1
|
Petrzik K. Evolutionary forces at work in partitiviruses. Virus Genes 2019; 55:563-573. [PMID: 31230256 DOI: 10.1007/s11262-019-01680-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023]
Abstract
The family Partitiviridae consists of dsRNA viruses with genome separated into two segments and encoding replicase and capsid protein only. We examined the nucleotide diversity expressed as the ratio dN/dS of nonsynonymous and synonymous substitutions, which has been calculated for 12 representative viruses of all five genera of partitiviruses. We can state that strong purifying selection works on both the RdRp and CP genes and propose that putative positive selection occurs also on the RdRp genes in two viruses. Among the 95 evaluated viruses, wherein both segments had been sequenced, 8 viruses in betapartitiviruses and 9 in alphapartitiviruses were identified as reassortment candidates because they differ extremely in their CP identity even as they are related in terms of RdRp. Furthermore, there are indications that reassortants are present among isolates of different viruses.
Collapse
Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic.
| |
Collapse
|
2
|
Abstract
My long career in virology has been a continuous learning exercise with a very modest start. Virology and related pertinent fields have changed significantly during my lifetime. Sometimes I wish that my career had just started and I could apply all available and state of the art technology to solving problems and explaining intriguing observations. I was always convinced that visiting growers' fields is essential for researchers to get firsthand observations and knowledge of virus disease problems under field conditions. I never thought I would pursue so many avenues of research, yet it is true that research never ends. I enjoyed dissecting strain diversity in a very important plant pathogen like bean pod mottle virus (BPMV) and using BPMV-based vectors to address fundamental virology questions. Lastly, solving the enigma of the transmissible disease of Helminthosporium victoriae and attempting to gain an understanding of the molecular basis of disease in a plant pathogenic fungus were thrilling.
Collapse
Affiliation(s)
- Said A Ghabrial
- Plant Pathology Department, University of Kentucky, Lexington, Kentucky 40546, USA;
| |
Collapse
|
3
|
An evolutionary analysis of the Secoviridae family of viruses. PLoS One 2014; 9:e106305. [PMID: 25180860 PMCID: PMC4152289 DOI: 10.1371/journal.pone.0106305] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/04/2014] [Indexed: 01/03/2023] Open
Abstract
The plant-infecting Secoviridae family of viruses forms part of the Picornavirales order, an important group of non-enveloped viruses that infect vertebrates, arthropods, plants and algae. The impact of the secovirids on cultivated crops is significant, infecting a wide range of plants from grapevine to rice. The overwhelming majority are transmitted by ecdysozoan vectors such as nematodes, beetles and aphids. In this study, we have applied a variety of computational methods to examine the evolutionary traits of these viruses. Strong purifying selection pressures were calculated for the coat protein (CP) sequences of nine species, although for two species evidence of both codon specific and episodic diversifying selection were found. By using Bayesian phylogenetic reconstruction methods CP nucleotide substitution rates for four species were estimated to range from between 9.29×10−3 to 2.74×10−3 (subs/site/year), values which are comparable with the short-term estimates of other related plant- and animal-infecting virus species. From these data, we were able to construct a time-measured phylogeny of the subfamily Comovirinae that estimated divergence of ninety-four extant sequences occurred less than 1,000 years ago with present virus species diversifying between 50 and 250 years ago; a period coinciding with the intensification of agricultural practices in industrial societies. Although recombination (modularity) was limited to closely related taxa, significant and often unique similarities in the protein domains between secovirid and animal infecting picorna-like viruses, especially for the protease and coat protein, suggested a shared ancestry. We discuss our results in a wider context and find tentative evidence to indicate that some members of the Secoviridae might have their origins in insects, possibly colonizing plants in a number of founding events that have led to speciation. Such a scenario; virus infection between species of different taxonomic kingdoms, has significant implications for virus emergence.
Collapse
|
4
|
Kwak HR, Kim MK, Lee YJ, Seo JK, Kim JS, Kim KH, Cha B, Choi HS. Molecular Characterization and Variation of the Broad bean wilt virus 2 Isolates Based on Analyses of Complete Genome Sequences. THE PLANT PATHOLOGY JOURNAL 2013; 29:397-409. [PMID: 25288968 PMCID: PMC4174820 DOI: 10.5423/ppj.oa.03.2013.0036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/26/2013] [Accepted: 05/26/2013] [Indexed: 05/10/2023]
Abstract
The full-genome sequences of fourteen isolates of Broad bean wilt virus 2 (BBWV2), collected from broad bean, pea, spinach, bell pepper and paprika plants in Korea during the years 2006-2012, were determined and analyzed comparatively along with fifteen previously reported BBWV2 genome sequences. Sequence analyses showed that RNA-1 and RNA-2 sequences of BBWV2 Korean isolates consisted of 5950-5956 and 3568-3604 nucleotides, respectively. Full-length genome sequence-based phylogenetic analyses revealed that the BBWV2 Korean isolates could be divided into three major groups comprising GS-I (isolates BB2 and RP7) along with isolate IP, GS-II (isolates BB5, P2, P3 and RP3) along with isolate B935, and GS-III including 16 BBWV2 Korean isolates. Interestingly, GS-III appears to be newly emerged and predominant in Korea. Recombination analyses identified two recombination events in the analyzed BBWV2 population: one in the RNA-1 of isolate K and another one in the RNA-2 of isolate XJ14-3. However, no recombination events were detected in the other 21 Korean isolates. On the other hand, out of 29 BBWV2 isolates, 16 isolates were found to be reassortants, of which each RNA segment (i.e. RNA1 and RNA2) was originated from different parental isolates. Our findings suggested that reassortment rather than recombination is a major evolutionary force in the genetic diversification of BBWV population in Korea.
Collapse
Affiliation(s)
- Hae-Ryun Kwak
- Crop Protection Division, National Academy of Agricultural Science, Suwon 441-707, Korea
- Department of Plant Medicine, Chungbuk National University, Cheongju 361-763, Korea
| | - Mi-Kyeong Kim
- Crop Protection Division, National Academy of Agricultural Science, Suwon 441-707, Korea
| | - Ye-Ji Lee
- Crop Protection Division, National Academy of Agricultural Science, Suwon 441-707, Korea
| | - Jang-Kyun Seo
- Crop Protection Division, National Academy of Agricultural Science, Suwon 441-707, Korea
| | - Jeong-Soo Kim
- Crop Protection Division, National Academy of Agricultural Science, Suwon 441-707, Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| | - Byeongjin Cha
- Department of Plant Medicine, Chungbuk National University, Cheongju 361-763, Korea
| | - Hong-Soo Choi
- Crop Protection Division, National Academy of Agricultural Science, Suwon 441-707, Korea
| |
Collapse
|
5
|
Genetic variability and evolution of broad bean wilt virus 1: role of recombination, selection and gene flow. Arch Virol 2013; 159:779-84. [DOI: 10.1007/s00705-013-1868-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/17/2013] [Indexed: 10/26/2022]
|
6
|
Wei QW, Yu C, Zhang SY, Yang CY, Miriam K, Zhang WN, Dou DL, Tao XR. One-step detection of Bean pod mottle virus in soybean seeds by the reverse-transcription loop-mediated isothermal amplification. Virol J 2012; 9:187. [PMID: 22958497 PMCID: PMC3479068 DOI: 10.1186/1743-422x-9-187] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 09/03/2012] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Bean pod mottle virus (BPMV) is a wide-spread and destructive virus that causes huge economic losses in many countries every year. A sensitive, reliable and specific method for rapid surveillance is urgently needed to prevent further spread of BPMV. METHODS A degenerate reverse-transcription loop-mediated isothermal amplification (RT-LAMP) primer set was designed on the conserved region of BPMV CP gene. The reaction conditions of RT-LAMP were optimized and the feasibility, specificity and sensitivity of this method to detect BPMV were evaluated using the crude RNA rapidly extracted from soybean seeds. RESULTS The optimized RT-LAMP parameters including 6 mM MgCl2, 0.8 M betaine and temperature at 62.5-65°C could successfully amplify the ladder-like bands from BPMV infected soybean seeds. The amplification was very specific to BPMV that no cross-reaction was observed with other soybean viruses. Inclusion of a fluorescent dye makes it easily be detected in-tube by naked eye. The sensitivity of RT-LAMP assay is higher than the conventional RT-PCR under the conditions tested, and the conventional RT-PCR couldn't be used for detection of BPMV using crude RNA extract from soybean seeds. CONCLUSION A highly efficient and practical method was developed for the detection of BPMV in soybean seeds by the combination of rapid RNA extraction and RT-LAMP. This RT-LAMP method has great potential for rapid BPMV surveillance and will assist in preventing further spread of this devastating virus.
Collapse
Affiliation(s)
- Qi-Wei Wei
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Cui Yu
- Shanghai Entry Exit Inspection and Quarantine Bureau, Shanghai 200135, People’s Republic of China
| | - Shu-Ya Zhang
- Shanghai Entry Exit Inspection and Quarantine Bureau, Shanghai 200135, People’s Republic of China
| | - Cui-Yun Yang
- Shanghai Entry Exit Inspection and Quarantine Bureau, Shanghai 200135, People’s Republic of China
| | - Karwitha Miriam
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Wen-Na Zhang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Dao-Long Dou
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Xiao-Rong Tao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| |
Collapse
|
7
|
Abreu EFM, Tinoco MLP, Andrade EC, Aragão FJL. Diversity among isolates of cowpea severe mosaic virus infecting cowpeas in northeastern Brazil. GENETICS AND MOLECULAR RESEARCH 2012; 11:3146-53. [PMID: 23007993 DOI: 10.4238/2012.september.3.3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Eleven isolates of cowpea severe mosaic virus (CPSMV), a member of the genus Comovirus, were selected from 50 samples collected of nine cowpea fields in Northeastern Brazil (Piauí, Ceará, Rio Grande do Norte, Paraíba, Pernambuco, Alagoas, Sergipe, Bahia, and Distrito Federal) and partially sequenced. The RNA1 partial sequence, corresponding to the helicase, viral genome-linked protein, picornain 3C-like protease, and the RNA-directed RNA polymerase genes from CPSMV, had high identity among isolates, varying from 98 to 100%. No evidence was found for intermolecular or intramolecular recombination. Phylogenetic analysis confirmed that the Brazilian CPSMV isolates are substantially different from the CPSMV strain USA. Despite the low variability found among Brazilian CPSMV isolates, there were notable differences in the symptomatology of infected cowpea plants, ranging from mild to moderate. Previous reports have demonstrated an association between CPSMV symptom determinants and helicase. However, we found no correlation between the helicase mutations and symptoms caused by CPSMV. Nevertheless, all isolates with mutation R to K in the protease provoked severe symptoms. This type of information can provide a foundation for the development of strategies to produce durable resistant cowpea lines. It is crucial for strategies based on DNA sequence-dependent technologies, such as inhibition with RNAi.
Collapse
Affiliation(s)
- E F M Abreu
- Embrapa Mandioca e Fruticultura, Cruz das Almas, BA, Brasil
| | | | | | | |
Collapse
|
8
|
Bradshaw JD, Zhang C, Hill JH, Rice ME. Landscape epidemiology of bean pod mottle comovirus: molecular evidence of heterogeneous sources. Arch Virol 2011; 156:1615-9. [DOI: 10.1007/s00705-011-1005-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 04/19/2011] [Indexed: 01/08/2023]
|
9
|
Zhang C, Bradshaw JD, Whitham SA, Hill JH. The development of an efficient multipurpose bean pod mottle virus viral vector set for foreign gene expression and RNA silencing. PLANT PHYSIOLOGY 2010; 153:52-65. [PMID: 20200069 PMCID: PMC2862437 DOI: 10.1104/pp.109.151639] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 03/01/2010] [Indexed: 05/18/2023]
Abstract
Plant viral vectors are valuable tools for heterologous gene expression, and because of virus-induced gene silencing (VIGS), they also have important applications as reverse genetics tools for gene function studies. Viral vectors are especially useful for plants such as soybean (Glycine max) that are recalcitrant to transformation. Previously, two generations of bean pod mottle virus (BPMV; genus Comovirus) vectors have been developed for overexpressing and silencing genes in soybean. However, the design of the previous vectors imposes constraints that limit their utility. For example, VIGS target sequences must be expressed as fusion proteins in the same reading frame as the viral polyprotein. This requirement limits the design of VIGS target sequences to open reading frames. Furthermore, expression of multiple genes or simultaneous silencing of one gene and expression of another was not possible. To overcome these and other issues, a new BPMV-based vector system was developed to facilitate a variety of applications for gene function studies in soybean as well as in common bean (Phaseolus vulgaris). These vectors are designed for simultaneous expression of multiple foreign genes, insertion of noncoding/antisense sequences, and simultaneous expression and silencing. The simultaneous expression of green fluorescent protein and silencing of phytoene desaturase shows that marker gene-assisted silencing is feasible. These results demonstrate the utility of this BPMV vector set for a wide range of applications in soybean and common bean, and they have implications for improvement of other plant virus-based vector systems.
Collapse
Affiliation(s)
- Chunquan Zhang
- Department of Plant Pathology, Iowa State University, Ames, Iowa 50011, USA.
| | | | | | | |
Collapse
|
10
|
Hu X, Karasev AV, Brown CJ, Lorenzen JH. Sequence characteristics of potato virus Y recombinants. J Gen Virol 2009; 90:3033-3041. [PMID: 19692546 DOI: 10.1099/vir.0.014142-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Potato virus Y (PVY) is one of the most economically important plant pathogens. The PVY genome has a high degree of genetic variability and is also subject to recombination. New recombinants have been reported in many countries since the 1980s, but the origin of these recombinant strains and the physical and evolutionary mechanisms driving their emergence are not clear at the moment. The replicase-mediated template-switching model is considered the most likely mechanism for forming new RNA virus recombinants. Two factors, RNA secondary structure (especially stem-loop structures) and AU-rich regions, have been reported to affect recombination in this model. In this study, we investigated the influence of these two factors on PVY recombination from two perspectives: their distribution along the whole genome and differences between regions flanking the recombination junctions (RJs). Based on their distributions, only a few identified RJs in PVY genomes were located in lower negative FORS-D, i.e. having greater secondary-structure potential and higher AU-content regions, but most RJs had more negative FORS-D values upstream and/or higher AU content downstream. Our whole-genome analyses showed that RNA secondary structures and/or AU-rich regions at some sites may have affected PVY recombination, but in general they were not the main forces driving PVY recombination.
Collapse
Affiliation(s)
- Xiaojun Hu
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID 83844, USA
- Department of Plant, Soil, and Entomological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Alexander V Karasev
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID 83844, USA
- Department of Plant, Soil, and Entomological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Celeste J Brown
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID 83844, USA
| | - Jim H Lorenzen
- International Institute of Tropical Agriculture, Kampala, Uganda
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID 83844, USA
| |
Collapse
|
11
|
Vigne E, Marmonier A, Fuchs M. Multiple interspecies recombination events within RNA2 of Grapevine fanleaf virus and Arabis mosaic virus. Arch Virol 2008; 153:1771-6. [DOI: 10.1007/s00705-008-0182-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Accepted: 07/18/2008] [Indexed: 10/21/2022]
|