 10.7717/peerj.13562] [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: 02/11/2022] [Accepted: 05/19/2022] [Indexed: 01/17/2023] Open
Abstract
The ongoing prevailing COVID-19 pandemic caused by SARS-CoV-2 is becoming one of the major global health concerns worldwide. The SARS-CoV-2 genome encodes spike (S) glycoprotein that plays a very crucial role in viral entry into the host cell via binding of its receptor binding domain (RBD) to the host angiotensin converting enzyme 2 (ACE2) receptor. The continuously evolving SARS-CoV-2 genome results in more severe and transmissible variants characterized by the emergence of novel mutations called 'variants of concern' (VOC). The currently designated alpha, beta, gamma, delta and omicron VOC are the focus of this study due to their high transmissibility, increased virulence, and concerns for decreased effectiveness of the available vaccines. In VOC, the spike (S) gene and other non-structural protein mutations may affect the efficacies of the approved COVID-19 vaccines. To understand the diversity of SARS-CoV-2, several studies have been performed on a limited number of sequences. However, only a few studies have focused on codon usage bias (CUBs) pattern analysis of all the VOC strains. Therefore, to evaluate the evolutionary divergence of all VOC S-genes, we performed CUBs analysis on 300,354 sequences to understand the evolutionary relationship with its adaptation in different hosts, i.e., humans, bats, and pangolins. Base composition and RSCU analysis revealed the presence of 20 preferred AU-ended and 10 under-preferred GC-ended codons. In addition, CpG was found to be depleted, which may be attributable to the adaptive response by viruses to escape from the host defense process. Moreover, the ENC values revealed a higher bias in codon usage in the VOC S-gene. Further, the neutrality plot analysis demonstrated that S-genes analyzed in this study are under 83.93% influence of natural selection, suggesting its pivotal role in shaping the CUBs. The CUBs pattern of S-genes was found to be very similar among all the VOC strains. Interestingly, we observed that VOC strains followed a trend of antagonistic codon usage with respect to the human host. The identified CUBs divergence would help to understand the virus evolution and its host adaptation, thus help design novel vaccine strategies against the emerging VOC strains. To the best of our knowledge, this is the first report for identifying the evolution of CUBs pattern in all the currently identified VOC.
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Affiliation(s)
- Neetu Tyagi
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India, New Delhi, New Delhi, India,Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Rahila Sardar
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India, New Delhi, New Delhi, India,Biochemistry, Jamia Hamdard University, New Delhi, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India, New Delhi, New Delhi, India
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Li B, Wu H, Miao Z, Hu L, Zhou L, Lu Y. Codon Usage of Hepatitis E Viruses: A Comprehensive Analysis. Front Microbiol 2022; 13:938651. [PMID: 35801104 PMCID: PMC9253588 DOI: 10.3389/fmicb.2022.938651] [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] [Received: 05/07/2022] [Accepted: 05/30/2022] [Indexed: 11/25/2022] Open
Abstract
Hepatitis E virus (HEV) is an emerging zoonotic pathogen with multiple species and genotypes, which may be classified into human, animal, and zoonotic HEV. Codon usage bias of HEV remained unclear. This study aims to characterize the codon usage of HEV and elucidate the main drivers influencing the codon usage bias. A total of seven HEV genotypes, HEV-1 (human HEV), HEV-3 and HEV-4 (zoonotic HEV), HEV-8, HEV-B, HEV-C1, and HEV-C2 (emerging animal HEV), were included in the study. Complete coding sequences, ORF1, ORF2, and ORF3, were accordingly obtained in the GenBank. Except for HEV-8, the other six genotypes tended to use codons ending in G/C. Based on the analysis of relatively synonymous codon usage (RSCU) and principal component analysis (PCA), codon usage bias was determined for HEV genotypes. Codon usage bias differed widely across human, zoonotic, and animal HEV genotypes; furthermore, it varied within certain genotypes such as HEV-4, HEV-8, and HEV-C1. In addition, dinucleotide abundance revealed that HEV was affected by translation selection to form a unique dinucleotide usage pattern. Moreover, parity rule 2 analysis (PR2), effective codon number (ENC)-plot, and neutrality analysis were jointly performed. Natural selection played a leading role in forming HEV codon usage bias, which was predominant in HEV-1, HEV-3, HEV-B and HEV-C1, while affected HEV-4, HEV-8, and HEV-C2 in combination with mutation pressure. Our findings may provide insights into HEV evolution and codon usage bias.
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Affiliation(s)
- Bingzhe Li
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Han Wu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Ziping Miao
- Institute of Communicable Diseases Prevention and Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Linjie Hu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Lu Zhou
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Yihan Lu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
- *Correspondence: Yihan Lu,
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He Z, Qin L, Xu X, Ding S. Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases. Comput Struct Biotechnol J 2022; 20:2600-2610. [PMID: 35685354 PMCID: PMC9160401 DOI: 10.1016/j.csbj.2022.05.021] [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: 03/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 01/23/2023] Open
Abstract
During recent decades, many new emerging or re-emerging RNA viruses have been found in plants through the development of deep-sequencing technology and big data analysis. These findings largely changed our understanding of the origin, evolution and host range of plant RNA viruses. There is evidence that their genetic composition originates from viruses, and host populations play a key role in the evolution and host adaptability of plant RNA viruses. In this mini-review, we describe the state of our understanding of the evolution of plant RNA viruses in view of compositional biases and explore how they adapt to the host. It appears that adenine rich (A-rich) coding sequences, low CpG and UpA dinucleotide frequencies and lower codon usage patterns were found in the vast majority of plant RNA viruses. The codon usage pattern of plant RNA viruses was influenced by both natural selection and mutation pressure, and natural selection mostly from hosts was the dominant factor. The codon adaptation analyses support that plant RNA viruses probably evolved a dynamic balance between codon adaptation and deoptimization to maintain efficient replication cycles in multiple hosts with various codon usage patterns. In the future, additional combinations of computational and experimental analyses of the nucleotide composition and codon usage of plant RNA viruses should be addressed.
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Affiliation(s)
- Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
- Corresponding author.
| | - Lang Qin
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
| | - Xiaowei Xu
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
| | - Shiwen Ding
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
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Nambou K, Anakpa M, Tong YS. Human genes with codon usage bias similar to that of the nonstructural protein 1 gene of influenza A viruses are conjointly involved in the infectious pathogenesis of influenza A viruses. Genetica 2022; 150:97-115. [PMID: 35396627 PMCID: PMC8992787 DOI: 10.1007/s10709-022-00155-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 03/24/2022] [Indexed: 11/27/2022]
Abstract
Molecular mechanisms of the non-structural protein 1 (NS1) in influenza A-induced pathological changes remain ambiguous. This study explored the pathogenesis of human infection by influenza A viruses (IAVs) through identifying human genes with codon usage bias (CUB) similar to NS1 gene of these viruses based on the relative synonymous codon usage (RSCU). CUB of the IAV subtypes H1N1, H3N2, H3N8, H5N1, H5N2, H5N8, H7N9 and H9N2 was analyzed and the correlation of RSCU values of NS1 sequences with those of the human genes was calculated. The CUB of NS1 was uneven and codons ending with A/U were preferred. The ENC-GC3 and neutrality plots suggested natural selection as the main determinant for CUB. The RCDI, CAI and SiD values showed that the viruses had a high degree of adaptability to human. A total of 2155 human genes showed significant RSCU-based correlation (p < 0.05 and r > 0.5) with NS1 coding sequences and was considered as human genes with CUB similar to NS1 gene of IAV subtypes. Differences and similarities in the subtype-specific human protein–protein interaction (PPI) networks and their functions were recorded among IAVs subtypes, indicating that NS1 of each IAV subtype has a specific pathogenic mechanism. Processes and pathways involved in influenza, transcription, immune response and cell cycle were enriched in human gene sets retrieved based on the CUB of NS1 gene of IAV subtypes. The present work may advance our understanding on the mechanism of NS1 in human infections of IAV subtypes and shed light on the therapeutic options.
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Affiliation(s)
- Komi Nambou
- Shenzhen Nambou1 Biotech Company Limited, 998 Wisdom Valley, No. 38-56 Zhenming Road, Guangming District, Shenzhen, 518106, China.
| | - Manawa Anakpa
- Centre d'Informatique et de Calcul, Université de Lomé, Boulevard Gnassingbé Eyadema, 01 B.P. 1515, Lomé, Togo
| | - Yin Selina Tong
- Shenzhen Nambou1 Biotech Company Limited, 998 Wisdom Valley, No. 38-56 Zhenming Road, Guangming District, Shenzhen, 518106, China
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Zu Z, Lin H, Hu Y, Zheng X, Chen C, Zhao Y, He N. The genetic evolution and codon usage pattern of severe fever with thrombocytopenia syndrome virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105238. [PMID: 35144005 DOI: 10.1016/j.meegid.2022.105238] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 01/04/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Severe fever with thrombocytopenia syndrome (SFTS) is a newly emerging zoonotic infectious disease caused by the SFTS virus (SFTSV), which has been continuously circulating in Eastern Asia in recent years. Although the evolution of SFTSV has been investigated, the evolutionary changes associated with codon usage have not been reported. Thus, a comprehensive genetic and codon usage bias analysis of SFTSV was conducted to elucidate the genetic diversity and evolutionary relationships in a novel perspective. The study amplified and sequenced fifteen SFTSV strains from a prefecture of Zhejiang Province, Eastern China in 2020, where SFTS cases have been continuously reported in the past decade. Phylogenetic analysis was conducted based on the complete coding sequences of SFTSV segments. It suggested that all SFTSV strains circulating in Zhejiang were clustered with Japanese and Korean strains, which belonged to two different genotypes. Meanwhile, thirty-nine genetic reassortants classified into nineteen different reassortment forms were identified, while 45 recombination events in 41 SFTSV strains were found. Codon usage patterns were further analyzed to understand the evolutionary changes in relation to genotype and host. And it revealed that codon usage bias was mainly driven by natural selection rather than mutation pressure. In addition, the codon adaptation index (CAI) analysis demonstrated the strong adaptability of SFTSV to Gallus gallus and Homo sapiens. Similarity index (SiD) analysis indicated that Haemaphysalis longicornis posed a strong selection pressure to SFTSV. In conclusion, this study revealed that the genetic diversity of SFTSV is gradually increasing. The codon usage analysis suggested that codon usage bias of SFTSV was mainly driven by natural selection, and SFTSV has evolved host-specific codon usage patterns. This contributes to the development of control measures against SFTSV.
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Affiliation(s)
- Zhipeng Zu
- Department of Epidemiology, School of Public Health, and the Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Haijiang Lin
- Department of Epidemiology, School of Public Health, and the Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai 200032, China; Taizhou City Center for Disease Control and Prevention, Taizhou City, Zhejiang Province 318001, China
| | - Yafei Hu
- Taizhou City Center for Disease Control and Prevention, Taizhou City, Zhejiang Province 318001, China
| | - Xiang Zheng
- Taizhou City Center for Disease Control and Prevention, Taizhou City, Zhejiang Province 318001, China
| | - Cairong Chen
- Taizhou City Center for Disease Control and Prevention, Taizhou City, Zhejiang Province 318001, China
| | - Yishuang Zhao
- Taizhou City Center for Disease Control and Prevention, Taizhou City, Zhejiang Province 318001, China
| | - Na He
- Department of Epidemiology, School of Public Health, and the Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai 200032, China; Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai 200032, China.
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Joshi A, Krishnan S, Kaushik V. Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei. J Genet Eng Biotechnol 2022; 20:41. [PMID: 35254546 PMCID: PMC8899776 DOI: 10.1186/s43141-022-00324-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/22/2022] [Indexed: 12/18/2022]
Abstract
Background The Tropheryma whipplei causes acute gastroenteritis to neuronal damages in Homo sapiens. Genomics and codon adaptation studies would be helpful advancements of disease evolution prediction, prevention, and treatment of disease. The codon usage data and codon usage measurement tools were deployed to detect the rare, very rare codons, and also synonymous codons usage. The higher effective number of codon usage values indicates the low codon usage bias in T. whipplei and also in the 23S and 16S ribosomal RNA genes. Results In T. whipplei, it was found to hold low codon biasness in genomic sets. The synonymous codons possess the base content in 3rd position that was calculated as A3S% (24.47 and 22.88), C3S% (20.99 and 22.88), T3S% (21.47 and 19.53), and G3S% (33.08 and 34.71) for 23s and 16s rRNA, respectively. Conclusion Amino acids like valine, aspartate, leucine, and phenylalanine hold high codon usage frequency and also found to be present in epitopes KPSYLSALSAHLNDK and FKSFNYNVAIGVRQP that were screened from proteins excinuclease ABC subunit UvrC and 3-oxoacyl-ACP reductase FabG, respectively. This method opens novel ways to determine epitope-based peptide vaccines against different pathogenic organisms.
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Affiliation(s)
- Amit Joshi
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Sunil Krishnan
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Vikas Kaushik
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India.
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Abstract
Although lessons have been learned from previous severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) outbreaks, the rapid evolution of the viruses means that future outbreaks of a much larger scale are possible, as shown by the current coronavirus disease 2019 (COVID-19) outbreak. Therefore, it is necessary to better understand the evolution of coronaviruses as well as viruses in general. This study reports a comparative analysis of the amino acid usage within several key viral families and genera that are prone to triggering outbreaks, including coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2], SARS-CoV, MERS-CoV, human coronavirus-HKU1 [HCoV-HKU1], HCoV-OC43, HCoV-NL63, and HCoV-229E), influenza A (H1N1 and H3N2), flavivirus (dengue virus serotypes 1 to 4 and Zika) and ebolavirus (Zaire, Sudan, and Bundibugyo ebolavirus). Our analysis reveals that the distribution of amino acid usage in the viral genome is constrained to follow a linear order, and the distribution remains closely related to the viral species within the family or genus. This constraint can be adapted to predict viral mutations and future variants of concern. By studying previous SARS and MERS outbreaks, we have adapted this naturally occurring pattern to determine that although pangolin plays a role in the outbreak of COVID-19, it may not be the sole agent as an intermediate animal. In addition to this study, our findings contribute to the understanding of viral mutations for subsequent development of vaccines and toward developing a model to determine the source of the outbreak. IMPORTANCE This study reports a comparative analysis of amino acid usage within several key viral genera that are prone to triggering outbreaks. Interestingly, there is evidence that the amino acid usage within the viral genomes is not random but in a linear order.
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Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences. Viruses 2022; 14:v14010081. [PMID: 35062285 PMCID: PMC8778832 DOI: 10.3390/v14010081] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/31/2021] [Accepted: 12/31/2021] [Indexed: 01/01/2023] Open
Abstract
Porcine circoviruses (PCVs) are distributed in swine herds worldwide and represent a threat to the health of domestic pigs and the profits of the swine industry. Currently, four PCV species, including PCV-1, PCV-2, PCV-3 and PCV-4, have been identified in China. Considering the ubiquitous characteristic of PCVs, the new emerged PCV-4 and the large scale of swine breeding in China, an overall analysis on codon usage bias for Chinese PCV sequences was performed by using the major proteins coding sequences (ORF1 and ORF2) to better understand the relationship of these viruses with their host. The data from genome nucleotide frequency composition and relative synonymous codon usage (RSCU) analysis revealed an overrepresentation of AT pair and the existence of a certain codon usage bias in all PCVs. However, the values of an effective number of codons (ENC) revealed that the bias was of low magnitude. Principal component analysis, ENC-plot, parity rule two analysis and correlation analysis suggested that natural selection and mutation pressure were both involved in the shaping of the codon usage patterns of PCVs. However, a neutrality plot revealed a stronger effect of natural selection than mutation pressure on codon usage patterns. Good host adaptation was also shown by the codon adaptation index analysis for all these viruses. Interestingly, obtained data suggest that PCV-4 might be more adapted to its host compared to other PCVs. The present study obtained insights into the codon usage pattern of PCVs based on ORF1 and ORF2, which further helps the understanding the molecular evolution of these swine viruses.
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Nair RR, Mohan M, Rudramurthy GR, Vivekanandam R, Satheshkumar PS. Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus. Pathogens 2021; 10:1649. [PMID: 34959603 PMCID: PMC8703355 DOI: 10.3390/pathogens10121649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022] Open
Abstract
Trends associated with codon usage in molluscum contagiosum virus (MCV) and factors governing the evolution of codon usage have not been investigated so far. In this study, attempts were made to decipher the codon usage trends and discover the major evolutionary forces that influence the patterns of codon usage in MCV with special reference to sub-types 1 and 2, MCV-1 and MCV-2, respectively. Three hypotheses were tested: (1) codon usage patterns of MCV-1 and MCV-2 are identical; (2) SCUB (synonymous codon usage bias) patterns of MCV-1 and MCV-2 slightly deviate from that of human host to avoid affecting the fitness of host; and (3) translational selection predominantly shapes the SCUB of MCV-1 and MCV-2. Various codon usage indices viz. relative codon usage value, effective number of codons and codon adaptation index were calculated to infer the nature of codon usage. Correspondence analysis and correlation analysis were performed to assess the relative contribution of silent base contents and significance of codon usage indices in defining bias in codon usage. Among the tested hypotheses, only the second and third hypotheses were accepted.
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Affiliation(s)
- Rahul Raveendran Nair
- Centre for Evolutionary Ecology, Aushmath Biosciences, Vadavalli Post, Coimbatore 641041, India
| | - Manikandan Mohan
- College of Pharmacy, University of Georgia, Athens, GA 30605, USA;
| | | | - Reethu Vivekanandam
- Department of Biotechnology, Bharathiyar University, Coimbatore 641046, India;
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Zhang Z, Guo F, Roy A, Yang J, Luo W, Shen X, Irwin DM, Chen RA, Shen Y. Evolutionary perspectives and adaptation dynamics of human seasonal influenza viruses from 2009 to 2019: An insight from codon usage. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 96:105067. [PMID: 34487866 DOI: 10.1016/j.meegid.2021.105067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
The annually recurrent seasonal influenza viruses, namely, influenza A viruses (H1N1/pdm2009 and H3N2) and influenza B viruses, contribute substantially to human disease burden. Elucidation of host adaptation, population dynamics and evolutionary patterns of these viruses contribute to better control of current epidemic situation and bolster efforts towards pandemic preparedness. Present study has been addressed at unraveling the signatures of codon usage and dinucleotide distribution of these seasonal influenza viruses associating with their fitness and ongoing adaptive evolution in human population. Thorough analysis of codon usage adaptation revealed that H3N2 has been exhibited best adapted to human cellular system, which correlate with its highest epidemic intensity as compared with the other seasonal influenza viruses. CpG dinucleotide was found to be strongly avoided among the seasonal influenza viruses with more restraint among influenza B viruses than influenza A viruses, and might be accounted to the strategy of the viral pathogens in evading human immune signals. Dynamic scenes of ongoing evolution in codon usage and elimination of CpG motif among the viruses, which correlate with their distinct host adaption state, signifying the marked impact of selective force operational on the viral genomes, aimed at proficient circulation, enhanced fitness and successful infective manifestations in humans.
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Affiliation(s)
- Zhipeng Zhang
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Fucheng Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Ayan Roy
- Department of Biotechnology, Lovely Professional University, Punjab, India
| | - Jinjin Yang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Wen Luo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xuejuan Shen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M5S 1A8, Canada; Banting and Best Diabetes Centre, University of Toronto, Toronto M5S 1A8, Canada
| | - Rui-Ai Chen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Zhaoqing Institute of Biotechnology, Zhaoqing 526238, China.
| | - Yongyi Shen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; Zhaoqing Institute of Biotechnology, Zhaoqing 526238, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China.
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Li Y, Wang R, Wang H, Pu F, Feng X, Jin L, Ma Z, Ma XX. Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages. Front Cell Infect Microbiol 2021; 11:771010. [PMID: 34804999 PMCID: PMC8602353 DOI: 10.3389/fcimb.2021.771010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 (atg13) is one essential gene for autophagy initiation, yet the evolutionary trends of the atg13 gene at the usages of nucleotide and synonymous codon remains unexplored. According to phylogenetic analyses for the atg13 gene of 226 eukaryotic organisms at the nucleotide and amino acid levels, it is clear that their nucleotide usages exhibit more genetic information than their amino acid usages. Specifically, the overall nucleotide usage bias quantified by information entropy reflected that the usage biases at the first and second codon positions were stronger than those at the third position of the atg13 genes. Furthermore, the bias level of nucleotide ‘G’ usage is highest, while that of nucleotide ‘C’ usage is lowest in the atg13 genes. On top of that, genetic features represented by synonymous codon usage exhibits a species-specific pattern on the evolution of the atg13 genes to some extent. Interestingly, the codon usages of atg13 genes in the ancestor animals (Latimeria chalumnae, Petromyzon marinus, and Rhinatrema bivittatum) are strongly influenced by mutation pressure from nucleotide composition constraint. However, the distributions of nucleotide composition at different codon positions in the atg13 gene display that natural selection still dominates atg13 codon usages during organisms’ evolution.
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Affiliation(s)
- Yicong Li
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Rui Wang
- Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States
| | - Huihui Wang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Feiyang Pu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Xili Feng
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Li Jin
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Zhongren Ma
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Xiao-Xia Ma
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
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Si F, Jiang L, Yu R, Wei W, Li Z. Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype. Front Microbiol 2021; 12:738082. [PMID: 34733253 PMCID: PMC8558211 DOI: 10.3389/fmicb.2021.738082] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV), which classified in the genus Alphacoronavirus, family Coronaviridae, is one of the most important pathogens that cause heavy economic losses in pig industry. Although intensive mutation and recombination analysis of PEDV strains were provided, systematic genome analysis were needed to elucidate the evolution mechanism and codon usage adaptation profiles of the pathogen. Here, a comprehensive investigation was carried out to reveal the systematic evolutionary processes of synonymous codon usage and host-adapted evolution phenotype of PEDV genome. We found a low codon usage bias (CUB) in PEDV genome and that nucleotide compositions, natural selection, mutation pressure and geographical diversity shapes the codon usage patterns of PEDV, with natural selection dominated the overall codon usage bias in PEDV than the others. By using the relative codon deoptimization index (RCDI) and similarity index (SiD) analysis, we observed that genotype II PEDV strains showed the highest level of adaptation phenotype to Sus scrofa than another divergent clade. To the best of our knowledge, this is the first comprehensive report elaborating the codon usage and host adaptation of PEDV. The findings offer an insight into our understanding of factors involved in PEDV evolution, adaptation and fitness toward their hosts.
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Affiliation(s)
- Fusheng Si
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Li Jiang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Ruisong Yu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wenqiang Wei
- Department of Microbiology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Zhen Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Ramos-González PL, Pons T, Chabi-Jesus C, Arena GD, Freitas-Astua J. Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:771983. [PMID: 34804105 PMCID: PMC8602818 DOI: 10.3389/fpls.2021.771983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
The genus Cilevirus groups enveloped single-stranded (+) RNA virus members of the family Kitaviridae, order Martellivirales. Proteins P15, scarcely conserved polypeptides encoded by cileviruses, have no apparent homologs in public databases. Accordingly, the open reading frames (ORFs) p15, located at the 5'-end of the viral RNA2 molecules, are considered orphan genes (ORFans). In this study, we have delved into ORFs p15 and the relatively poorly understood biochemical properties of the proteins P15 to posit their importance for viruses across the genus and theorize on their origin. We detected that the ORFs p15 are under purifying selection and that, in some viral strains, the use of synonymous codons is biased, which might be a sign of adaptation to their plant hosts. Despite the high amino acid sequence divergence, proteins P15 show the conserved motif [FY]-L-x(3)-[FL]-H-x-x-[LIV]-S-C-x-C-x(2)-C-x-G-x-C, which occurs exclusively in members of this protein family. Proteins P15 also show a common predicted 3D structure that resembles the helical scaffold of the protein ORF49 encoded by radinoviruses and the phosphoprotein C-terminal domain of mononegavirids. Based on the 3D structural similarities of P15, we suggest elements of common ancestry, conserved functionality, and relevant amino acid residues. We conclude by postulating a plausible evolutionary trajectory of ORFans p15 and the 5'-end of the RNA2 of cileviruses considering both protein fold superpositions and comparative genomic analyses with the closest kitaviruses, negeviruses, nege/kita-like viruses, and unrelated viruses that share the ecological niches of cileviruses.
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Affiliation(s)
- Pedro L. Ramos-González
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
| | - Tirso Pons
- National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Camila Chabi-Jesus
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | - Gabriella Dias Arena
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
| | - Juliana Freitas-Astua
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
- Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
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50
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Yi K, Kim SY, Bleazard T, Kim T, Youk J, Ju YS. Mutational spectrum of SARS-CoV-2 during the global pandemic. Exp Mol Med 2021; 53:1229-1237. [PMID: 34453107 PMCID: PMC8393781 DOI: 10.1038/s12276-021-00658-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023] Open
Abstract
Viruses accumulate mutations under the influence of natural selection and host-virus interactions. Through a systematic comparison of 351,525 full viral genome sequences collected during the recent COVID-19 pandemic, we reveal the spectrum of SARS-CoV-2 mutations. Unlike those of other viruses, the mutational spectrum of SARS-CoV-2 exhibits extreme asymmetry, with a much higher rate of C>U than U>C substitutions, as well as a higher rate of G>U than U>G substitutions. This suggests directional genome sequence evolution during transmission. The substantial asymmetry and directionality of the mutational spectrum enable pseudotemporal tracing of SARS-CoV-2 without prior information about the root sequence, collection time, and sampling region. This shows that the viral genome sequences collected in Asia are similar to the original genome sequence. Adjusted estimation of the dN/dS ratio accounting for the asymmetrical mutational spectrum also shows evidence of negative selection on viral genes, consistent with previous reports. Our findings provide deep insights into the mutational processes in SARS-CoV-2 viral infection and advance the understanding of the history and future evolution of the virus.
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Affiliation(s)
- Kijong Yi
- grid.37172.300000 0001 2292 0500Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Korea
| | - Su Yeon Kim
- grid.37172.300000 0001 2292 0500Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Korea
| | - Thomas Bleazard
- grid.70909.370000 0001 2199 6511National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, EN6 3QG UK
| | - Taewoo Kim
- grid.37172.300000 0001 2292 0500Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Korea
| | - Jeonghwan Youk
- grid.37172.300000 0001 2292 0500Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Korea ,grid.511166.4GENOME INSIGHT Inc, Daejeon, 34051 Korea
| | - Young Seok Ju
- grid.37172.300000 0001 2292 0500Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Korea ,grid.511166.4GENOME INSIGHT Inc, Daejeon, 34051 Korea
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