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Sharma D, Chakraborty S. RNA editing sites and triplet usage in exomes of bat RNA virus genomes of the family Paramyxoviridae. Microb Pathog 2024; 194:106796. [PMID: 39025379 DOI: 10.1016/j.micpath.2024.106796] [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: 02/29/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Bats contain a diverse spectrum of viral species in their bodies. The RNA virus family Paramyxoviridae tends to infect several vertebrate species, which are accountable for a variety of devastating infections in both humans and animals. Viruses of this kind include measles, mumps, and Hendra. Some synonymous codons are favoured over others in mRNAs during gene-to-protein synthesis process. Such phenomenon is termed as codon usage bias (CUB). Our research emphasized many aspects that shape the CUB of genes in the Paramyxoviridae family found in bats. Here, the nitrogenous base A occurred the most. AT was found to be abundant in the coding sequences of the Paramyxoviridae family. RSCU data revealed that A or T ending codons occurred more frequently than predicted. Furthermore, 3 overrepresented codons (CAT, AGA, and GCA) and 7 underrepresented codons (CCG, TCG, CGC, CGG, CGT, GCG and ACG) were detected in the viral genomes. Correspondence analysis, neutrality plot, and parity plots highlight the combined impact of mutational pressure and natural selection on CUB. The neutrality plot of GC12 against GC3 yielded a regression coefficient value of 0.366, indicating that natural selection had a significant (63.4 %) impact. Moreover, RNA editing analysis was done, which revealed the highest frequency of C to T mutations. The results of our research revealed the pattern of codon usage and RNA editing sites in Paramyxoviridae genomes.
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Affiliation(s)
- Deepika Sharma
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
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Kang Q, Ning S, Sui L, Lu Y, Zhao Y, Shi W, Li Q, Zhang Z. Transcriptomic analysis of entomopathogenic fungus Beauveria bassiana infected by a hypervirulent polymycovirus BbPmV-4. Fungal Biol 2023; 127:958-967. [PMID: 36906386 DOI: 10.1016/j.funbio.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 12/30/2022] [Accepted: 02/15/2023] [Indexed: 02/22/2023]
Abstract
Polymycoviridae is a recently established family of mycoviruses. Beauveria bassiana polymycovirus 4 (BbPmV-4) was previously reported. However, the effect of the virus on host fungus B. bassiana was not clarified. Here, a comparison between virus-free and virus-infected isogenic lines of B. bassiana revealed that BbPmV-4 infection of B. bassiana changes morphology and could lead to decreases in conidiation and increases in virulence against Ostrinia furnacalis larvae. The differential expression of genes between virus-free and virus-infected strains was compared by RNA-Seq and was consistent with the phenotype of B. bassiana. The enhanced pathogenicity may be related to the significant up-regulation of genes encoding mitogen activated protein kinase, cytochrome P450, and polyketide synthase. The results enable studies of the mechanism of interaction between BbPmV-4 and B. bassiana.
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Affiliation(s)
- Qin Kang
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, Jilin Province, PR China; Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, PR China
| | - Siyu Ning
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, Jilin Province, PR China; Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, PR China
| | - Li Sui
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, Jilin Province, PR China
| | - Yang Lu
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, Jilin Province, PR China
| | - Yu Zhao
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, Jilin Province, PR China
| | - Wangpeng Shi
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, PR China.
| | - Qiyun Li
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, Jilin Province, PR China; Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, PR China.
| | - Zhengkun Zhang
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of Agriculture and Rural Areas, Changchun, 130033, Jilin Province, PR 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:ijms23137441. [PMID: 35806445 PMCID: PMC9267111 DOI: 10.3390/ijms23137441] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [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
- Correspondence: ; Tel.: +86-185-027-36960
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Characterization of a Novel Mitovirus of the Sand Fly Lutzomyia longipalpis Using Genomic and Virus-Host Interaction Signatures. Viruses 2020; 13:v13010009. [PMID: 33374584 PMCID: PMC7822452 DOI: 10.3390/v13010009] [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: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Hematophagous insects act as the major reservoirs of infectious agents due to their intimate contact with a large variety of vertebrate hosts. Lutzomyia longipalpis is the main vector of Leishmania chagasi in the New World, but its role as a host of viruses is poorly understood. In this work, Lu. longipalpis RNA libraries were subjected to progressive assembly using viral profile HMMs as seeds. A sequence phylogenetically related to fungal viruses of the genus Mitovirus was identified and this novel virus was named Lul-MV-1. The 2697-base genome presents a single gene coding for an RNA-directed RNA polymerase with an organellar genetic code. To determine the possible host of Lul-MV-1, we analyzed the molecular characteristics of the viral genome. Dinucleotide composition and codon usage showed profiles similar to mitochondrial DNA of invertebrate hosts. Also, the virus-derived small RNA profile was consistent with the activation of the siRNA pathway, with size distribution and 5′ base enrichment analogous to those observed in viruses of sand flies, reinforcing Lu. longipalpis as a putative host. Finally, RT-PCR of different insect pools and sequences of public Lu. longipalpis RNA libraries confirmed the high prevalence of Lul-MV-1. This is the first report of a mitovirus infecting an insect host.
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Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts. Viruses 2019; 11:v11080752. [PMID: 31416257 PMCID: PMC6722529 DOI: 10.3390/v11080752] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023] Open
Abstract
Potato virus M (PVM) is a member of the genus Carlavirus of the family Betaflexviridae and causes large economic losses of nightshade crops. Several previous studies have elucidated the population structure, evolutionary timescale and adaptive evolution of PVM. However, the synonymous codon usage pattern of PVM remains unclear. In this study, we performed comprehensive analyses of the codon usage and composition of PVM based on 152 nucleotide sequences of the coat protein (CP) gene and 125 sequences of the cysteine-rich nucleic acid binding protein (NABP) gene. We observed that the PVM CP and NABP coding sequences were GC-and AU-rich, respectively, whereas U- and G-ending codons were preferred in the PVM CP and NABP coding sequences. The lower codon usage of the PVM CP and NABP coding sequences indicated a relatively stable and conserved genomic composition. Natural selection and mutation pressure shaped the codon usage patterns of PVM, with natural selection being the most important factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analysis revealed that the greatest adaption of PVM was to pepino, followed by tomato and potato. Moreover, similarity Index (SiD) analysis showed that pepino had a greater impact on PVM than tomato and potato. Our study is the first attempt to evaluate the codon usage pattern of the PVM CP and NABP genes to better understand the evolutionary changes of a carlavirus.
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