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Tripathi JN, Ntui VO, Tripathi L. Precision genetics tools for genetic improvement of banana. THE PLANT GENOME 2024; 17:e20416. [PMID: 38012108 DOI: 10.1002/tpg2.20416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/22/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023]
Abstract
Banana is an important food security crop for millions of people in the tropics but it faces challenges from diseases and pests. Traditional breeding methods have limitations, prompting the exploration of precision genetic tools like genetic modification and genome editing. Extensive efforts using transgenic approaches have been made to develop improved banana varieties with resistance to banana Xanthomonas wilt, Fusarium wilt, and nematodes. However, these efforts should be extended for other pests, diseases, and abiotic stresses. The commercialization of transgenic crops still faces continuous challenges with regulatory and public acceptance. Genome editing, particularly CRISPR/Cas, offers precise modifications to the banana genome and has been successfully applied in the improvement of banana. Targeting specific genes can contribute to the development of improved banana varieties with enhanced resistance to various biotic and abiotic constraints. This review discusses recent advances in banana improvement achieved through genetic modification and genome editing.
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Affiliation(s)
| | | | - Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
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2
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Tennant P, Rampersad S, Alleyne A, Johnson L, Tai D, Amarakoon I, Roye M, Pitter P, Chang PG, Myers Morgan L. Viral Threats to Fruit and Vegetable Crops in the Caribbean. Viruses 2024; 16:603. [PMID: 38675944 PMCID: PMC11053604 DOI: 10.3390/v16040603] [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: 01/26/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Viruses pose major global challenges to crop production as infections reduce the yield and quality of harvested products, hinder germplasm exchange, increase financial inputs, and threaten food security. Small island or archipelago habitat conditions such as those in the Caribbean are particularly susceptible as the region is characterized by high rainfall and uniform, warm temperatures throughout the year. Moreover, Caribbean islands are continuously exposed to disease risks because of their location at the intersection of transcontinental trade between North and South America and their role as central hubs for regional and global agricultural commodity trade. This review provides a summary of virus disease epidemics that originated in the Caribbean and those that were introduced and spread throughout the islands. Epidemic-associated factors that impact disease development are also discussed. Understanding virus disease epidemiology, adoption of new diagnostic technologies, implementation of biosafety protocols, and widespread acceptance of biotechnology solutions to counter the effects of cultivar susceptibility remain important challenges to the region. Effective integrated disease management requires a comprehensive approach that should include upgraded phytosanitary measures and continuous surveillance with rapid and appropriate responses.
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Affiliation(s)
- Paula Tennant
- Department of Life Sciences, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica;
- Biotechnology Centre, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica; (D.T.); (M.R.); (P.P.)
| | - Sephra Rampersad
- Department of Life Sciences, The University of the West Indies, St. Augustine 999183, Trinidad and Tobago;
| | - Angela Alleyne
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill, Bridgetown BB11000, Barbados;
| | - Lloyd Johnson
- Department of Life Sciences, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica;
| | - Deiondra Tai
- Biotechnology Centre, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica; (D.T.); (M.R.); (P.P.)
| | - Icolyn Amarakoon
- Department of Basic Medical Sciences, Biochemistry Section, Faculty of Medical Sciences Teaching and Research Complex, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica;
| | - Marcia Roye
- Biotechnology Centre, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica; (D.T.); (M.R.); (P.P.)
| | - Patrice Pitter
- Biotechnology Centre, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica; (D.T.); (M.R.); (P.P.)
- Ministry of Agriculture, Bodles Research Station, Old Harbour, St. Catherine JMACE18, Jamaica; (P.-G.C.); (L.M.M.)
| | - Peta-Gaye Chang
- Ministry of Agriculture, Bodles Research Station, Old Harbour, St. Catherine JMACE18, Jamaica; (P.-G.C.); (L.M.M.)
| | - Lisa Myers Morgan
- Ministry of Agriculture, Bodles Research Station, Old Harbour, St. Catherine JMACE18, Jamaica; (P.-G.C.); (L.M.M.)
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3
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Ricciuti E, Laboureau N, Noumbissié G, Chabannes M, Sukhikh N, Pooggin MM, Iskra-Caruana ML. Extrachromosomal viral DNA produced by transcriptionally active endogenous viral elements in non-infected banana hybrids impedes quantitative PCR diagnostics of banana streak virus infections in banana hybrids. J Gen Virol 2021; 102. [PMID: 34726592 DOI: 10.1099/jgv.0.001670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The main edible and cultivated banana varieties are intra- and interspecific hybrids of the two main Musa species, Musa acuminata and Musa balbisiana, having diploid genomes denoted A and B, respectively. The B genome naturally hosts sequences of banana streak virus (BSV) named endogenous BSV (eBSV). Upon stress, eBSVs are identified as the origin of BSV infection for at least three BSV species, causing banana streak disease. For each of the three species, BSV and eBSV share >99.9 % sequence identity, complicating PCR-based diagnosis of viral infection in the B genome-containing bananas. Here, we designed a quantitative PCR-based method to only quantify episomal BSV particles produced, overcoming the limitation of eBSV also being detected by qPCR by using it as a 'calibrator'. However, our results revealed unexpected variation of eBSV amplification in calibrator plants composed of a clonal population of 53 replicating virus-free banana hybrids with the same AAB genotype. Our in-depth molecular analyses suggest that this calibrator variation is due to the variable abundance of non-encapsidated extrachromosomal viral DNA, likely produced via the transcription of eBSVs, followed by occasional reverse transcription. We also present evidence that accumulation of viral transcripts in AAB plants is downregulated both at post-transcriptional and transcriptional levels by an RNA interference mechanism that keeps the plants free of virus infection. Finally, we recommend that such eBSV amplification variation be taken into account to establish a quantitative viral diagnostic for banana plants with the B genome.
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Affiliation(s)
- Emeline Ricciuti
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France
| | - Nathalie Laboureau
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France.,CIRAD, UMR PHIM, 34090 Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, INRAE, IRD, CIRAD, Institut Agro, Montpellier, France
| | - Guy Noumbissié
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France
| | - Matthieu Chabannes
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France.,CIRAD, UMR AGAP Intitute, F-34398 Montpellier, France.,AGAP Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Natalia Sukhikh
- PHIM Plant Health Institute, Univ Montpellier, INRAE, IRD, CIRAD, Institut Agro, Montpellier, France.,Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences. Moscow, 119071, Russia
| | - Mikhail M Pooggin
- PHIM Plant Health Institute, Univ Montpellier, INRAE, IRD, CIRAD, Institut Agro, Montpellier, France
| | - Marie-Line Iskra-Caruana
- CIRAD, UMR BGPI, Univ Montpellier, INRAE, Montpellier SupAgro, Montpellier, 34984, France.,CIRAD, DGD-RS, F-34398 Montpellier, France
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Chabannes M, Gabriel M, Aksa A, Galzi S, Dufayard J, Iskra‐Caruana M, Muller E. Badnaviruses and banana genomes: a long association sheds light on Musa phylogeny and origin. MOLECULAR PLANT PATHOLOGY 2021; 22:216-230. [PMID: 33231927 PMCID: PMC7814968 DOI: 10.1111/mpp.13019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/07/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
Badnaviruses are double-stranded DNA pararetroviruses of the family Caulimoviridae. Badnaviral sequences found in banana are distributed over three main clades of the genus Badnavirus and exhibit wide genetic diversity. Interestingly, the nuclear genome of many plants, including banana, is invaded by numerous badnaviral sequences although badnaviruses do not require an integration step to replicate, unlike animal retroviruses. Here, we confirm that banana streak viruses (BSVs) are restricted to clades 1 and 3. We also show that only BSVs from clade 3 encompassing East African viral species are not integrated into Musa genomes, unlike BSVs from clade 1. Finally, we demonstrate that sequences from clade 2 are definitively integrated into Musa genomes with no evidence of episomal counterparts; all are phylogenetically distant from BSVs known to date. Using different molecular approaches, we dissected the coevolution between badnaviral sequences of clade 2 and banana by comparing badnavirus integration patterns across a banana sampling representing major Musa speciation events. Our data suggest that primary viral integrations occurred millions of years ago in banana genomes under different possible scenarios. Endogenous badnaviral sequences can be used as powerful markers to better characterize the Musa phylogeny, narrowing down the likely geographical origin of the Musa ancestor.
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Affiliation(s)
- Matthieu Chabannes
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
| | - Marc Gabriel
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
| | - Abderrahmane Aksa
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
| | - Serge Galzi
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
| | - Jean‐François Dufayard
- CIRAD, UMR AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance
| | | | - Emmanuelle Muller
- CIRAD, UMR BGPI, University of Montpellier, Montpellier SupAgroMontpellierFrance
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Tripathi L, Ntui VO, Tripathi JN, Kumar PL. Application of CRISPR/Cas for Diagnosis and Management of Viral Diseases of Banana. Front Microbiol 2021; 11:609784. [PMID: 33584573 PMCID: PMC7873300 DOI: 10.3389/fmicb.2020.609784] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/29/2020] [Indexed: 12/26/2022] Open
Abstract
Viral diseases are significant biotic constraints for banana (Musa spp.) production as they affect the yield and limit the international movement of germplasm. Among all the viruses known to infect banana, the banana bunchy top virus and banana streak viruses are widespread and economically damaging. The use of virus-resistant bananas is the most cost-effective option to minimize the negative impacts of viral-diseases on banana production. CRISPR/Cas-based genome editing is emerging as the most powerful tool for developing virus-resistant crop varieties in several crops, including the banana. The availability of a vigorous genetic transformation and regeneration system and a well-annotated whole-genome sequence of banana makes it a compelling candidate for genome editing. A robust CRISPR/Cas9-based genome editing of the banana has recently been established, which can be applied in developing disease-resistant varieties. Recently, the CRISPR system was exploited to detect target gene sequences using Cas9, Cas12, Cas13, and Cas14 enzymes, thereby unveiling the use of this technology for virus diagnosis. This article presents a synopsis of recent advancements and perspectives on the application of CRISPR/Cas-based genome editing for diagnosing and developing resistance against banana viruses and challenges in genome-editing of banana.
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Affiliation(s)
- Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | | | | | - P. Lava Kumar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
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6
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A Complex of Badnavirus Species Infecting Cacao Reveals Mixed Infections, Extensive Genomic Variability, and Interspecific Recombination. Viruses 2020; 12:v12040443. [PMID: 32295173 PMCID: PMC7232428 DOI: 10.3390/v12040443] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/09/2020] [Accepted: 04/11/2020] [Indexed: 12/04/2022] Open
Abstract
The incidence of cacao swollen shoot disease (CSSD) in cacao (Theobroma cacao L.) has increased in West Africa since ~2000. To investigate the genomic and species diversity of the CSSD-badnaviruses infecting cacao in Côte d’Ivoire and Ghana, symptomatic leaves were subjected to high-throughput sequencing. Among the 30 newly determined genomes, three badnaviruses were identified, Cacao swollen shoot Togo B virus (CSSTBV), Cacao swollen shoot CD virus, and Cacao swollen shoot CE virus (CSSCEV). The phylogenetic trees reconstructed for the reverse transcriptase (RT) and ribonuclease H (RNase H) sequences were incongruent with the complete viral genomes, which had the most robust statistical support. Recombination seems to be involved in the CSSD-badnavirus diversification. The genomic diversity varied among different CSSD-badnaviruses, with CSSTBV showing the lowest nucleotide diversity (π = 0.06236), and CSSCEV exhibiting the greatest variability (π = 0.21911). Evidence of strong purifying selection was found in the coding regions of the CSSTBV isolates.
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Basso MF, Lourenço-Tessutti IT, Busanello C, Pinto CEM, de Oliveira Freitas E, Ribeiro TP, de Almeida Engler J, de Oliveira AC, Morgante CV, Alves-Ferreira M, Grossi-de-Sa MF. Insights obtained using different modules of the cotton uceA1.7 promoter. PLANTA 2020; 251:56. [PMID: 32006110 DOI: 10.1007/s00425-020-03348-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
The structure of the cotton uceA1.7 promoter and its modules was analyzed; the potential of their key sequences has been confirmed in different tissues, proving to be a good candidate for the development of new biotechnological tools. Transcriptional promoters are among the primary genetic engineering elements used to control genes of interest (GOIs) associated with agronomic traits. Cotton uceA1.7 was previously characterized as a constitutive promoter with activity higher than that of the constitutive promoter from the Cauliflower mosaic virus (CaMV) 35S gene in various plant tissues. In this study, we generated Arabidopsis thaliana homozygous events stably overexpressing the gfp reporter gene driven by different modules of the uceA1.7 promoter. The expression level of the reporter gene in different plant tissues and the transcriptional stability of these modules was determined compared to its full-length promoter and the 35S promoter. The full-length uceA1.7 promoter exhibited higher activity in different plant tissues compared to the 35S promoter. Two modules of the promoter produced a low and unstable transcription level compared to the other promoters. The other two modules rich in cis-regulatory elements showed similar activity levels to full-length uceA1.7 and 35S promoters but were less stable. This result suggests the location of a minimal portion of the promoter that is required to initiate transcription properly (the core promoter). Additionally, the full-length uceA1.7 promoter containing the 5'-untranslated region (UTR) is essential for higher transcriptional stability in various plant tissues. These findings confirm the potential use of the full-length uceA1.7 promoter for the development of new biotechnological tools (NBTs) to achieve higher expression levels of GOIs in, for example, the root or flower bud for the efficient control of phytonematodes and pest-insects, respectively, in important crops.
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Affiliation(s)
- Marcos Fernando Basso
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil.
| | | | - Carlos Busanello
- Federal University of Pelotas, Capão Do Leão, RS, 96160-000, Brazil
| | - Clidia Eduarda Moreira Pinto
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- Federal University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Elínea de Oliveira Freitas
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- Federal University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Thuanne Pires Ribeiro
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
| | | | | | - Carolina Vianna Morgante
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- Embrapa Semi Arid, Petrolina, PE, 56302-970, Brazil
| | | | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil.
- Catholic University of Brasília, Brasília, DF, 71966-700, Brazil.
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Abstract
Mealybug wilt of pineapple (MWP) is a disease of pineapple that has a long history in Hawaii, but is present throughout the world where pineapples are grown in tropical regions. The disease has an interesting etiology that is poorly understood but involves an association with virus particles, mealybug vectors, and ants which spread the mealybug vectors. Several distinct pineapple mealybug wilt-associated virus (PMWaV) species have been identified thus far with potential further member species yet to be characterized. Pineapple mealybug wilt-associated viruses are member species of the Ampelovirus genus of the Closteroviridae family. Ampeloviruses are split into two subgroups, subgroup I and subgroup II. PMWaV-2 is a subgroup II member, and these have a longer and more complex genome with additional genes on the 3’ terminus of the RNA genome compared to subgroup I ampeloviruses. PMWaV-2, along with the presence of mealybug vectors, have been shown to be necessary factors in symptom development in Hawaii. Some of these extra genes in the 3’ of PMWaV-2 have recently been shown to function as silencing suppressors, and may play a role in the virulence of PMWaV-2 and symptom development. In other regions of the world, reports of symptomatic plants without PMWaV-2 infection, but with PMWaV-1, -3 or some combination, contradict the requirement of PMWaV-2 for symptom development in MWP. It is possible that further, uncharacterized PMWaVs may be present in symptomatic pineapple plants that test negative for PMWaV-2, explaining the inconsistency in symptom development. More research is necessary to explore the confusing etiology of the MWP disease, and to perhaps shed light upon the symptom development.
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Muller E, Ravel S, Agret C, Abrokwah F, Dzahini-Obiatey H, Galyuon I, Kouakou K, Jeyaseelan EC, Allainguillaume J, Wetten A. Next generation sequencing elucidates cacao badnavirus diversity and reveals the existence of more than ten viral species. Virus Res 2017; 244:235-251. [PMID: 29169831 DOI: 10.1016/j.virusres.2017.11.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/15/2017] [Accepted: 11/18/2017] [Indexed: 11/18/2022]
Abstract
Cacao swollen shoot virus is a member of the family Caulimoviridae, genus Badnavirus and is naturally transmitted to Theobroma cacao (L.) by several mealybug species. CSSV populations in West African countries are highly variable and genetically structured into several different groups based on the diversity in the first part of ORF3 which encodes the movement protein. To unravel the extent of isolate diversity and address the problems of low titer and mixed viral sequences in samples, we used Illumina MiSeq and HiSeq technology. We were able to reconstruct de novo 20 new complete genomes from cacao samples collected in the Cocoa Research Institute of Ghana (CRIG) Museum and from the field samples collected in Côte d'Ivoire or Ghana. Based on the 20% threshold of nucleotide divergence in the reverse transcriptase/ribonuclease H (RT/RNase H) region which denotes species demarcation, we conclude there exist seven new species associated with the cacao swollen shoot disease. These new species along with the three already described leads to ten, the total number of the complex of viral species associated with the disease. A sample from Sri Lanka exhibiting similar leaf symptomology to West African CSSD-affected plants was also included in the study and the corresponding sequence represents the genome of a new virus named cacao bacilliform SriLanka virus (CBSLV).
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Affiliation(s)
- E Muller
- CIRAD, UMR BGPI, 34398, Montpellier, France; BGPI, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
| | - S Ravel
- CIRAD, UMR BGPI, 34398, Montpellier, France; BGPI, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - C Agret
- CIRAD, UMR AGAP, 34398, Montpellier, France; AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - F Abrokwah
- Department of Biochemistry, University of Cape Coast, Ghana
| | | | - I Galyuon
- Department of Molecular Biology and Biotechnology, University of Cape Coast, Ghana
| | - K Kouakou
- World Cocoa Foundation, Abidjan, Cote d'Ivoire
| | - E C Jeyaseelan
- University of Jaffna, Faculty of Science, Department of Botany, Jaffna, Sri Lanka
| | - J Allainguillaume
- University of the West of England, Frenchay Campus, Coldharbour Lane, Bristol, BS16 1QY, United Kingdom
| | - A Wetten
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 7BE, United Kingdom
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10
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PCR-DGGE Analysis: Unravelling Complex Mixtures of Badnavirus Sequences Present in Yam Germplasm. Viruses 2017; 9:v9070181. [PMID: 28696406 PMCID: PMC5537673 DOI: 10.3390/v9070181] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/29/2017] [Accepted: 07/04/2017] [Indexed: 12/19/2022] Open
Abstract
Badnaviruses (family Caulimoviridae, genus Badnavirus) have emerged as serious pathogens especially affecting the cultivation of tropical crops. Badnavirus sequences can be integrated in host genomes, complicating the detection of episomal infections and the assessment of viral genetic diversity in samples containing a complex mixture of sequences. Yam (Dioscorea spp.) plants are hosts to a diverse range of badnavirus species, and recent findings have suggested that mixed infections occur frequently in West African yam germplasm. Historically, the determination of the diversity of badnaviruses present in yam breeding lines has been achieved by cloning and sequencing of polymerase chain reaction (PCR) products. In this study, the molecular diversity of partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences from yam badnaviruses was analysed using PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE). This resulted in the identification of complex ‘fingerprints’ composed of multiple sequences of Dioscorea bacilliform viruses (DBVs). Many of these sequences show high nucleotide identities to endogenous DBV (eDBV) sequences deposited in GenBank, and fall into six monophyletic species groups. Our findings highlight PCR-DGGE as a powerful tool in badnavirus diversity studies enabling a rapid indication of sequence diversity as well as potential candidate integrated sequences revealed by their conserved nature across germplasm.
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Du K, Liu S, Chen Z, Fan Z, Wang H, Tian G, Zhou T. Full genome sequence of jujube mosaic-associated virus, a new member of the family Caulimoviridae. Arch Virol 2017; 162:3221-3224. [DOI: 10.1007/s00705-017-3438-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/22/2017] [Indexed: 10/19/2022]
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12
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Vo JN, Campbell PR, Mahfuz NN, Ramli R, Pagendam D, Barnard R, Geering ADW. Characterization of the banana streak virus capsid protein and mapping of the immunodominant continuous B-cell epitopes to the surface-exposed N terminus. J Gen Virol 2016; 97:3446-3457. [DOI: 10.1099/jgv.0.000643] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Jenny N. Vo
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland 4001, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
- Plant Biosecurity Cooperative Research Centre, LPO Box 5012, Bruce, Australian Capital Territory 2617, Australia
| | - Paul R. Campbell
- Plant Biosecurity Cooperative Research Centre, LPO Box 5012, Bruce, Australian Capital Territory 2617, Australia
- Queensland Department of Agriculture, Fisheries and Forestry, GPO Box 267, Brisbane, Queensland 4001, Australia
| | - Nur N. Mahfuz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Ras Ramli
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Daniel Pagendam
- CSIRO Mathematics, Informatics and Statistics, Ecosciences Precinct, 41 Boggo Road, Dutton Park, Queensland 4102, Australia
| | - Ross Barnard
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Andrew D. W. Geering
- Plant Biosecurity Cooperative Research Centre, LPO Box 5012, Bruce, Australian Capital Territory 2617, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland 4001, Australia
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Bömer M, Turaki AA, Silva G, Kumar PL, Seal SE. A Sequence-Independent Strategy for Amplification and Characterisation of Episomal Badnavirus Sequences Reveals Three Previously Uncharacterised Yam Badnaviruses. Viruses 2016; 8:E188. [PMID: 27399761 PMCID: PMC4974523 DOI: 10.3390/v8070188] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/24/2016] [Accepted: 06/30/2016] [Indexed: 12/17/2022] Open
Abstract
Yam (Dioscorea spp.) plants are potentially hosts to a diverse range of badnavirus species (genus Badnavirus, family Caulimoviridae), but their detection is complicated by the existence of integrated badnavirus sequences in some yam genomes. To date, only two badnavirus genomes have been characterised, namely, Dioscorea bacilliform AL virus (DBALV) and Dioscorea bacilliform SN virus (DBSNV). A further 10 tentative species in yam have been described based on their partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences, generically referred to here as Dioscorea bacilliform viruses (DBVs). Further characterisation of DBV species is necessary to determine which represent episomal viruses and which are only present as integrated badnavirus sequences in some yam genomes. In this study, a sequence-independent multiply-primed rolling circle amplification (RCA) method was evaluated for selective amplification of episomal DBV genomes. This resulted in the identification and characterisation of nine complete genomic sequences (7.4-7.7 kbp) of existing and previously undescribed DBV phylogenetic groups from Dioscorea alata and Dioscorea rotundata accessions. These new yam badnavirus genomes expand our understanding of the diversity and genomic organisation of DBVs, and assist the development of improved diagnostic tools. Our findings also suggest that mixed badnavirus infections occur relatively often in West African yam germplasm.
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Affiliation(s)
- Moritz Bömer
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, Kent ME4 4TB, UK.
| | - Aliyu A Turaki
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, Kent ME4 4TB, UK.
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, Kent ME4 4TB, UK.
| | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria.
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, Kent ME4 4TB, UK.
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Bhat AI, Hohn T, Selvarajan R. Badnaviruses: The Current Global Scenario. Viruses 2016; 8:E177. [PMID: 27338451 PMCID: PMC4926197 DOI: 10.3390/v8060177] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/18/2016] [Accepted: 05/25/2016] [Indexed: 12/16/2022] Open
Abstract
Badnaviruses (Family: Caulimoviridae; Genus: Badnavirus) are non-enveloped bacilliform DNA viruses with a monopartite genome containing about 7.2 to 9.2 kb of dsDNA with three to seven open reading frames. They are transmitted by mealybugs and a few species by aphids in a semi-persistent manner. They are one of the most important plant virus groups and have emerged as serious pathogens affecting the cultivation of several horticultural crops in the tropics, especially banana, black pepper, cocoa, citrus, sugarcane, taro, and yam. Some badnaviruses are also known as endogenous viruses integrated into their host genomes and a few such endogenous viruses can be awakened, e.g., through abiotic stress, giving rise to infective episomal forms. The presence of endogenous badnaviruses poses a new challenge for the fool-proof diagnosis, taxonomy, and management of the diseases. The present review aims to highlight emerging disease problems, virus characteristics, transmission, and diagnosis of badnaviruses.
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Affiliation(s)
| | - Thomas Hohn
- UNIBAS, Botanical Institute, 4056 Basel, Switzerland.
| | - Ramasamy Selvarajan
- ICAR-National Research Centre for Banana, Tiruchirapalli 620102, Tamil Nadu, India.
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15
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Duroy PO, Perrier X, Laboureau N, Jacquemoud-Collet JP, Iskra-Caruana ML. How endogenous plant pararetroviruses shed light on Musa evolution. ANNALS OF BOTANY 2016; 117:625-41. [PMID: 26971286 PMCID: PMC4817503 DOI: 10.1093/aob/mcw011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/06/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Banana genomes harbour numerous copies of viral sequences derived from banana streak viruses (BSVs) - dsDNA viruses belonging to the family Caulimoviridae.These viral integrants (eBSVs) are mostly defective, probably as a result of 'pseudogenization' driven by host genome evolution. However, some can give rise to infection by releasing a functional viral genome following abiotic stresses. These distinct infective eBSVs correspond to the three main widespread BSV species (BSOLV, BSGFV and BSIMV), fully described within the Musa balbisiana B genomes of the seedy diploid 'Pisang Klutuk Wulung' (PKW). METHODS We characterize eBSV distribution among a Musa sampling including seedy BB diploids and interspecific hybrids with Musa acuminate exhibiting different levels of ploidy for the B genome (ABB, AAB, AB). We used representative samples of the two areas of sympatry between M. acuminate and M. balbisiana species representing the native area of the most widely cultivated AAB cultivars (in India and in East Asia, ranging from the Philippines to New Guinea). Seventy-seven accessions were characterized using eBSV-related PCR markers and Southern hybridization approaches. We coded both sets of results to create a common dissimilarity matrix with which to interpret eBSV distribution. KEY RESULTS We propose a Musa phylogeny driven by the M. balbisiana genome based on a dendrogram resulting from a joint neighbour-joining analysis of the three BSV species, showing for the first time lineages between BB and ABB/AAB hybrids. eBSVs appear to be relevant phylogenetic markers that can illustrate theM. balbisiana phylogeography story. CONCLUSION The theoretical implications of this study for further elucidation of the historical and geographical process of Musa domestication are numerous. Discovery of banana plants with B genome non-infective for eBSV opens the way to the introduction of new genitors in programmes of genetic banana improvement.
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16
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Kazmi SA, Yang Z, Hong N, Wang G, Wang Y. Characterization by Small RNA Sequencing of Taro Bacilliform CH Virus (TaBCHV), a Novel Badnavirus. PLoS One 2015. [PMID: 26207896 PMCID: PMC4514669 DOI: 10.1371/journal.pone.0134147] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
RNA silencing is an antiviral immunity that regulates gene expression through the production of small RNAs (sRNAs). In this study, deep sequencing of small RNAs was used to identify viruses infecting two taro plants. Blast searching identified five and nine contigs assembled from small RNAs of samples T1 and T2 matched onto the genome sequences of badnaviruses in the family Caulimoviridae. Complete genome sequences of two isolates of the badnavirus determined by sequence specific amplification comprised of 7,641 nucleotides and shared overall nucleotide similarities of 44.1%‒55.8% with other badnaviruses. Six open reading frames (ORFs) were identified on the plus strand, showed amino acid similarities ranging from 59.8% (ORF3) to 10.2% (ORF6) to the corresponding proteins encoded by other badnaviruses. Phylogenetic analysis also supports that the virus is a new member in the genus Badnavirus. The virus is tentatively named as Taro bacilliform CH virus (TaBCHV), and it is the second badnavirus infecting taro plants, following Taro bacilliform virus (TaBV). In addition, analyzes of viral derived small RNAs (vsRNAs) from TaBCHV showed that almost equivalent number of vsRNAs were generated from both strands and the most abundant vsRNAs were 21 nt, with uracil bias at 5' terminal. Furthermore, TaBCHV vsRNAs were asymmetrically distributed on its entire circular genome at both orientations with the hotspots mainly generated in the ORF5 region.
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Affiliation(s)
- Syeda Amber Kazmi
- State Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zuokun Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ni Hong
- State Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
| | - Guoping Wang
- State Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanfen Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
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17
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Stainton D, Halafihi M, Collings DA, Varsani A. Genome Sequence of Banana Streak MY Virus from the Pacific Ocean Island of Tonga. GENOME ANNOUNCEMENTS 2015; 3:e00543-15. [PMID: 26021925 PMCID: PMC4447910 DOI: 10.1128/genomea.00543-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 04/29/2015] [Indexed: 11/20/2022]
Abstract
Banana streak disease is caused by a variety of banana-infecting badnaviruses. A genome of the episomal form of a banana streak MY virus was recovered from an infected banana plant sampled on Vava'u Island, Tonga, and shares >98% pairwise identity with the six other genomes available in public databases.
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Affiliation(s)
- Daisy Stainton
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mana'ia Halafihi
- Ministry of Agriculture and Food, Forests and Fisheries of Tonga, Nuku-alofa, Kingdom of Tonga
| | - David A Collings
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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18
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Sharma SK, Vignesh Kumar P, Geetanjali AS, Pun KB, Baranwal VK. Subpopulation level variation of banana streak viruses in India and common evolution of banana and sugarcane badnaviruses. Virus Genes 2015; 50:450-65. [PMID: 25672291 DOI: 10.1007/s11262-015-1179-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 01/31/2015] [Indexed: 01/21/2023]
Abstract
Genome sequences of three episomal Banana streak MY virus (BSMYV) isolates sampled from triploid banana hybrids (Chini Champa: AAB; Malbhog: AAB and Monthan: ABB), grown in North-East and South India are reported in this study by sequence-independent improved rolling circle amplification (RCA). RCA coupled with restriction fragment length polymorphism revealed diverse restriction profiles of five BSMYV isolates. Nucleotide substitution rates of BSMYV subpopulation and Banana streak OL virus subpopulation was 7.13 × 10(-3) to 1.59 × 10(-2) and 2.65 × 10(-3) to 5.49 × 10(-3), respectively, for the different coding regions. Analysis of the genetic diversity of banana and sugarcane badnaviruses revealed a total of 32 unique recombination events among banana and sugarcane badnaviruses (inter BSV-SCBV), in addition to the extensive recombination with in banana streak viruses and sugarcane bacilliform viruses (intra-BSV and intra-SCBV). Many unique fragments were shown to contain similar ruminant sequence fragments which indicated the possibility that the two groups of badnaviruses or their ancestors to colonise same host before making the host shift. The distribution of recombination events, hot-spots (intergenic region and C-terminal of ORF3) as well as cold-spots (distributed in ORF3) displayed the mirroring of recombination traces in both group of badnaviruses. These results support the hypothesis of relatedness of banana and sugarcane badnaviruses and the host and geographical shifts that followed the fixation of the species complex appear to be a recent event.
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Affiliation(s)
- Susheel Kumar Sharma
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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19
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Kumar PL, Selvarajan R, Iskra-Caruana ML, Chabannes M, Hanna R. Biology, etiology, and control of virus diseases of banana and plantain. Adv Virus Res 2014; 91:229-69. [PMID: 25591881 DOI: 10.1016/bs.aivir.2014.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Banana and plantain (Musa spp.), produced in 10.3 million ha in the tropics, are among the world's top 10 food crops. They are vegetatively propagated using suckers or tissue culture plants and grown almost as perennial plantations. These are prone to the accumulation of pests and pathogens, especially viruses which contribute to yield reduction and are also barriers to the international exchange of germplasm. The most economically important viruses of banana and plantain are Banana bunchy top virus (BBTV), a complex of banana streak viruses (BSVs) and Banana bract mosaic virus (BBrMV). BBTV is known to cause the most serious economic losses in the "Old World," contributing to a yield reduction of up to 100% and responsible for a dramatic reduction in cropping area. The BSVs exist as episomal and endogenous forms are known to be worldwide in distribution. In India and the Philippines, BBrMV is known to be economically important but recently the virus was discovered in Colombia and Costa Rica, thus signaling its spread into the "New World." Banana and plantain are also known to be susceptible to five other viruses of minor significance, such as Abaca mosaic virus, Abaca bunchy top virus, Banana mild mosaic virus, Banana virus X, and Cucumber mosaic virus. Studies over the past 100 years have contributed to important knowledge on disease biology, distribution, and spread. Research during the last 25 years have led to a better understanding of the virus-vector-host interactions, virus diversity, disease etiology, and epidemiology. In addition, new diagnostic tools were developed which were used for surveillance and the certification of planting material. Due to a lack of durable host resistance in the Musa spp., phytosanitary measures and the use of virus-free planting material are the major methods of virus control. The state of knowledge on BBTV, BBrMV, and BSVs, and other minor viruses, disease spread, and control are summarized in this review.
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Affiliation(s)
- P Lava Kumar
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria.
| | - Ramasamy Selvarajan
- National Research Center for Banana, Tiruchirapalli, PIN # 620102, TN, India
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20
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Evasion of short interfering RNA-directed antiviral silencing in Musa acuminata persistently infected with six distinct banana streak pararetroviruses. J Virol 2014; 88:11516-28. [PMID: 25056897 DOI: 10.1128/jvi.01496-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Vegetatively propagated crop plants often suffer from infections with persistent RNA and DNA viruses. Such viruses appear to evade the plant defenses that normally restrict viral replication and spread. The major antiviral defense mechanism is based on RNA silencing generating viral short interfering RNAs (siRNAs) that can potentially repress viral genes posttranscriptionally through RNA cleavage and transcriptionally through DNA cytosine methylation. Here we examined the RNA silencing machinery of banana plants persistently infected with six pararetroviruses after many years of vegetative propagation. Using deep sequencing, we reconstructed consensus master genomes of the viruses and characterized virus-derived and endogenous small RNAs. Consistent with the presence of endogenous siRNAs that can potentially establish and maintain DNA methylation, the banana genomic DNA was extensively methylated in both healthy and virus-infected plants. A novel class of abundant 20-nucleotide (nt) endogenous small RNAs with 5'-terminal guanosine was identified. In all virus-infected plants, 21- to 24-nt viral siRNAs accumulated at relatively high levels (up to 22% of the total small RNA population) and covered the entire circular viral DNA genomes in both orientations. The hotspots of 21-nt and 22-nt siRNAs occurred within open reading frame (ORF) I and II and the 5' portion of ORF III, while 24-nt siRNAs were more evenly distributed along the viral genome. Despite the presence of abundant viral siRNAs of different size classes, the viral DNA was largely free of cytosine methylation. Thus, the virus is able to evade siRNA-directed DNA methylation and thereby avoid transcriptional silencing. This evasion of silencing likely contributes to the persistence of pararetroviruses in banana plants. IMPORTANCE We report that DNA pararetroviruses in Musa acuminata banana plants are able to evade DNA cytosine methylation and transcriptional gene silencing, despite being targeted by the host silencing machinery generating abundant 21- to 24-nucleotide short interfering RNAs. At the same time, the banana genomic DNA is extensively methylated in both healthy and virus-infected plants. Our findings shed light on the siRNA-generating gene silencing machinery of banana and provide a possible explanation why episomal pararetroviruses can persist in plants whereas true retroviruses with an obligatory genome-integration step in their replication cycle do not exist in plants.
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21
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Sharma SK, Kumar PV, Baranwal VK. Immunodiagnosis of episomal Banana streak MY virus using polyclonal antibodies to an expressed putative coat protein. J Virol Methods 2014; 207:86-94. [PMID: 24977315 DOI: 10.1016/j.jviromet.2014.06.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 06/17/2014] [Accepted: 06/20/2014] [Indexed: 11/24/2022]
Abstract
A cryptic Badnavirus species complex, known as banana streak viruses (BSV) poses a serious threat to banana production and genetic improvement worldwide. Due to the presence of integrated BSV sequences in the banana genome, routine detection is largely based on serological and nucleo-serological diagnostic methods which require high titre specific polyclonal antiserum. Viral structural proteins like coat protein (CP) are the best target for in vitro expression, to be used as antigen for antiserum production. However, in badnaviruses precise CP sequences are not known. In this study, two putative CP coding regions (p48 and p37) of Banana streak MY virus (BSMYV) were identified in silico by comparison with caulimoviruses, retroviruses and Rice tungro bacilliform virus. The putative CP coding region (p37) was in vitro expressed in pMAL system and affinity purified. The purified fusion protein was used as antigen for raising polyclonal antiserum in rabbit. The specificity of antiserum was confirmed in Western blots, immunosorbent electron microscopy (ISEM) and antigen coated plate-enzyme linked immunosorbent assay (ACP-ELISA). The antiserum (1:2000) was successfully used in ACP-ELISA for specific detection of BSMYV infection in field and tissue culture raised banana plants. The antiserum was also utilized in immuno-capture PCR (IC-PCR) based indexing of episomal BSMYV infection. This is the first report of in silico identification of putative CP region of BSMYV, production of polyclonal antiserum against recombinant p37 and its successful use in immunodetection.
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Affiliation(s)
- Susheel Kumar Sharma
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - P Vignesh Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Virendra Kumar Baranwal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India.
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22
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Wang Y, Cheng X, Wu X, Wang A, Wu X. Characterization of complete genome and small RNA profile of pagoda yellow mosaic associated virus, a novel badnavirus in China. Virus Res 2014; 188:103-8. [PMID: 24751798 DOI: 10.1016/j.virusres.2014.04.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/06/2014] [Accepted: 04/09/2014] [Indexed: 12/16/2022]
Abstract
A new badnavirus was discovered from pagoda trees showing yellow mosaic symptoms on the leaves by high throughput sequencing of small RNAs. The complete genome of this virus was determined to comprise 7424 nucleotides, and the virus shared 40.4-45.1% identity with that of other badnaviruses. The genome encodes five open reading frames (ORFs) on the plus strand, which includes three conserved badnaviral ORFs. These results suggest that this virus is a new member of the genus Badnavirus in the family Caulimoviridae. The virus is tentatively named pagoda yellow mosaic associated virus (PYMAV). Phylogenetic analysis suggested that this virus together with gooseberry vein banding virus (GVBV) and grapevine vein-clearing virus (GVCV) forms a separate group that is distinct two other well characterized badnaviral groups. Additionally, the viral derived small RNA (vsRNA) profile of PYMAV was analyzed and compared with that of viruses within the same family. Results showed that the most abundant PYMAV vsRNAs were 21-nt, whereas other viruses in the same family have a predominance of 22- or 24-nt vsRNA. The percentage of sense PYMAV vsRNA was almost equal to that of antisense vsRNA, whereas vsRNAs of other viruses in the family display preferences toward the sense strand of their genome. Furthermore, PYMAV vsRNAs were symmetrically distributed along the genome with no obvious vsRNA generating hotspots.
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Affiliation(s)
- Yilun Wang
- College of Agricultural and Food Science, Zhejiang Agricultural and Forestry University, Lin'an 311300, Zhejiang, PR China
| | - Xiaofei Cheng
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, Zhejiang, PR China; Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London N5V 4T3, Ontario, Canada
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Key Laboratory of Soybean Biology, Ministry of Education, Harbin 150030, Heilongjiang, PR China
| | - Aiming Wang
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London N5V 4T3, Ontario, Canada
| | - Xiaoyun Wu
- College of Agricultural and Food Science, Zhejiang Agricultural and Forestry University, Lin'an 311300, Zhejiang, PR China.
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The common evolutionary history of badnaviruses and banana. INFECTION GENETICS AND EVOLUTION 2013; 21:83-9. [PMID: 24184704 DOI: 10.1016/j.meegid.2013.10.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/13/2013] [Accepted: 10/15/2013] [Indexed: 12/12/2022]
Abstract
Recent plant genome sequencing efforts have revealed myriad viral sequences suggesting a cryptic interaction between both partners. Interestingly, no integration step has ever been reported as an obligatory step in the life cycle of plant viruses. Circular dsDNA viruses belonging to the family Caulimoviridae are the most abundant among integrated plant viral sequences. In this review, we describe how this hitherto hidden interaction could inform the evolutionary history of both partners badnaviruses and banana plants.
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Baranwal VK, Sharma SK, Khurana D, Verma R. Sequence analysis of shorter than genome length episomal Banana streak OL virus like sequences isolated from banana in India. Virus Genes 2013; 48:120-7. [PMID: 24101342 DOI: 10.1007/s11262-013-0984-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/16/2013] [Indexed: 01/30/2023]
Abstract
Electron microscopy and sequencing of reverse transcriptase and ribonuclease H (RT/RNase H) region of Badnavirus genome from two banana cultivars: Poovan (triploid: AAB) and Safed velchi (diploid: AB), exhibiting leaf streak symptoms, confirmed the association of Banana streak OL virus (BSOLV). As per ICTV species demarcation threshold of 80 % identity in RT/RNase H region, both the isolates were identified as BSOLV. Rolling circle and end-to-end amplification showed the association of two short episomal BSOLV variants: BSOLV-IN1 and BSOLV-IN2 from Poovan and Safed velchi banana, respectively. The genome sizes of both isolates were 6,950 nucleotides long, but shorter than the typical BSOLV genome of 7,389 bp. Open reading frames (ORFs) 1 and 2 of shorter BSOLV isolates shared almost complete nucleotide identity (>99 %) to that of BSOLV. However, the ORF 3 (5,130 bp) and intergenic region (IGR), 886 bp, showed deletions compared with ORF 3 (5,499 bp) and IGR (956 bp) of BSOLV. In phylogenetic analysis for ORF 3 polyprotein, both the isolates clustered with BSOLV, Banana streak CA virus (BSCAV), and Sugarcane bacilliform GA virus (SCBGAV). Identical ORF 1, ORF 2, and the presence of all the conserved domains in short ORF 3 and promoter elements in IGR indicated that these isolates represent replicationally competent shorter variants of BSOLV. These two shorter-than-BSOLV genome sequences and two other identical banana streak virus sequences in GenBank (BSV-TRY; DQ859899 and BSV-GD; DQ451009) might have evolved due to error-prone reverse transcription and splicing or excision from the integrated sequences by homologous recombination in natural banana hybrids under field conditions.
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Affiliation(s)
- Virendra K Baranwal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012, India,
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Borah BK, Sharma S, Kant R, Johnson AMA, Saigopal DVR, Dasgupta I. Bacilliform DNA-containing plant viruses in the tropics: commonalities within a genetically diverse group. MOLECULAR PLANT PATHOLOGY 2013; 14:759-71. [PMID: 23763585 PMCID: PMC6638767 DOI: 10.1111/mpp.12046] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
UNLABELLED Plant viruses, possessing a bacilliform shape and containing double-stranded DNA, are emerging as important pathogens in a number of agricultural and horticultural crops in the tropics. They have been reported from a large number of countries in African and Asian continents, as well as from islands from the Pacific region. The viruses, belonging to two genera, Badnavirus and Tungrovirus, within the family Caulimoviridae, have genomes displaying a common plan, yet are highly variable, sometimes even between isolates of the same virus. In this article, we summarize the current knowledge with a view to revealing the common features embedded within the genetic diversity of this group of viruses. TAXONOMY Virus; order Unassigned; family Caulimoviridae; genera Badnavirus and Tungrovirus; species Banana streak viruses, Bougainvillea spectabilis chlorotic vein banding virus, Cacao swollen shoot virus, Citrus yellow mosaic badnavirus, Dioscorea bacilliform viruses, Rice tungro bacilliform virus, Sugarcane bacilliform viruses and Taro bacilliform virus. MICROBIOLOGICAL PROPERTIES Bacilliform in shape; length, 60-900 nm; width, 35-50 nm; circular double-stranded DNA of approximately 7.5 kbp with one or more single-stranded discontinuities. HOST RANGE Each virus generally limited to its own host, including banana, bougainvillea, black pepper, cacao, citrus species, Dioscorea alata, rice, sugarcane and taro. DISEASE SYMPTOMS Foliar streaking in banana and sugarcane, swelling of shoots in cacao, yellow mosaic in leaves and stems in citrus, brown spot in the tubers in yam and yellow-orange discoloration and stunting in rice. USEFUL WEBSITES http://www.dpvweb.net.
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Affiliation(s)
- Basanta K Borah
- Department of Plant Molecular Biology, Delhi University South Campus, New Delhi 110021, India
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Abstract
Plant pararetroviruses integrate serendipitously into their host genomes. The banana genome harbors integrated copies of banana streak virus (BSV) named endogenous BSV (eBSV) that are able to release infectious pararetrovirus. In this investigation, we characterized integrants of three BSV species-Goldfinger (eBSGFV), Imove (eBSImV), and Obino l'Ewai (eBSOLV)-in the seedy Musa balbisiana Pisang klutuk wulung (PKW) by studying their molecular structure, genomic organization, genomic landscape, and infectious capacity. All eBSVs exhibit extensive viral genome duplications and rearrangements. eBSV segregation analysis on an F1 population of PKW combined with fluorescent in situ hybridization analysis showed that eBSImV, eBSOLV, and eBSGFV are each present at a single locus. eBSOLV and eBSGFV contain two distinct alleles, whereas eBSImV has two structurally identical alleles. Genotyping of both eBSV and viral particles expressed in the progeny demonstrated that only one allele for each species is infectious. The infectious allele of eBSImV could not be identified since the two alleles are identical. Finally, we demonstrate that eBSGFV and eBSOLV are located on chromosome 1 and eBSImV is located on chromosome 2 of the reference Musa genome published recently. The structure and evolution of eBSVs suggest sequential integration into the plant genome, and haplotype divergence analysis confirms that the three loci display differential evolution. Based on our data, we propose a model for BSV integration and eBSV evolution in the Musa balbisiana genome. The mutual benefits of this unique host-pathogen association are also discussed.
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Molecular characterization of Banana streak virus isolate from Musa Acuminata in China. Virol Sin 2011; 26:393-402. [PMID: 22160939 DOI: 10.1007/s12250-011-3212-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 10/24/2011] [Indexed: 12/24/2022] Open
Abstract
Banana streak virus (BSV), a member of genus Badnavirus, is a causal agent of banana streak disease throughout the world. The genetic diversity of BSVs from different regions of banana plantations has previously been investigated, but there are relatively few reports of the genetic characteristic of episomal (non-integrated) BSV genomes isolated from China. Here, the complete genome, a total of 7722bp (GenBank accession number DQ092436), of an isolate of Banana streak virus (BSV) on cultivar Cavendish (BSAcYNV) in Yunnan, China was determined. The genome organises in the typical manner of badnaviruses. The intergenic region of genomic DNA contains a large stem-loop, which may contribute to the ribosome shift into the following open reading frames (ORFs). The coding region of BSAcYNV consists of three overlapping ORFs, ORF1 with a non-AUG start codon and ORF2 encoding two small proteins are individually involved in viral movement and ORF3 encodes a polyprotein. Besides the complete genome, a defective genome lacking the whole RNA leader region and a majority of ORF1 and which encompasses 6525bp was also isolated and sequenced from this BSV DNA reservoir in infected banana plants. Sequence analyses showed that BSAcYNV has closest similarity in terms of genome organization and the coding assignments with an BSV isolate from Vietnam (BSAcVNV). The corresponding coding regions shared identities of 88% and -95% at nucleotide and amino acid levels, respectively. Phylogenetic analysis also indicated BSAcYNV shared the closest geographical evolutionary relationship to BSAcVNV among sequenced banana streak badnaviruses.
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Muller E, Dupuy V, Blondin L, Bauffe F, Daugrois JH, Nathalie L, Iskra-Caruana ML. High molecular variability of sugarcane bacilliform viruses in Guadeloupe implying the existence of at least three new species. Virus Res 2011; 160:414-9. [PMID: 21741419 DOI: 10.1016/j.virusres.2011.06.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 06/21/2011] [Accepted: 06/22/2011] [Indexed: 12/13/2022]
Abstract
Thirty-five unique partial sugarcane bacilliform virus (SCBV) sequences extending over 529 bp were identified in sugarcane samples from Guadeloupe diagnosed by Immunocapture-PCR (IC-PCR) using specific badnavirus primers. Phylogenetic analysis of these sequences along with the two known genome sequences of Sugarcane bacilliform Mor virus (SCBMV) and Sugarcane bacilliform IM virus (SCBIMV) revealed high molecular variability in the SCBV genome. Seven phylogenetic groups, named A to G, were characterized: virus isolates from groups A-B, C and D are proposed to be members of three additional SCBV species. The two (7446 and 7444 bp) and one (7317 bp) complete sequences of SCBV isolates from groups A and D, respectively, likely represented the genome of two new species. Phylogenetic analysis of the complete genome and RT/RNase H sequences confirmed the polyphyletic structure of SCBV isolates and the absence of a clear separation between SCBV and Banana streak virus (BSV) isolates within badnavirus group 1. These results showed that reconsideration of taxonomy and classification of SCBV and BSV are necessary.
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29
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Molecular analysis of the complete genomic sequences of four isolates of Gooseberry vein banding associated virus. Virus Genes 2011; 43:130-7. [PMID: 21533750 DOI: 10.1007/s11262-011-0614-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 04/12/2011] [Indexed: 10/18/2022]
Abstract
The presence of Gooseberry vein banding associated virus (GVBaV), a badnavirus in the family Caulimoviridae, is strongly correlated with gooseberry vein banding disease in Ribes spp. In this study, full-length genomic sequences of four GVBaV isolates from different hosts and geographic regions were determined to be 7649-7663 nucleotides. These isolates share identities of 96.4-97.3% for the complete genomic sequence, indicating low genetic diversity among them. The GVBaV genome contains three open reading frames (ORFs) on the plus strand that potentially encode proteins of 26, 16, and 216 kDa. The size and organization of GVBaV ORFs 1-3 are similar to those of most other badnaviruses. The putative amino acid sequence of GVBaV ORF 3 contained motifs that are conserved among badnavirus proteins including aspartic protease, reverse transcriptase, and ribonuclease H. The highly conserved putative plant tRNA(met)-binding site is also present in the 935-bp intergenic region of GVBaV. The identities of the genomic sequences of GVBaV and other badnaviruses range from 49.1% (Sugarcane bacilliform Mor virus) to 51.7% (Pelargonium vein banding virus, PVBV). Phylogenetic analysis using the amino acid sequence of the ORF 3 putative protein shows that GVBaV groups most closely to Dioscorea bacilliform virus, PVBV, and Taro bacilliform virus. These results confirm that GVBaV is a pararetrovirus of the genus Badnavirus in the family Caulimoviridae.
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30
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James AP, Geijskes RJ, Dale JL, Harding RM. Development of a Novel Rolling-Circle Amplification Technique to Detect Banana streak virus that also Discriminates Between Integrated and Episomal Virus Sequences. PLANT DISEASE 2011; 95:57-62. [PMID: 30743660 DOI: 10.1094/pdis-07-10-0519] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Banana plants are hosts to a large number of Banana streak virus (BSV) species. However, diagnostic methods for BSV are inadequate because of the considerable genetic and serological diversity among BSV isolates and the presence of integrated BSV sequences in some banana cultivars which leads to false positives. In this study, a sequence-nonspecific, rolling-circle amplification (RCA) technique was developed and shown to overcome these limitations for the detection and subsequent characterization of BSV isolates infecting banana. This technique was shown to discriminate between integrated and episomal BSV DNA, specifically detecting the latter in several banana cultivars known to contain episomal or integrated sequences of Banana streak Mysore virus (BSMyV), Banana streak OL virus (BSOLV), and Banana streak GF virus (BSGFV). Using RCA, the presence of BSMyV and BSOLV was confirmed in Australia, while BSOLV, BSGFV, Banana streak Uganda I virus (BSUgIV), Banana streak Uganda L virus (BSUgLV), and Banana streak Uganda M virus (BSUgMV) were detected in Uganda. This is the first confirmed report of episomally-derived BSUglV, BSUgLV, and BSUgMV in Uganda. As well as its ability to detect BSV, RCA was shown to detect two other pararetroviruses, Sugarcane bacilliform virus in sugarcane and Cauliflower mosaic virus in turnip.
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Affiliation(s)
- A P James
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - R J Geijskes
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - J L Dale
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - R M Harding
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4001, Australia
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31
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Iskra-Caruana ML, Baurens FC, Gayral P, Chabannes M. A four-partner plant–virus interaction: enemies can also come from within. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:1394-1402. [PMID: 20923349 DOI: 10.1094/mpmi-05-10-0107] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Plant viruses are disseminated by either vertical (vegetative multiplication or sexual reproduction) or horizontal (vector-mediated) propagation. Plant pararetroviruses—members of the Caulimoviridae family—have developed an alternative strategy for vertical propagation via integration within the host plant genome, although integration is not required for viral replication. Integrated endogenous pararetrovirus (EPRV) sequences have undergone extensive viral genome rearrangements and contain more than one copy of the viral genome. Furthermore, EPRV can become infectious upon spontaneous escape of active virus following stresses such as wounding, tissue culture, or interspecific crosses. Such infectious EPRV are of great importance, not only in terms of their ability to precipitate epidemic outbreaks but also because of their effect on breeding of numerous plant genomes in temperate and tropical crops. This is especially true for banana, a crop susceptible to banana streak viruses, the causative agents of banana streak disease. Thus, the classical three-component banana–Banana streak virus (BSV)–mealybug pathosystem can be expanded to include endogenous BSV as an alternative source of active virions. The BSV-banana pathosystem is one of only three pathosystems known to date to harbor this remarkable feature, and the present review focuses exclusively on it to illustrate this four-partner interaction.
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32
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Gayral P, Iskra-Caruana ML. Phylogeny of Banana Streak Virus reveals recent and repetitive endogenization in the genome of its banana host (Musa sp.). J Mol Evol 2009; 69:65-80. [PMID: 19517051 DOI: 10.1007/s00239-009-9253-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 05/05/2009] [Accepted: 05/26/2009] [Indexed: 12/11/2022]
Abstract
Banana streak virus (BSV) is a plant dsDNA pararetrovirus (family Caulimoviridae, genus badnavirus). Although integration is not an essential step in the BSV replication cycle, the nuclear genome of banana (Musa sp.) contains BSV endogenous pararetrovirus sequences (BSV EPRVs). Some BSV EPRVs are infectious by reconstituting a functional viral genome. Recent studies revealed a large molecular diversity of episomal BSV viruses (i.e., nonintegrated) while others focused on BSV EPRV sequences only. In this study, the evolutionary history of badnavirus integration in banana was inferred from phylogenetic relationships between BSV and BSV EPRVs. The relative evolution rates and selective pressures (d(N)/d(S) ratio) were also compared between endogenous and episomal viral sequences. At least 27 recent independent integration events occurred after the divergence of three banana species, indicating that viral integration is a recent and frequent phenomenon. Relaxation of selective pressure on badnaviral sequences that experienced neutral evolution after integration in the plant genome was recorded. Additionally, a significant decrease (35%) in the EPRV evolution rate was observed compared to BSV, reflecting the difference in the evolution rate between episomal dsDNA viruses and plant genome. The comparison of our results with the evolution rate of the Musa genome and other reverse-transcribing viruses suggests that EPRVs play an active role in episomal BSV diversity and evolution.
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Affiliation(s)
- Philippe Gayral
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, Montpellier, France
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33
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Bousalem M, Durand O, Scarcelli N, Lebas BSM, Kenyon L, Marchand JL, Lefort F, Seal SE. Dilemmas caused by endogenous pararetroviruses regarding the taxonomy and diagnosis of yam (Dioscorea spp.) badnaviruses: analyses to support safe germplasm movement. Arch Virol 2009; 154:297-314. [PMID: 19190853 DOI: 10.1007/s00705-009-0311-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 12/12/2008] [Indexed: 11/25/2022]
Abstract
The discovery of endogenous pararetroviral sequences (EPRVs) has had a deep impact on the approaches needed for diagnosis, taxonomy, safe movement of germplasm and management of diseases caused by pararetroviruses. In this article, we illustrate this through the example of yam (Dioscorea spp.) badnaviruses. To enable progress, it is first necessary to clarify the taxonomical status of yam badnavirus sequences. Phylogeny and pairwise sequence comparison of 121 yam partial reverse transcriptase sequences provided strong support for the identification of 12 yam badnavirus species, of which ten have not been previously named. Virus prevalence data were obtained, and they support the presence of EPRVs in D. rotundata, but not in D. praehensilis, D. abyssinica, D. alata or D. trifida. Five yam badnavirus species characterised by a wide host range seem to be of African origin. Seven other yam badnavirus species with a limited host range are probably of Asian-Pacific origin. Recombination under natural circumstances appears to be rare. Average values of nucleotide intra-species genetic distances are comparable to data obtained for other RNA and DNA virus families. The dispersion scenarios proposed here, combined with the fact that host-switching events appear common for some yam badnaviruses, suggest that the risks linked to introduction via international plant material exchanges are high.
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Affiliation(s)
- Mustapha Bousalem
- INRA-URPV, Domaine Duclos, Prise d'Eau, 9170 Petit-Bourg, Guadeloupe, France.
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34
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Eni AO, Hughes JD, Asiedu R, Rey MEC. Sequence diversity among badnavirus isolates infecting yam (Dioscorea spp.) in Ghana, Togo, Benin and Nigeria. Arch Virol 2008; 153:2263-72. [PMID: 19030955 DOI: 10.1007/s00705-008-0258-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 10/21/2008] [Indexed: 11/29/2022]
Abstract
We analysed the sequence diversity in the reverse transcriptase (RT)/ribonuclease H (RNaseH) coding region of 19 badnavirus isolates infecting yam (Dioscorea spp.) in Ghana, Togo, Benin, and Nigeria. Phylogenetic analysis of the deduced amino acid sequences revealed that the isolates are broadly divided into two distinct species, each clustering with Dioscorea alata bacilliform virus (DaBV) and Dioscorea sansibarensis bacilliform virus (DsBV). Fourteen isolates had 90-96% amino acid identity with DaBV, while four isolates had 83-84% amino acid identity with DsBV. One isolate from Benin, BN4Dr, was distinct and had 77 and 75% amino acid identity with DaBV and DsBV, respectively, and may be a member of a new badnavirus species infecting yam in West Africa. Viruses of the two main species were present in Ghana, Togo and Benin and were observed to infect both D. alata and D. rotundata indiscriminately. This is the first confirmed report of DsBV infection in yam in Ghana and Togo. The results of this study demonstrate that members of two distinct species of badnaviruses infect yam in the West African yam zone and suggest a putative new species, BN4Dr. We also conclude that these species are not confined to limited geographic regions or specific for yam host species. However, the three badnavirus species are serologically related. The sequence information obtained from this study can be used to develop PCR-based diagnostics to detect members of the various species and/or strains of badnaviruses infecting yam in West Africa.
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Affiliation(s)
- A O Eni
- International Institute of Tropical Agriculture, Oyo Road, Ibadan, Nigeria.
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35
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Meyer JB, Kasdorf GGF, Nel LH, Pietersen G. Transmission of Activated-Episomal Banana streak OL (badna)virus (BSOLV) to cv. Williams Banana (Musa sp.) by Three Mealybug Species. PLANT DISEASE 2008; 92:1158-1163. [PMID: 30769482 DOI: 10.1094/pdis-92-8-1158] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Four different mealybug species (Dysmicoccus brevipes, Planococcus citri, P. ficus, and Pseudococcus longispinus) were evaluated for their ability to transmit putative activated-episomal Banana streak OL (badna)virus (BSOLV) to banana cv. Williams (Cavendish subgroup, AAA). Expressible endogenous sequences of banana streak viruses (BSVs) have been reported to be present in the DNA of various Musa hybrids, including FHIA-21 (AAAB). To obtain activated episomal BSOLV for this experimental transmission study, intentional stress by tissue culture propagation was applied to indexed FHIA-21 which, while free of other viruses, can contain activated episomal BSOLV. Immunocapture polymerase chain reaction and triple-antibody sandwich enzyme-linked immunosorbent assay results revealed that 13.4% of the derived progeny of the mother plants were infected with episomal BSOLV. Four of these BSOLV-infected progeny were used as sources of episomal virus for transmission studies. D. brevipes, Planococcus citri, and P. ficus mealybugs were able to transmit the putative activated episomal BSOLV. Control plants for the transmission experiments included FHIA-21 corms with no background history of tissue culture, as well as virus-free Williams plants. Episomal Banana streak GF (badna)virus (BSGFV) was transmitted from asymptomatic corm-derived FHIA-21 plants by P. citri and P. ficus. This is the first report of P. ficus as a vector of BSVs.
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Affiliation(s)
- J B Meyer
- Du Roi Laboratory, Letsitele, 0885, South Africa
| | - G G F Kasdorf
- ARC-Plant Protection Research Institute, Queenswood, 0121, South Africa
| | - L H Nel
- Department of Microbiology and Plant Pathology, University of Pretoria, 0002, South Africa
| | - G Pietersen
- Citrus Research International, c/o Department of Microbiology and Plant Pathology, University of Pretoria, 0002, South Africa
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36
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Bousalem M, Douzery EJP, Seal SE. Taxonomy, molecular phylogeny and evolution of plant reverse transcribing viruses (family Caulimoviridae) inferred from full-length genome and reverse transcriptase sequences. Arch Virol 2008; 153:1085-102. [PMID: 18483693 DOI: 10.1007/s00705-008-0095-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 03/20/2008] [Indexed: 11/26/2022]
Abstract
This study constitutes the first evaluation and application of quantitative taxonomy to the family Caulimoviridae and the first in-depth phylogenetic study of the family Caulimoviridae that integrates the common origin between LTR retrotransposons and caulimoviruses. The phylogenetic trees and PASC analyses derived from the full genome and from the corresponding partial RT concurred, providing strong support for the current genus classification based mainly on genome organisation and use of partial RT sequence as a molecular marker. The PASC distributions obtained are multimodal, making it possible to distinguish between genus, species and strain. The taxonomy of badnaviruses infecting banana (Musa spp.) was clarified, and the consequence of endogenous badnaviruses on the genetic diversity and evolution of caulimoviruses is discussed. The use of LTR retrotransposons as outgroups reveals a structured bipolar topology separating the genus Badnavirus from the other genera. Badnaviruses appear to be the most recent genus, with the genus Tungrovirus in an intermediary position. This structuring intersects the one established by genomic and biological properties and allows us to make a correlation between phylogeny and biogeography. The variability shown between members of the family Caulimoviridae is in a similar range to that reported within other DNA and RNA plant virus families.
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Affiliation(s)
- M Bousalem
- INRA Antilles-Guyane, UR979 Productions Végétales, Domaine Duclos, 97170 Petit-Bourg, Guadeloupe.
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37
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Yams (Dioscorea spp.) from the South Pacific Islands contain many novel badnaviruses: implications for international movement of yam germplasm. Arch Virol 2008; 153:877-89. [PMID: 18330495 DOI: 10.1007/s00705-008-0062-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Accepted: 09/25/2007] [Indexed: 10/22/2022]
Abstract
Yam (Dioscorea spp.) samples (n = 690) from seven South Pacific Islands were screened for badnavirus infection by ELISA using two antisera to African badnaviruses. Positive readings were obtained for 26.4-34.6% of samples representing both known (D. bulbifera, D. nummularia and D. pentaphylla) and unreported host species (D. alata, D. esculenta, D. rotundata and D. trifida) in this region. Total DNAs were extracted from 25 ELISA-positive plants and 4 ELISA-negative controls and subjected to PCR amplification with badnavirus-specific primers targeting the reverse transcriptase (RT)-RNaseH genes. All 29 samples yielded the expected size PCR-product for badnaviruses, which were cloned and sequenced. Phylogenetic analyses of the resulting 45 partial (500-527 bp) RT-RNaseH sequences revealed 11 new sequence groups with <79% nucleotide identity to each other or any EMBL sequence. Three sequences (two groups) were highly divergent to the other nine new South Pacific yam badnavirus groups (47.9-57.2% identity) and probably represent either new Caulimoviridae genera or endogenous pararetrovirus sequences. Some sequence groups appeared specific to particular Dioscorea host species. Four 99.9% identical RT-RNaseH sequences possessing nine amino acid deletions from D. esculenta from three islands represent a putative integrated sequence group. The distribution of sequence groups across the islands indicates that badnaviruses have spread extensively between islands and continents through infected germplasm.
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38
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Kek Heng C, . SMN, . TSY, . RYO. Biopanning for Banana streak virus Binding Peptide by Phage Display Peptide Library. ACTA ACUST UNITED AC 2007. [DOI: 10.3923/jbs.2007.1382.1387] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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39
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Su L, Gao S, Huang Y, Ji C, Wang D, Ma Y, Fang R, Chen X. Complete genomic sequence of Dracaena mottle virus, a distinct badnavirus. Virus Genes 2007; 35:423-9. [PMID: 17497213 DOI: 10.1007/s11262-007-0102-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Accepted: 04/02/2007] [Indexed: 10/23/2022]
Abstract
The genome of Dracaena mottle virus (DrMV) was cloned from infected Dracaena sanderiana plants, and its complete nucleotide sequence was determined and analyzed. The circular DNA genome consists of 7531 base pairs (bp) and possesses seven putative open reading frames (ORFs) on the plus-strand that potentially encode proteins of 17.6, 14.9, 215.0, 11.9, 11.3, 16.1, and 11.0 kDa, respectively. ORF 3, the largest ORF, encodes a putative polyprotein that contains sequences for viral aspartyl proteinase, reverse transcriptase (RT) and ribonuclease H (RNase H), characteristic of pararetroviruses. Phylogenetic analysis based on the amino acid sequence of ORF 3 showed that DrMV is related to other badnaviruses. However, the nucleotide sequence coding for the RT and RNase H domain of DrMV shares less than 68% homology with that of any known badnaviruses. The seventh ORF of DrMV is not found in other badnaviruses described before. Our results strongly support that DrMV is a distinct species of the genus Badnavirus, family Caulimoviridae. Evidence that the DrMV sequence is integrated in the D. sanderiana genome is presented and discussed.
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Affiliation(s)
- Lei Su
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China.
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40
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Lheureux F, Laboureau N, Muller E, Lockhart BEL, Iskra-Caruana ML. Molecular characterization of banana streak acuminata Vietnam virus isolated from Musa acuminata siamea (banana cultivar). Arch Virol 2007; 152:1409-16. [PMID: 17431738 DOI: 10.1007/s00705-007-0946-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2006] [Accepted: 01/22/2007] [Indexed: 10/23/2022]
Abstract
An isolate of banana streak virus (BSV) that does not also occur as an integrant in the Musa balbisiana genome was sought in order to investigate the biological role of BSV in the evolution of either the Musa genome or of the virus itself. We isolated BSV virions from a Musa acuminata siamea accession from Vietnam and sequenced the entire viral genome. The molecular organization is similar to that described for other BSV but slightly larger (7801 bp vs. 1611-7568 bp), and ORF I has a non-conventional start codon. This genome was sufficiently different to propose it as a member of a distinct species named Banana streak virus strain acuminata Vietnam (BSAcVNV).
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Affiliation(s)
- F Lheureux
- CIRAD/UMR BGPI TA A54/K, Montpellier, France
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41
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Seal S, Muller E. Molecular analysis of a full-length sequence of a new yam badnavirus from Dioscorea sansibarensis. Arch Virol 2007; 152:819-25. [PMID: 17195956 DOI: 10.1007/s00705-006-0888-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2006] [Accepted: 11/06/2006] [Indexed: 11/24/2022]
Abstract
Badnavirus-like particles were observed by ISEM in viral preparations from yam (Dioscorea sansibarensis) leaves from Benin. Use of the viral preparation as template for PCR amplification with badnavirus-specific primers gave rise to a 579-bp product with most nucleotide identity (70.8%) to Dioscorea alata bacilliform virus (DaBV, Accession numbers X94575-X94582), the only other yam badnavirus sequenced to date. A full-length badnavirus sequence was generated, which consisted of 7261 nucleotides with a typical Badnavirus genome organisation. The full-length sequence shared most identity (61.9%) to DaBV (Accession numbers X94575-X94582) and hence represents a member of a new badnavirus species termed Dioscorea sansibarensis bacilliform virus (DsBV).
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Affiliation(s)
- S Seal
- Natural Resources Institute, The University of Greenwich at Medway, Chatham Maritime, UK.
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42
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Le Provost G, Iskra-Caruana ML, Acina I, Teycheney PY. Improved detection of episomal Banana streak viruses by multiplex immunocapture PCR. J Virol Methods 2006; 137:7-13. [PMID: 16857272 DOI: 10.1016/j.jviromet.2006.05.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Revised: 05/17/2006] [Accepted: 05/25/2006] [Indexed: 11/28/2022]
Abstract
Banana streak viruses (BSV) are currently the main viral constraint to Musa germplasm movement, genetic improvement and mass propagation. Therefore, it is necessary to develop and implement BSV detection strategies that are both reliable and sensitive, such as PCR-based techniques. Unfortunately, BSV endogenous pararetrovirus sequences (BSV EPRVs) are present in the genome of Musa balbisiana. They interfere with PCR-based detection of episomal BSV in infected banana and plantain, such as immunocapture PCR. Therefore, a multiplex, immunocapture PCR (M-IC-PCR) was developed for the detection of BSV. Musa sequence tagged microsatellite site (STMS) primers were selected and used in combination with BSV species-specific primers in order to monitor possible contamination by Musa genomic DNA, using multiplex PCR. Furthermore, immunocapture conditions were optimized in order to prevent Musa DNA from interfering with episomal BSV DNA during the PCR step. This improved detection method successfully allowed the accurate, specific and sensitive detection of episomal DNA only from distinct BSV species. Its implementation should benefit PCR-based detection of viruses for which homologous sequences are present in the genome of their hosts, including transgenic plants expressing viral sequences.
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Affiliation(s)
- Grégoire Le Provost
- CIRAD, UMR BGPI, Campus International de Baillarguet, F-34398 Montpellier Cedex 5, France
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43
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Fargette D, Konaté G, Fauquet C, Muller E, Peterschmitt M, Thresh JM. Molecular ecology and emergence of tropical plant viruses. ANNUAL REVIEW OF PHYTOPATHOLOGY 2006; 44:235-60. [PMID: 16784403 DOI: 10.1146/annurev.phyto.44.120705.104644] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
An appreciation of the risks caused by emergent plant viruses is critical in tropical areas that rely heavily on agriculture for subsistence and rural livelihood. Molecular ecology, within 10 years, has unraveled the factors responsible for the emergence of several of the economically most important tropical plant viruses: Rice yellow mottle virus (RYMV), Cassava mosaic geminiviruses (CMGs), Maize streak virus (MSV), and Banana streak virus (BSV). A large range of mechanisms--most unsuspected until recently--were involved: recombination and synergism between virus species, new vector biotypes, genome integration of the virus, host adaptation, and long-distance dispersal. A complex chain of molecular and ecological events resulted in novel virus-vector-plant-environment interactions that led to virus emergence. It invariably involved a major agricultural change: crop introduction, cultural intensification, germplasm movement, and new genotypes. A current challenge is now to complement the analysis of the causes by an assessment of the risks of emergence. Recent attempts to assess the risks of emergence of virulent virus strains are described.
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Affiliation(s)
- D Fargette
- IRD BP 64501, 34394 Montpellier Cedex 5, France.
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Hansen CN, Harper G, Heslop-Harrison JS. Characterisation of pararetrovirus-like sequences in the genome of potato (Solanum tuberosum). Cytogenet Genome Res 2005; 110:559-65. [PMID: 16093709 DOI: 10.1159/000084989] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2003] [Accepted: 02/19/2004] [Indexed: 11/19/2022] Open
Abstract
Three families of pararetrovirus-like sequences were isolated from the genome of potato using PCR of a characteristic fragment extending from the end of the transactivator domain. The potato pararetrovirus-like sequences are abundant in the nuclear genome of potato as demonstrated by their hybridisation to high-molecular weight DNA in Southern transfers and by fluorescence in situ hybridisation. Sequencing of cloned PCR products demonstrated that the potato pararetrovirus-like sequences were similar to other pararetroviral sequences and also to some expressed sequences from tobacco and tomato, notably from callus and Agrobacterium-infected tissue. It is possible that the potato pararetroviral sequences defend against viral genes via silencing mechanisms, although, as in Petunia or banana, their transcription and recombination may cause infection under stress conditions.
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Affiliation(s)
- C N Hansen
- Department of Biology, University of Leicester, Leicester, UK
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Jaufeerally-Fakim Y, Khorugdharry A, Harper G. Genetic variants of Banana streak virus in Mauritius. Virus Res 2005; 115:91-8. [PMID: 16143419 DOI: 10.1016/j.virusres.2005.06.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Revised: 06/22/2005] [Accepted: 06/22/2005] [Indexed: 11/20/2022]
Abstract
Genetic variations among isolates of Banana streak virus (BSV) were assessed using two sets of primers. The virus, found in banana accessions in Mauritius, was compared to a Nigerian isolate from cultivar Obino l'Ewai (BSOEV). On the basis of the observed size of amplicons, some Mauritius strains were different from l'Ewai BSOEV. Both Southern blot hybridization and the nucleotide sequences of the PCR products confirmed that they were of episomal BSV origin. An isolate of sugarcane bacilliform virus (SCBV) was found to be also very similar to the BSV isolated from banana samples. Nucleotide sequence analysis showed that even the same size PCR products had differing sequences. The dendrogram placed the isolates from Mauritius in a cluster separate from BSV and SCBV from other geographical locations.
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Affiliation(s)
- Y Jaufeerally-Fakim
- Biotechnology Unit, Faculty of Agriculture, University of Mauritius, Reduit, Mauritius.
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Harper G, Hart D, Moult S, Hull R, Geering A, Thomas J. The diversity of Banana streak virus isolates in Uganda. Arch Virol 2005; 150:2407-20. [PMID: 16096705 DOI: 10.1007/s00705-005-0610-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2005] [Accepted: 06/24/2005] [Indexed: 11/29/2022]
Abstract
In a study of the variation among isolates of Banana streak virus (BSV) in Uganda, 140 sequences were obtained from 49 samples by PCR across the conserved reverse transcriptase/RNaseH region of the genome. Pairwise comparison of these sequences suggested that they represented 15 different species and phylogenetic analyses showed that all species fell into three major clades based on 28% sequence difference. In addition to the Ugandan sequences, clade I also contained BSV species that are known as both integrated sequences and episomal viruses; clade II also contained integrated BSV sequences but which have not previously been identified as episomal viruses. Clade III comprised of Sugarcane bacilliform virus isolates and Ugandan BSV sequences and for which there is no evidence of integration. The possible reasons for the extraordinary levels of virus sequence variation and the potential origins and epidemiology of these viruses causing banana streak disease are discussed.
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Affiliation(s)
- G Harper
- Department of Disease and Stress Biology, John Innes Centre, Colney Lane, Norwich, UK.
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Remans T, Grof CPL, Ebert PR, Schenk PM. Identification of functional sequences in the pregenomic RNA promoter of the Banana streak virus Cavendish strain (BSV-Cav). Virus Res 2005; 108:177-86. [PMID: 15681068 DOI: 10.1016/j.virusres.2004.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2004] [Revised: 05/30/2004] [Accepted: 09/27/2004] [Indexed: 01/10/2023]
Abstract
The promoter regions of plant pararetroviruses direct transcription of the full-length viral genome into a pregenomic RNA that is an intermediate in the replication of the virus. It serves as template for reverse transcription and as polycistronic mRNA for translation to viral proteins. We have identified functional promoter elements in the intergenic region of the Cavendish isolate of Banana streak virus (BSV-Cav), a member of the genus Badnavirus. Potential binding sites for plant transcription factors were found both upstream and downstream of the transcription start site by homology search in the PLACE database of plant cis-acting elements. The functionality of these putative cis-acting elements was tested by constructing loss-of-function and "regain"-of-function mutant promoters whose activity was quantified in embryogenic sugarcane suspension cells. Four regions that are important for activity of the BSV-Cav promoter were identified: the region containing an as-1-like element, the region around -141 and down to -77, containing several putative transcription factor binding sites, the region including the CAAT-box, and the leader region. The results could help explain the high BSV-Cav promoter activity that was observed previously in transgenic sugarcane plants and give more insight into the plant cell-mediated replication of the viral genome in banana streak disease.
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Affiliation(s)
- Tony Remans
- Department of Biochemistry and Molecular Biology, 306 Carmody Road, St. Lucia, Qld. 4072, Australia.
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Yang Z, Nicolaisen M, Olszewski NE, Lockhart BEL. Sequencing, Improved Detection, and a Novel Form of Kalanchoë top-spotting virus. PLANT DISEASE 2005; 89:298-302. [PMID: 30795353 DOI: 10.1094/pd-89-0298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Virions of Kalanchoë top-spotting virus (KTSV) were purified from infected leaf tissue of Kalanchoë blossfeldiana using a procedure that prevented loss of virus in the initial extraction step. The double-stranded DNA viral genome was cloned and sequenced. The KTSV genome was 7,591 bp in size and contained three open reading frames capable of encoding proteins of 21, 14, and 223 kDa, respectively. The size and organization of the KTSV genome were similar to those of other mealybug-transmitted badnaviruses. Several oligonucleotide primer pairs, based on the KTSV genomic sequence, were used to efficiently detect the virus in plants, thereby removing a major constraint to reliable screening of kalanchoë propagating stock and breeding lines for KTSV infection. Two KTSV sequences, one symptom-inducing and the other not, were identified and differentiated by polymerase chain reaction (PCR) amplification and digestion of the resulting amplicon with restriction endonucleases. Preliminary results from graft-transmission tests and PCR indexing suggest that the nonsymptomatic form of KTSV may represent an integrated viral element. The occurrence of such integrated pararetroviral elements poses practical problems for routine PCR indexing of breeding and propagating stock, and also raises the possibility of symptomatic episomal infections arising from these viral integrants.
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Affiliation(s)
- Zihong Yang
- Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | - Mogens Nicolaisen
- Danish Institute of Agriculture Sciences, Department of Crop Protection, Flakkebjerg, Denmark
| | - Neil E Olszewski
- Department of Plant Biology, University of Minnesota, St. Paul 55108
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Braithwaite KS, Geijskes RJ, Smith GR. A variable region of the sugarcane bacilliform virus (SCBV) genome can be used to generate promoters for transgene expression in sugarcane. PLANT CELL REPORTS 2004; 23:319-26. [PMID: 15309498 DOI: 10.1007/s00299-004-0817-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2004] [Revised: 05/01/2004] [Accepted: 05/04/2004] [Indexed: 05/03/2023]
Abstract
Four promoters derived from sugarcane bacilliform virus (SCBV) were compared and characterised. Three were obtained by PCR amplification of purified virion DNA extracted from three sugarcane cultivars. The fourth promoter was obtained by subcloning from an almost genome-length clone of SCBV. All promoters were able to drive stable expression of beta-glucuronidase in sugarcane. The PCR-derived promoter sequences shared more DNA homology with banana streak virus than to the subcloned SCBV. The subcloned promoter was the strongest expressing and was able to drive reporter gene expression in vitro and in the leaves, meristems and roots of glasshouse-grown sugarcane. Expression levels were at least equal to or higher than those measured for the maize polyubiquitin promoter.
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Affiliation(s)
- K S Braithwaite
- David North Plant Research Centre, BSES Limited, P.O. Box 86, Indooroopilly, Queensland, 4068, Australia.
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Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution. BMC Genomics 2004; 5:80. [PMID: 15488154 PMCID: PMC526188 DOI: 10.1186/1471-2164-5-80] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Accepted: 10/18/2004] [Indexed: 11/10/2022] Open
Abstract
Background Plant genomes contain various kinds of repetitive sequences such as transposable elements, microsatellites, tandem repeats and virus-like sequences. Most of them, with the exception of virus-like sequences, do not allow us to trace their origins nor to follow the process of their integration into the host genome. Recent discoveries of virus-like sequences in plant genomes led us to set the objective of elucidating the origin of the repetitive sequences. Endogenous rice tungro bacilliform virus (RTBV)-like sequences (ERTBVs) have been found throughout the rice genome. Here, we reconstructed putative virus structures from RTBV-like sequences in the rice genome and characterized to understand evolutionary implication, integration manner and involvements of endogenous virus segments in the corresponding disease response. Results We have collected ERTBVs from the rice genomes. They contain rearranged structures and no intact ORFs. The identified ERTBV segments were shown to be phylogenetically divided into three clusters. For each phylogenetic cluster, we were able to make a consensus alignment for a circular virus-like structure carrying two complete ORFs. Comparisons of DNA and amino acid sequences suggested the closely relationship between ERTBV and RTBV. The Oryza AA-genome species vary in the ERTBV copy number. The species carrying low-copy-number of ERTBV segments have been reported to be extremely susceptible to RTBV. The DNA methylation state of the ERTBV sequences was correlated with their copy number in the genome. Conclusions These ERTBV segments are unlikely to have functional potential as a virus. However, these sequences facilitate to establish putative virus that provided information underlying virus integration and evolutionary relationship with existing virus. Comparison of ERTBV among the Oryza AA-genome species allowed us to speculate a possible role of endogenous virus segments against its related disease.
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