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Tavoosi M, Moradi Z, Mehrvar M. First report of Turnip mosaic virus infecting saffron in Iran. Virusdisease 2022; 33:489-491. [PMID: 36447818 PMCID: PMC9701283 DOI: 10.1007/s13337-022-00798-4] [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: 08/27/2022] [Accepted: 10/03/2022] [Indexed: 11/30/2022] Open
Abstract
Saffron (Crocus sativus) is widely used as an important herbal medicine crop worldwide. Iran is the largest producer and exporter of saffron in the world. Turnip mosaic virus (TuMV) is a species of the genus Potyvirus, which infects a wide range of plants species. During the autumn of 2019, saffron plants with symptoms including colour breaking of the flowers, chlorosis and mild mosaic of leaves were collected from the major saffron cultivation areas of Iran. After the isolation of total RNA from diseased samples, RT-PCR was done using TuMV-specific primers. Amplicons of two selected isolates were purified, cloned, and sequenced. BLASTn of obtained sequences indicated high similarity with TuMV sequences. To the best of our knowledge, this is the first finding of TuMV infection in the saffron plant of Iran.
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Affiliation(s)
- Masoumeh Tavoosi
- Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, P.O. BOX 91779-1163, Mashhad, Iran
| | - Zohreh Moradi
- Department of Plant Pathology, Faculty of Crop Sciences, Sari Agricultural Sciences and Natural Resources University, P.O. BOX 578, Sari, Iran
| | - Mohsen Mehrvar
- Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, P.O. BOX 91779-1163, Mashhad, Iran
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2
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Muhammad K, Herath V, Ahmed K, Tahir M, Verchot J. Genetic diversity and molecular evolution of sugarcane mosaic virus, comparing whole genome and coat protein sequence phylogenies. Arch Virol 2022; 167:2239-2247. [PMID: 35999328 PMCID: PMC9556425 DOI: 10.1007/s00705-022-05572-x] [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: 04/04/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022]
Abstract
Sugarcane mosaic virus (SCMV) is a widely distributed potyvirus that causes mosaic disease in sugarcane, maize, sorghum, canna, and other monocot species worldwide. This study used 139 SCMV full-length genome sequences to analyze the phylogenetic relatedness of geographically distinct isolates. The phylogenetic analysis revealed four major groups of SCMV isolates that relate to their primary host. The geographic locations for some isolates appear to be mismatched within the tree, suggesting either that convergent molecular evolution has occurred or that the tree reconstruction produces statistically significant incongruences that create uncertainty in the true evolutionary relationships of these virus isolates. Recombination analysis showed hot spots across most of the genome except in the coat protein (CP) coding region. We examined 161 SCMV CP sequences from the GenBank database, including sequences from samples collected in Pakistan, a region that has not been included in prior phylogenetic studies. These data suggest that the SCMV isolates from sugarcane (Saccharum officinarum) predate isolates from all other hosts, regardless of their geographic origins.
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Affiliation(s)
- Khalid Muhammad
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Venura Herath
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA.,Department of Agriculture Biology, Faculty of Agriculture, University of Peradeniya, 20400, Peradeniya, Sri Lanka
| | - Khadija Ahmed
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Tahir
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA.
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3
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Bashir S, Naqvi SMS, Muhammad A, Hussain I, Ali K, Khan MR, Farrakh S, Yasmin T, Hyder MZ. Banana bunchy top virus genetic diversity in Pakistan and association of diversity with recombination in its genomes. PLoS One 2022; 17:e0263875. [PMID: 35255085 PMCID: PMC8901069 DOI: 10.1371/journal.pone.0263875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/30/2022] [Indexed: 11/30/2022] Open
Abstract
Banana Bunchy top virus (BBTV) is a multipartite circular single strand DNA virus that belongs to genus Babuvirus and family Nanoviridae. It causes significant crop losses worldwide and also in Pakistan. BBTV is present in Pakistan since 1988 however, till now only few (about twenty only) sequence of genomic components have been reported from the country. To have insights into current genetic diversity in Pakistan fifty-seven genomic components including five complete genomes (comprises of DNA-R, -U3, -S, -M, -C and -N components) were sequenced in this study. The genetic diversity analysis of populations from Pakistan showed that DNA-R is highly conserved followed by DNA-N, whereas DNA-U3 is highly diverse with the most diverse Common Region Stem-loop (CR-SL) in BBTV genome, a functional region, which previously been reported to have undergone recombination in Pakistani population. A Maximum Likelihood (ML) phylogenetic analysis of entire genomes of isolates by using sequence of all the components concatenated together with the reported genomes around the world revealed deeper insights about the origin of the disease in Pakistan. A comparison of the genetic diversity of Pakistani and entire BBTV populations around the world indicates that there exists a correlation between genetic diversity and recombination. Population genetics analysis indicated that the degree of selection pressure differs depending on the area and genomic component. A detailed analysis of recombination across various components and functional regions suggested that recombination is closely associated with the functional parts of BBTV genome showing high genetic diversity. Both genetic diversity and recombination analyses suggest that the CR-SL is a recombination hotspot in all BBTV genomes and among the six components DNA-U3 is the only recombined component that has extensively undergone inter and intragenomic recombination. Diversity analysis of recombinant regions results on average one and half fold increase and, in some cases up to four-fold increase due to recombination. These results suggest that recombination is significantly contributing to the genetic diversity of BBTV populations around the world.
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Affiliation(s)
- Sana Bashir
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Aish Muhammad
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Iqbal Hussain
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Kazim Ali
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Sumaira Farrakh
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Tayyaba Yasmin
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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He Z, Qin L, Wang W, Ding S, Xu X, Zhang S. The dinucleotide composition of sugarcane mosaic virus is shaped more by protein coding regions than by host species. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105165. [PMID: 34861431 DOI: 10.1016/j.meegid.2021.105165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022]
Abstract
Sugarcane mosaic virus (SCMV), which belongs to the Potyvirus genus of the family Potyviridae, causes mosaic diseases in canna, sugarcane and maize worldwide. Previously, the genetic variations, timescale, codon usage patterns and host adaptions of SCMV were determined. However, the dinucleotide composition and the dinucleotide bias from hosts or the protein coding regions of the virus have yet to be investigated. In this study, comprehensive analyses of the dinucleotide composition and dinucleotide bias from hosts, lineages and protein coding regions of SCMV were performed using 131 complete genomic sequences. We found that UpG and CpA were largely overrepresented while UpA, CpC, and CpG were largely underrepresented in the polyprotein and 11 protein coding region data sets. SCMV dinucleotide composition bias is more strongly dependent on the protein coding regions than on hosts. A weak association between the dinucleotide composition and SCMV lineages was also observed. Our analysis provides a novel perspective on the molecular evolutionary mechanisms of SCMV and may provide a better understanding of future research on the origin and evolutionary patterns of SCMV.
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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.
| | - Lang Qin
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, Jiangsu Province, PR China
| | - Wenzhi Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Shiwen Ding
- 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
| | - Shuzhen Zhang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.
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Hincapie M, Sood S, Mollov D, Odero DC, Grisham M, Rott P. Eight Species of Poaceae Are Hosting Different Genetic and Pathogenic Strains of Sugarcane Mosaic Virus in the Everglades Agricultural Area. PHYTOPATHOLOGY 2021; 111:1862-1869. [PMID: 33622050 DOI: 10.1094/phyto-11-20-0489-r] [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] [Indexed: 06/12/2023]
Abstract
Sugarcane mosaic virus (SCMV) was detected by reverse transcription polymerase chain reaction in eight different species of the Poaceae family in the Everglades Agricultural Area (EAA) of south Florida: broadleaf signalgrass (Urochloa platyphylla), Columbus grass (Sorghum almum), goosegrass (Eleusine indica), maize (Zea mays), sorghum (Sorghum bicolor), St. Augustine grass (Stenotaphrum secundatum), southern crabgrass (Digitaria ciliaris), and sugarcane (Saccharum interspecific hybrids). Based on their coat protein (CP) gene sequence, 62 isolates of SCMV from Florida and 29 worldwide isolates representing the known genetic diversity of this virus were distributed into eight major phylogenetic groups. SCMV isolates infecting Columbus grass, maize, and sorghum in Florida formed a unique group, whereas virus isolates infecting sugarcane in the United States (Florida and Louisiana) clustered with isolates from other countries. Based on the entire genome coding region, SCMV isolates infecting sugarcane in Florida were closest to virus isolates infecting sorghum species or St. Augustine grass. Virus isolates from Columbus grass, St. Augustine grass, and sugarcane showed different virulence patterns after mechanical inoculation of Columbus grass, St. Augustine grass, and sugarcane plants, thus proving that these isolates were different pathogenic strains. Sugarcane was symptomless and tested negative for SCMV by tissue blot immunoassay after inoculation with crude sap from SCMV-infected Columbus grass, indicating that Columbus grass was not a reservoir for SCMV infecting sugarcane in the EAA. Close CP sequence identity between isolates of SCMV from Columbus grass, maize, and sorghum suggested that the same virus strain was naturally spreading between these three plants in south Florida.
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Affiliation(s)
- Martha Hincapie
- University of Florida, Everglades Research and Education Center, Plant Pathology Department, Belle Glade, FL 33430, U.S.A
| | - Sushma Sood
- USDA-ARS, Sugarcane Field Station, Canal Point, FL 33438, U.S.A
| | - Dimitre Mollov
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD 20705, U.S.A
| | - D Calvin Odero
- University of Florida, Everglades Research and Education Center, Agronomy Department, Belle Glade, FL 33430, U.S.A
| | | | - Philippe Rott
- University of Florida, Everglades Research and Education Center, Plant Pathology Department, Belle Glade, FL 33430, U.S.A
- CIRAD, UMR PHIM, 34398 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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6
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Widyaningrum S, Pujiasih DR, Sholeha W, Harmoko R, Sugiharto B. Induction of resistance to sugarcane mosaic virus by RNA interference targeting coat protein gene silencing in transgenic sugarcane. Mol Biol Rep 2021; 48:3047-3054. [PMID: 33837900 DOI: 10.1007/s11033-021-06325-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/31/2021] [Indexed: 11/27/2022]
Abstract
Sugarcane mosaic virus (SCMV) is a serious disease of monocotyledonous plants, including sugarcane, causing deterioration in both growth and productivity. RNA interference (RNAi) inhibits gene expression through RNA-mediated sequence-specific interactions and is considered an effective approach to control viral infection in plants. In this study, the SCMVCp gene encoding the coat protein (CP) was inserted into the pGreen-0179 plasmid in both sense and antisense orientations. Cauliflower mosaic virus (CaMV) and Zea mays ubiquitin (Ubi) promoters were selected to drive the transcription of the intron-hairpin constructs, called HpSCMVCp-CaMV and HpSCMVCp-Ubi, respectively. Transgenic sugarcane expressing these constructs was generated through Agrobacterium-mediated transformation. This transformation method produced a high percentage of transgenic plants for both HpSCMVCp-CaMV and HpSCMVCp-Ubi, as confirmed by PCR analysis. Southern blotting revealed a single stable insertion of the DNA target in the genome of transgenic sugarcane lines. After artificial virus infection, lines that developed mosaic symptoms were classified as susceptible, whereas those that remained green without symptoms were classified as resistant at 42 days post-inoculation. Immunoblotting revealed CP expression at 37 kDa in susceptible and non-transgenic sugarcane, but not in resistant lines. RT-PCR analysis confirmed viral Cp and Nib gene expression in susceptible lines and their absence in resistant lines. Interestingly, upon comparison of effectivity, CaMV and Ubi promoter-driven gene expression resulted in 57.69% and 82.35% resistant sugarcane lines, respectively. Thus, we concluded that RNAi is effective for inducing resistance against SCMV and that the Ubi promoter is an effective promoter for producing transgenic sugarcane.
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Affiliation(s)
- Suvia Widyaningrum
- Laboratory of Molecular Biology and Biotechnology, Center for Development of Advanced Science and Technology (CDAST), Jember University, Jln. Kalimantan 37, Jember, 68121, Indonesia.,Postgraduate Program in Biotechnology, Jember University, Jln. Kalimantan 37, Jember, 68121, Indonesia
| | - Dwi Ratna Pujiasih
- Laboratory of Molecular Biology and Biotechnology, Center for Development of Advanced Science and Technology (CDAST), Jember University, Jln. Kalimantan 37, Jember, 68121, Indonesia.,Department of Biology, Faculty of Mathematics and Natural Sciences, Jember University, Jln. Kalimantan 37, Jember, 68121, Indonesia
| | - Wardatus Sholeha
- Laboratory of Molecular Biology and Biotechnology, Center for Development of Advanced Science and Technology (CDAST), Jember University, Jln. Kalimantan 37, Jember, 68121, Indonesia.,Department of Biology, Faculty of Mathematics and Natural Sciences, Jember University, Jln. Kalimantan 37, Jember, 68121, Indonesia
| | - Rikno Harmoko
- Indonesian Institute of Sciences, Jl. Raya Jakarta-Bogor, Cibinong, Bogor, 16911, Indonesia
| | - Bambang Sugiharto
- Laboratory of Molecular Biology and Biotechnology, Center for Development of Advanced Science and Technology (CDAST), Jember University, Jln. Kalimantan 37, Jember, 68121, Indonesia. .,Postgraduate Program in Biotechnology, Jember University, Jln. Kalimantan 37, Jember, 68121, Indonesia. .,Department of Biology, Faculty of Mathematics and Natural Sciences, Jember University, Jln. Kalimantan 37, Jember, 68121, Indonesia.
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7
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Cho M, Kim H, Je M, Son HS. Analysis of Codon Usage Patterns in the Human Papillomavirus Oncogenes. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200614173136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Background:
Persistent high-risk genital human papillomavirus (HPV) infection is a major cause of cervical
cancer in women. The products of the viral transforming genes E6 and E7 in the high-risk HPVs are known to be similar
in their amino acid composition and structure. We performed a comparative analysis of codon usage patterns in the E6
and E7 genes of HPVs.
Methods:
The E6 and E7 gene sequences of eight HPV subtypes were analyzed to determine their nucleotide
composition, relative synonymous codon usage (RSCU), effective number of codons (ENC), neutrality, genetic
variability, selection pressure, and codon adaptation index (CAI). Additionally, a correspondence analysis (CoA) was
performed.
Results:
The analysis to determine the effects of differences in composition on the codon usage patterns revealed that
there may be usage bias for ‘A’ nucleotides. This was consistent with the results of the RSCU analysis, which
demonstrated that the selection of A/T-rich patterns and the preference for A/T-ended codons in HPVs are influenced by
compositional constraints. Moreover, the results reveal that selection pressure plays an important role in the CoA results
for the RSCU values, Tajima’s D tests, and neutrality tests.
Conclusion:
The results of this study are consistent with previous findings that most papillomavirus genes are under
purifying selection pressure, which limits changes to the encoded proteins. Natural selection and mutation pressures
resulting in changes in the nucleotide composition and codon usage bias in the two tumor genes of HPV act differently
during the evolution of the HPV subtype; thus, throughout the viral life cycle, HPV can constantly evolve to adapt to a
new environment.
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Affiliation(s)
- Myeongji Cho
- Laboratory of Computational Biology & Bioinformatics, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826,Korea
| | - Hayeon Kim
- Department of Biomedical Laboratory Science, Kyungdong University, 815 Gyeonhwon-ro, Munmak, Wonju, Gangwondo, 24695,Korea
| | - Mikyeong Je
- Laboratory of Computational Biology & Bioinformatics, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826,Korea
| | - Hyeon S. Son
- Laboratory of Computational Biology & Bioinformatics, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826,Korea
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Xu XJ, Li HG, Cheng DJ, Liu LZ, Geng C, Tian YP, Li XD. A Spontaneous Complementary Mutation Restores the RNA Silencing Suppression Activity of HC-Pro and the Virulence of Sugarcane Mosaic Virus. FRONTIERS IN PLANT SCIENCE 2020; 11:1279. [PMID: 32973838 PMCID: PMC7472499 DOI: 10.3389/fpls.2020.01279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/05/2020] [Indexed: 05/26/2023]
Abstract
Cross-protection is a promising measure to control plant viral diseases. Reverse genetics had been recently adopted to generate attenuated mutants that have potential in cross-protection. But studies on the variability of the progeny viruses of the attenuated mutants are scarce. Sugarcane mosaic virus (SCMV; genus Potyvirus, family Potyviridae) is the prevalent virus inducing maize dwarf mosaic disease in China. Here, we showed that the substitution of arginine with isoleucine in the FRNK motif at position 184 of helper component-proteinase (HC-Pro) abolished its RNA silencing suppression (RSS) activity, drastically reduced the virulence and accumulation level of SCMV, and impaired the synergism between SCMV and maize chlorotic mottle virus. The attenuated mutant could protect maize plants from a severe infection of SCMV. However, a spontaneous mutation of glycine at position 440 to arginine in HC-Pro rescued the virulence and synergism with maize chlorotic mottle virus of SCMV and the RSS activity of HC-Pro. Similar results were obtained with tobacco vein banding mosaic virus and watermelon mosaic virus. These results provide novel evidence for the complementary mutation of potyviruses in maintaining the HC-Pro RSS activity and potyviral virulence and remind us of evaluating the potential risk of attenuated mutants thoroughly before applying for the control of plant viral diseases via cross-protection.
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Affiliation(s)
- Xiao-Jie Xu
- Shandong Province Key Laboratory for Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Huan-Gai Li
- Protein Science Laboratory of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
| | - De-Jie Cheng
- Shandong Province Key Laboratory for Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Ling-Zhi Liu
- Shandong Province Key Laboratory for Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Chao Geng
- Shandong Province Key Laboratory for Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Yan-Ping Tian
- Shandong Province Key Laboratory for Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Xiang-Dong Li
- Shandong Province Key Laboratory for Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, China
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He Z, Dong Z, Gan H. Genetic changes and host adaptability in sugarcane mosaic virus based on complete genome sequences. Mol Phylogenet Evol 2020; 149:106848. [PMID: 32380283 DOI: 10.1016/j.ympev.2020.106848] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/10/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022]
Abstract
Sugarcane mosaic virus (SCMV), a member of the genus Potyvirus in the family Potyviridae, is an important pathogen that causes mosaic diseases in maize, sugarcane, canna and other graminaceous species worldwide. Previously, several reports have showed the genetic variation and population structure of SCMV. However, the evolutionary dynamics, synonymous codon usage pattern and adaptive evolution of the virus is unclear. In this study, we performed comprehensive analyses of phylodynamics, composition bias and codon usage of SCMV using 108 complete genomic sequences. Our phylogenetic analysis found six host- and geographically confined phylogenetic lineages within the SCMV non-recombinant isolates. We found a relatively stable and conserved genomic composition with a lower codon usage choice in the SCMV protein coding sequences. Mutation pressure and natural selection have shaped the codon usage patterns of the SCMV protein coding sequences with natural selection being the dominant factor. The codon adaptation index (CAI), relative codon deoptimization index (RCDI) and similarity index (SiD) analyses revealed a stronger correlation between SCMV and maize than between SCMV and sugarcane or canna. Our study is the first to evaluate the codon usage pattern of SCMV based on complete sequences and may provide a better understanding of the origin of SCMV and its evolutionary patterns for future research.
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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.
| | - Zhuozhuo Dong
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
| | - Haifeng Gan
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
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10
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Cho M, Kim H, Son HS. Codon usage patterns of LT-Ag genes in polyomaviruses from different host species. Virol J 2019; 16:137. [PMID: 31727090 PMCID: PMC6854729 DOI: 10.1186/s12985-019-1245-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/17/2019] [Indexed: 11/10/2022] Open
Abstract
Background Polyomaviruses (PyVs) have a wide range of hosts, from humans to fish, and their effects on hosts vary. The differences in the infection characteristics of PyV with respect to the host are assumed to be influenced by the biochemical function of the LT-Ag protein, which is related to the cytopathic effect and tumorigenesis mechanism via interaction with the host protein. Methods We carried out a comparative analysis of codon usage patterns of large T-antigens (LT-Ags) of PyVs isolated from various host species and their functional domains and sequence motifs. Parity rule 2 (PR2) and neutrality analysis were applied to evaluate the effects of mutation and selection pressure on codon usage bias. To investigate evolutionary relationships among PyVs, we carried out a phylogenetic analysis, and a correspondence analysis of relative synonymous codon usage (RSCU) values was performed. Results Nucleotide composition analysis using LT-Ag gene sequences showed that the GC and GC3 values of avian PyVs were higher than those of mammalian PyVs. The effective number of codon (ENC) analysis showed host-specific ENC distribution characteristics in both the LT-Ag gene and the coding sequences of its domain regions. In the avian and fish PyVs, the codon diversity was significant, whereas the mammalian PyVs tended to exhibit conservative and host-specific evolution of codon usage bias. The results of our PR2 and neutrality analysis revealed mutation bias or highly variable GC contents by showing a narrow GC12 distribution and wide GC3 distribution in all sequences. Furthermore, the calculated RSCU values revealed differences in the codon usage preference of the LT-AG gene according to the host group. A similar tendency was observed in the two functional domains used in the analysis. Conclusions Our study showed that specific domains or sequence motifs of various PyV LT-Ags have evolved so that each virus protein interacts with host cell targets. They have also adapted to thrive in specific host species and cell types. Functional domains of LT-Ag, which are known to interact with host proteins involved in cell proliferation and gene expression regulation, may provide important information, as they are significantly related to the host specificity of PyVs.
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Affiliation(s)
- Myeongji Cho
- Laboratory of Computational Biology & Bioinformatics, Institute of Public Health and Environment, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Hayeon Kim
- Department of Biomedical Laboratory Science, Kyungdong University, 815 Gyeonhwon-ro, Munmak, Wonju, Gangwondo, 24695, South Korea
| | - Hyeon S Son
- Laboratory of Computational Biology & Bioinformatics, Institute of Public Health and Environment, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea. .,SNU Bioinformatics Institute, Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea.
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11
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Moradi Z, Mehrvar M, Nazifi E. Genetic diversity and biological characterization of sugarcane streak mosaic virus isolates from Iran. Virusdisease 2018; 29:316-323. [PMID: 30159366 DOI: 10.1007/s13337-018-0461-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/29/2018] [Indexed: 11/26/2022] Open
Abstract
Sugarcane streak mosaic virus (SCSMV; genus Poacevirus, family Potyviridae) is a major causal agent of sugarcane mosaic disease in Asia. A survey of SCSMV was conducted in cultivated fields in Khuzestan province, southwestern Iran. Sixty-five sugarcane leaf samples showing mosaic symptoms were collected and investigated by RT-PCR. Almost one-fourth of the samples were found to be infected by SCSMV. To verify molecular variability, 12 SCSMV isolates were sequenced and analyzed by comparing partial NIb-CP gene sequences. The nucleotide identity among Iranian isolates was 83.1-99.8%, indicating high nucleotide variability, while amino acid identity was 95.2-100%, which suggesting selection for amino acid conservation. They shared nucleotide identities of 76.2-99.1% with those of other SCSMV isolates available in GenBank, the highest with isolates from Pakistan (PAK), India (IND671) and China (M117, KT257289). Further analysis was conducted based on complete CI coding region to gain more insight into the phylogenetic relationships of Iranian SCSMV compared to those from other Asian countries. Iranian isolates shared identities of 79.8-89.0% (nucleotide) and 94.8-98.6% (amino acid) with those from other geographical regions in the CI gene. The highest nucleotide identity of Iranian isolates was with isolates PAK (Pakistan), M121 (JQ975096, China) and IND671 (India), respectively. The phylogenetic trees (based on CI and NIb-CP) revealed the segregation of SCSMV isolates into two major divergent evolutionary lineages that reflect geographical origin of the isolates (with minor exception). Phylogenetic analyses grouped Iranian SCSMV isolates together with isolates from Pakistan, India and just one Chinese isolate in group II. Biological results showed that Iranian SCSMV isolates infect sugarcane, sorghum, maize and some wild grasses, causing mosaic symptoms on the leaves.
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Affiliation(s)
- Zohreh Moradi
- 1Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohsen Mehrvar
- 1Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ehsan Nazifi
- 2Department of Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran
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