1
|
Ishwara Bhat A, Selvarajan R, Balasubramanian V. Emerging and Re-Emerging Diseases Caused by Badnaviruses. Pathogens 2023; 12:pathogens12020245. [PMID: 36839517 PMCID: PMC9963457 DOI: 10.3390/pathogens12020245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
New and emerging plant diseases are caused by different pathogens including viruses that often cause significant crop losses. Badnaviruses are pararetroviruses that contain a single molecule of ds DNA genome of 7 to 9 kb in size and infect a large number of economically important crops such as banana and plantains, black pepper, cacao, citrus, grapevine, pineapple, sugarcane, sweet potato, taro, and yam, causing significant yield losses. Many of the species in the genus have a restricted host range and several of them are known to infect a single crop. Combined infections of different virus species and strains offer conditions that favor the development of new strains via recombination, especially in vegetatively propagated crops. The primary spread of badnaviruses is through vegetative propagating materials while for the secondary spread, they depend on insects such as mealybugs and aphids. Disease emerges as a consequence of the interactions between host and pathogens under favorable environmental conditions. The viral genome of the pararetroviruses is known to be integrated into the chromosome of the host and a few plants with integrants when subjected to different kinds of abiotic stress will give rise to episomal forms of the virus and cause disease. Attempts have been made to develop management strategies for badnaviruses both conventionally and using precision breeding techniques such as genome editing. Until 2016 only 32 badnavirus species infecting different crops were known, but in a span of six years, this number has gone up to 68. The current review highlights the emerging disease problems and management options for badnaviruses infecting economically important crops.
Collapse
Affiliation(s)
- Alangar Ishwara Bhat
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Kozhikode 673012, Kerala, India
| | - Ramasamy Selvarajan
- Division of Crop Protection, ICAR-National Research Centre for Banana, Trichy 620102, Tamil Nadu, India
| | - Velusamy Balasubramanian
- Division of Crop Protection, ICAR-National Research Centre for Banana, Trichy 620102, Tamil Nadu, India
| |
Collapse
|
2
|
Vakić M, Stainton D, Delić D, Tzanetakis IE. Characterization of the first Rubus yellow net virus genome from blackberry. Virus Genes 2022; 58:594-597. [PMID: 35941271 DOI: 10.1007/s11262-022-01926-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/07/2022] [Indexed: 11/29/2022]
Abstract
Rubus yellow net virus (RYNV) is a badnavirus that infects Rubus spp. Mixed infections with black raspberry necrosis virus and raspberry leaf mottle virus cause raspberry mosaic, a disease that leads to significant losses and even plant death. RYNV has been reported in several European countries and the Americas yet there is substantial lack of knowledge, especially when it comes to virus diversity and the evolutionary forces that affect virus fitness outside its primary host, raspberry. Herein, we report the first RYNV episomal genome isolated from blackberry and this is the first report of the virus in Bosnia and Herzegovina. The isolate has five open reading frames (ORFs) and, when compared with other fully sequenced counterparts, showed 82-97% nucleotide pairwise identity. This communication adds to our limited knowledge on RYNV and addresses some of the gaps in RYNV genetics when it comes to the coding capacity of episomal isolates and the probability of the first fully sequenced isolate of the virus being integrated in the raspberry genome.
Collapse
Affiliation(s)
- Mišaela Vakić
- Faculty of Agriculture, University of Banja Luka, Banja Luka, Bosnia and Herzegovina
| | - Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR, 72701, USA
| | - Duška Delić
- Faculty of Agriculture, University of Banja Luka, Banja Luka, Bosnia and Herzegovina
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR, 72701, USA.
| |
Collapse
|
3
|
Hu X, Boeckman CJ, Cong B, Steimel JP, Richtman NM, Sturtz K, Wang Y, Walker CA, Yin J, Unger A, Farris C, Lu AL. Characterization of DvSSJ1 transcripts targeting the smooth septate junction (SSJ) of western corn rootworm (Diabrotica virgifera virgifera). Sci Rep 2020; 10:11139. [PMID: 32636422 PMCID: PMC7341793 DOI: 10.1038/s41598-020-68014-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 06/17/2020] [Indexed: 11/29/2022] Open
Abstract
Transgenic maize plants expressing dsRNA targeting western corn rootworm (WCR, Diabrotica virgifera virgifera) DvSSJ1 mRNA, a Drosophila snakeskin (ssk) ortholog, show insecticidal activity and significant plant protection from WCR damage. The gene encodes a membrane protein associated with the smooth sepate junction (SSJ) which is required for intestinal barrier function. To understand the active RNA form that leads to the mortality of WCR larvae by DvSSJ1 RNA interference (RNAi), we characterized transgenic plants expressing DvSSJ1 RNA transcripts targeting WCR DvSSJ1 mRNA. The expression of the silencing cassette results in the full-length transcript of 901 nucleotides containing a 210 bp inverted fragment of the DvSSJ1 gene, the formation of a double-stranded RNA (dsRNA) transcript and siRNAs in transgenic plants. Our artificial diet-feeding study indicates that dsRNAs greater than or equal to approximately 60 base-pairs (bp) are required for DvSSJ1 insecticidal activity. Impact of specificity of dsRNA targeting DvSSJ1 mRNA on insecticidal activities was also evaluated in diet bioassay, which showed a single nucleotide mutation can have a significant impact or abolish diet activities against WCR. These results provide insights as to the functional forms of plant-delivered dsRNA for the protection of transgenic maize from WCR feeding damage and information contributing to the risk assessment of transgenic maize expressing insecticidal dsRNA.
Collapse
Affiliation(s)
- Xu Hu
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA.
| | - Chad J Boeckman
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA.
| | - Bin Cong
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA.
| | - Joe P Steimel
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Nina M Richtman
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Kristine Sturtz
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Yiwei Wang
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Carl A Walker
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Jiaming Yin
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Anita Unger
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Caitlin Farris
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Albert L Lu
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| |
Collapse
|
4
|
Abstract
Promoters regulate gene expression, and are essential biotechnology tools. Since its introduction in the mid-1990s, biotechnology has greatly enhanced maize productivity primarily through the development of insect control and herbicide tolerance traits. Additional biotechnology applications include improving seed nutrient composition, industrial protein production, therapeutic production, disease resistance, abiotic stress resistance, and yield enhancement. Biotechnology has also greatly expanded basic research into important mechanisms that govern plant growth and reproduction. Many novel promoters have been developed to facilitate this work, but only a few are widely used. Transgene optimization includes a variety of strategies some of which effect promoter structure. Recent reviews examine the state of the art with respect to transgene design for biotechnology applications. This chapter examines the use of transgene technology in maize, focusing on the way promoters are selected and used. The impact of new developments in genomic technology on promoter structure is also discussed.
Collapse
|
5
|
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: 65] [Impact Index Per Article: 8.1] [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.
Collapse
Affiliation(s)
| | - Thomas Hohn
- UNIBAS, Botanical Institute, 4056 Basel, Switzerland.
| | - Ramasamy Selvarajan
- ICAR-National Research Centre for Banana, Tiruchirapalli 620102, Tamil Nadu, India.
| |
Collapse
|
6
|
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.
Collapse
|
7
|
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.
Collapse
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
| | | |
Collapse
|
8
|
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.
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Iskra-Caruana ML, Chabannes M, Duroy PO, Muller E. A possible scenario for the evolution of Banana streak virus in banana. Virus Res 2014; 186:155-62. [PMID: 24457073 DOI: 10.1016/j.virusres.2014.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 12/18/2013] [Accepted: 01/10/2014] [Indexed: 01/15/2023]
Abstract
Outbreaks of Banana streak virus (BSV) have been recorded worldwide where Musa spp. is grown during the last 20 years with no convincing evidence of epidemics. Epidemics were previously reported in Uganda where BSV is currently endemic. BSV is a plant pararetrovirus of the family Caulimoviridae, genus Badnavirus it causes chlorosis leaf streak disease. The information currently available on banana streak disease makes it possible to identify a complex of distinct BSV species each causing the same disease. BSV exists in two states: one as an episomal form, infecting plant cells; the other as viral DNA integrated within the B genome of banana (endogenous BSV-eBSV) forming a viral genome for de novo viral particles. Both forms can be infectious in banana plants. The BSV phylogeny is polyphyletic with BSV distributed in two clades. Clade 1 clusters BSV species that occur worldwide and may have an eBSV counterpart, whereas Clade 3 only comprises BSV species from Uganda. Clearly, two distinct origins explain such BSV diversity. However, the epidemiology/outbreaks of BSV remains unclear and the role of eBSV needs to be clarified. In this review, the biodiversity of BSV is explained and discussed in the light of field and molecular epidemiology data. A scheme is proposed for the co-evolution of BSV and banana based on old or recent infection hypotheses related to African domestication sites and banana dissemination to explain the disease context.
Collapse
|
11
|
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.
Collapse
|
12
|
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.
Collapse
Affiliation(s)
- Virendra K Baranwal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012, India,
| | | | | | | |
Collapse
|
13
|
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.
Collapse
Affiliation(s)
- Basanta K Borah
- Department of Plant Molecular Biology, Delhi University South Campus, New Delhi 110021, India
| | | | | | | | | | | |
Collapse
|
14
|
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.
Collapse
|
15
|
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.
Collapse
|
16
|
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.
Collapse
|
17
|
Geering ADW, Parry JN, Thomas JE. Complete genome sequence of a novel badnavirus, banana streak IM virus. Arch Virol 2011; 156:733-7. [PMID: 21347843 DOI: 10.1007/s00705-011-0946-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 02/03/2011] [Indexed: 11/25/2022]
Abstract
In 1999, banana streak disease outbreaks occurred at two locations in Australia in new banana hybrids that were being screened for fusarium wilt resistance. Two different badnaviruses, banana streak GF virus and a newly discovered virus called banana streak IM virus (BSIMV), were detected in these plants. The complete nucleotide sequence of the BSIMV genome was determined and comprised 7768 nt. Three open reading frames were detected, the first beginning with a non-conventional start codon (CUG). A 55-nt repetition in the putative pregenomic RNA promoter was also identified. Phylogenetic analysis suggests that BSIMV is most closely related to banana streak VN virus.
Collapse
Affiliation(s)
- Andrew D W Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Brisbane, QLD 4001, Australia.
| | | | | |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Gayral P, Blondin L, Guidolin O, Carreel F, Hippolyte I, Perrier X, Iskra-Caruana ML. Evolution of endogenous sequences of banana streak virus: what can we learn from banana (Musa sp.) evolution? J Virol 2010; 84:7346-59. [PMID: 20427523 PMCID: PMC2898222 DOI: 10.1128/jvi.00401-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 04/22/2010] [Indexed: 11/20/2022] Open
Abstract
Endogenous plant pararetroviruses (EPRVs) are viral sequences of the family Caulimoviridae integrated into the nuclear genome of numerous plant species. The ability of some endogenous sequences of Banana streak viruses (eBSVs) in the genome of banana (Musa sp.) to induce infections just like the virus itself was recently demonstrated (P. Gayral et al., J. Virol. 83:6697-6710, 2008). Although eBSVs probably arose from accidental events, infectious eBSVs constitute an extreme case of parasitism, as well as a newly described strategy for vertical virus transmission in plants. We investigated the early evolutionary stages of infectious eBSV for two distinct BSV species-GF (BSGFV) and Imové (BSImV)-through the study of their distribution, insertion polymorphism, and structure evolution among selected banana genotypes representative of the diversity of 60 wild Musa species and genotypes. To do so, the historical frame of host evolution was analyzed by inferring banana phylogeny from two chloroplast regions-matK and trnL-trnF-as well as from the nuclear genome, using 19 microsatellite loci. We demonstrated that both BSV species integrated recently in banana evolution, circa 640,000 years ago. The two infectious eBSVs were subjected to different selective pressures and showed distinct levels of rearrangement within their final structure. In addition, the molecular phylogenies of integrated and nonintegrated BSVs enabled us to establish the phylogenetic origins of eBSGFV and eBSImV.
Collapse
|
20
|
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.
Collapse
Affiliation(s)
- Philippe Gayral
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, Montpellier, France
| | | |
Collapse
|
21
|
Gayral P, Noa-Carrazana JC, Lescot M, Lheureux F, Lockhart BEL, Matsumoto T, Piffanelli P, Iskra-Caruana ML. A single Banana streak virus integration event in the banana genome as the origin of infectious endogenous pararetrovirus. J Virol 2008; 82:6697-710. [PMID: 18417582 PMCID: PMC2447048 DOI: 10.1128/jvi.00212-08] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 04/07/2008] [Indexed: 12/15/2022] Open
Abstract
Sequencing of plant nuclear genomes reveals the widespread presence of integrated viral sequences known as endogenous pararetroviruses (EPRVs). Banana is one of the three plant species known to harbor infectious EPRVs. Musa balbisiana carries integrated copies of Banana streak virus (BSV), which are infectious by releasing virions in interspecific hybrids. Here, we analyze the organization of the EPRV of BSV Goldfinger (BSGfV) present in the wild diploid M. balbisiana cv. Pisang Klutuk Wulung (PKW) revealed by the study of Musa bacterial artificial chromosome resources and interspecific genetic cross. cv. PKW contains two similar EPRVs of BSGfV. Genotyping of these integrants and studies of their segregation pattern show an allelic insertion. Despite the fact that integrated BSGfV has undergone extensive rearrangement, both EPRVs contain the full-length viral genome. The high degree of sequence conservation between the integrated and episomal form of the virus indicates a recent integration event; however, only one allele is infectious. Analysis of BSGfV EPRV segregation among an F1 population from an interspecific genetic cross revealed that these EPRV sequences correspond to two alleles originating from a single integration event. We describe here for the first time the full genomic and genetic organization of the two EPRVs of BSGfV present in cv. PKW in response to the challenge facing both scientists and breeders to identify and generate genetic resources free from BSV. We discuss the consequences of this unique host-pathogen interaction in terms of genetic and genomic plant defenses versus strategies of infectious BSGfV EPRVs.
Collapse
Affiliation(s)
- Philippe Gayral
- CIRAD BIOS, UMR BGPI, Campus International de Baillarguet, TA A-54/K, 34398 Montpellier Cedex 5, France
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Pest risk assessment made by France on Banana streak virus (BSV) considered by France as harmful in French overseas departments of French Guiana, Guadeloupe, Martinique and Réunion ‐ Scientific Opinion of the Panel on Plant Health. EFSA J 2008. [DOI: 10.2903/j.efsa.2008.667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|