Genome Of Banana Bunchy Top Virus Research Articles

UJI KETAHANAN TIGA VARIETAS PISANG (Musa sp.) TERHADAP ISOLAST BANANA BUNCHY TOP VIRUS (BBTV)

Banana is a horticultural crop that has economic value and is widely cultivated in tropical countries. Banana Bunchy Top Virus (BBTV) is the cause of dwarf disease in banana plants (Musa. sp). The vector for the spread of this banana dwarf disease is the banana aphid (Pentalonia nigronervosa). BBTV has been reported in various regions of Indonesia, having been reported in Bengkulu in 2020. However, data on the resistance of BBTV infections in Indonesia are still very limited. This study aimed to evaluate the resistance of three types of bananas (Barangan, Kepok, and Ambon Hijau) to BBTV infection. In this study, two treatments were carried out, namely inoculated and without BBTV virus inoculation with three types of bananas. BBTV detection was carried out using the PCR method. BBTV transmission using aphids succeeded in infecting the test plants with a disease incidence of 12.5% ​​to 75.0% at 30 DAI. The most common symptom seen is, slightly yellowed leaf edges. the severity of BBTV on the Barangan banana plant was 20.83%, kepok was 4.17% and Ambon Hijau was 25.00%. Samples on the leaves of the test banana plant that showed symptoms of BBTV were taken for detection using Polymerase Chain Reaction (PCR) with a pair of related NSP primers in the BBTV genome with a size of ± 500 bp. The results of the detection of BBTV virus showed that the types of bananas that were resistant to BBTV were Kepok bananas, Barangan bananas and Ambon Hijau types which showed moderate resistance to BBTV

Banana bunchy top virus genetic diversity in Pakistan and association of diversity with recombination in its genomes

Banana Bunchy top virus (BBTV) is a multipartite circular single strand DNA virus that belongs to genus Babuvirus and family Nanoviridae. It causes significant crop losses worldwide and also in Pakistan. BBTV is present in Pakistan since 1988 however, till now only few (about twenty only) sequence of genomic components have been reported from the country. To have insights into current genetic diversity in Pakistan fifty-seven genomic components including five complete genomes (comprises of DNA-R, -U3, -S, -M, -C and -N components) were sequenced in this study. The genetic diversity analysis of populations from Pakistan showed that DNA-R is highly conserved followed by DNA-N, whereas DNA-U3 is highly diverse with the most diverse Common Region Stem-loop (CR-SL) in BBTV genome, a functional region, which previously been reported to have undergone recombination in Pakistani population. A Maximum Likelihood (ML) phylogenetic analysis of entire genomes of isolates by using sequence of all the components concatenated together with the reported genomes around the world revealed deeper insights about the origin of the disease in Pakistan. A comparison of the genetic diversity of Pakistani and entire BBTV populations around the world indicates that there exists a correlation between genetic diversity and recombination. Population genetics analysis indicated that the degree of selection pressure differs depending on the area and genomic component. A detailed analysis of recombination across various components and functional regions suggested that recombination is closely associated with the functional parts of BBTV genome showing high genetic diversity. Both genetic diversity and recombination analyses suggest that the CR-SL is a recombination hotspot in all BBTV genomes and among the six components DNA-U3 is the only recombined component that has extensively undergone inter and intragenomic recombination. Diversity analysis of recombinant regions results on average one and half fold increase and, in some cases up to four-fold increase due to recombination. These results suggest that recombination is significantly contributing to the genetic diversity of BBTV populations around the world.

Survey and detection of Banana bunchy top virus in Java

Banana bunchy top virus (BBTV) is one of the most important virus causing disease on banana plantation. Infection of BBTV is indicated by unique symptoms involving yellowing and curling of leaf margin, and stunting of plant. Research was conducted to determine the distribution of banana bunchy top disease (BBTD) in West Java (Bogor and Sukabumi), Central Java (Pati and Magelang), and East Java (Malang and Banyuwangi) based on symptom variations and disease severity. Field samples was then confirmed by polymerase chain reaction (PCR) detection method using four specific primers, each amplified different region of BBTV genome, i.e CP1/2 which amplified coat protein gene in DNA S, mRep1/2, BBT1/2, and BBTV-F/-R which amplified replication gene in DNA R in different region. Symptoms and incidence of BBTD was varied across banana plantation in Java. The most common symptoms observed in the field includes chlorotic, green mosaic, narrow, and upright appearance of the leaves, and stunting of the plant. Incidence of BBTV was found more severe in West Java than those in Central Java and East Java. All primers used in the detection method was successfully amplified the target DNA fragment. DNA R primers were more sensitive than DNA S primers and the better amplification result was achieved using BBT1/2 and BBTVR-F/-R primers.

Cloning of BBTV (Banana Bunchy Top Virus) components and screening of BBTV using functionalized gold nanoparticles.

Banana bunchy top virus (BBTV) affects all varieties of banana plants and causes heavy economic loss in most of the banana cultivating areas. The BBTV genome comprises of six DNA components; in this study, we have cloned the six BBTV-DNA components from one of the BBTV-infected plants (Tri-8) and were submitted to GenBank. Analysis of the BBTV DNA-R component showed that it belonged to south Pacific group. Resistance against BBTV has not been observed so far in banana plants and removal and killing of the infected plants has been routinely practiced. Hence, early detection of BBTV infection would be desirable and various detection methods routinely employed include enzyme linked immunosorbent assay (antigen-antibody based) and molecular-based methods such as polymerase chain reaction (PCR), qPCR, or LAMP PCR. Most of these methods require enzymes or antibodies for detection and hence are expensive. Here, we report a visual detection method (AuNP probe assay) using gold nanoparticles (AuNPs) functionalized with an ssDNA-thiolated probe (CR1). This method is based on the hybridization of the functionalized AuNPs with the target DNA (BBTV). In the AuNP probe assay, the functionalized AuNPs retains red colour when BBTV DNA is present, and in the absence of BBTV DNA, the colour of the functionalized AuNPs changes to purple when salt is added. The AuNP probe assay was compared with PCR for the detection of banana plants and it was found that AuNP probe assay was better than PCR in detecting BBTV infection (86.5% for AuNP probe assay and 65% for PCR). The AuNP probe assay was found to be highly specific to BBTV and was found to detect up to 1pg/μl of the plasmid (pTZBBTri 4, BBTV DNA) mixed with healthy banana DNA.

Banana bunchy top virus and the bunchy top disease

Banana bunchy top virus (BBTV) is a circular single-stranded (ss) plant DNA virus and the type member of the genus Babuvirus in the family Nanoviridae. BBTV causes bunchy top disease of banana and plantain. Its integral genome consists of at least six circular ssDNA genome components and is associated with all geographical isolates of BBTV. BBTV is a phloem-limited virus that is transmitted from plant to plant by the aphid vector, and long-distance spread is through the movement of infected plant material. BBTV is an economically important plant pathogen causing substantial damage to banana crops worldwide. In the past 2 decades, with the advent of molecular techniques, the genome of BBTV has been elucidated, and its genetic diversity has been studied extensively. However, the molecular interactions of viral proteins with host metabolites and proteins have not been studied in depth. Protein functions and viral interactions of BBTV are comparable to the other group of single-stranded plant DNA viruses, Geminiviridae. However in many other aspects, BBTV is clearly distinct from geminiviruses. Further research is required to better elucidate the virus–host interactions and protein functions of this pathogen.

Application of Motif-Based Tools on Evolutionary Analysis of Multipartite Single-Stranded DNA Viruses

Multipartite viruses contain more than one distinctive genome component, and the origin of multipartite viruses has been suggested to evolve from a non-segmented wild-type virus. To explore whether recombination also plays a role in the evolution of the genomes of multipartite viruses, we developed a systematic approach that employs motif-finding tools to detect conserved motifs from divergent genomic regions and applies statistical approaches to select high-confidence motifs. The information that this approach provides helps us understand the evolution of viruses. In this study, we compared our motif-based strategy with current alignment-based recombination-detecting methods and applied our methods to the analysis of multipartite single-stranded plant DNA viruses, including bipartite begomoviruses, Banana bunchy top virus (BBTV) (consisting of 6 genome components) and Faba bean necrotic yellows virus (FBNYV) (consisting of 8 genome components). Our analysis revealed that recombination occurred between genome components in some begomoviruses, BBTV and FBNYV. Our data also show that several unusual recombination events have contributed to the evolution of BBTV genome components. We believe that similar approaches can be applied to resolve the evolutionary history of other viruses.

Evidence of recombination in the Banana bunchy top virus genome

Viruses serve as good model for evolutionary studies, owing to their short generation times and small genomes. Banana bunchy top virus (BBTV) is a significant subject being multicomponent circular single stranded DNA virus. BBTV belongs to family Nanoviridae and contains DNA-R, -U3, -S, -M, -C, and -N as integral genomic components. Evolutionary studies have shown genetic re-assortment of components among its isolates and revealed a concerted type evolution in non-coding regions of its genome. The DNA U3 having been shown as the most diverse component in our previous studies, was subjected to sequencing from some Pakistani isolates for the first time. Sequence analysis revealed intergenomic recombination in DNA-U3 among the isolates of two sub-groups and a very rare intragenomic recombination in Pakistani BBTV population. This indicates that like other evolutionary processes including intergenomic recombination, intragenomic recombination among the genomic components of the same isolate may also have a significant contribution in the evolution of BBTV genome. Intragenomic recombination therefore appears to be a unique way to generate genetic diversity in the multicomponent ssDNA viruses.

MOLECULAR CHARACTERIZATION AND PHYLOGENETIC STUDIES OF COMPONENT SIX OF BANANA BUNCHY TOP BABUVIRUS (BBTV DNA-6)

Banana and plantations (Musa sp.) are the most fourth most important global food crop after rice, wheat and maize (Piertersen and Thomas, 2001). Banana plantations are subjected to various natural climates but diseases; in particular, viral diseases constitute a major setback to this crop worldwide. Among viral infections, Banana Bunchy Top Virus (BBTV) is the most serious virus affecting banana in Egypt as well as the world (Dale, 1987; Othman et al., 1996; Harish et al., 2008) and is responsible for the massive reduction in banana crop yield. The symptoms of BBTD are yellowing, dark green streaks on midrib, petioles, extending down into pseudostem, dark green dots and dashes along the minor leaf veins, stunted growth with bunchy top appearance (Magee, 1940; Vetten et al., 2005). BBTV belong to genus Babuvirus and family Nanoviridae with isometric particles of 18-20 nm in diameter. It is naturally transmitted, in persistence manner, by banana aphid Pentalonia nigronervosa (Hu et al., 1996). BBTV is identified as a phloem-limited virus used to occur in low concentration in banana-infected plants (Harding et al., 1991 and 2000). The virus has a single coat protein with molecular weight (Mr.) of about 20-21kDa (Dietzgen and Thomas, 1991; Harding et al., 1991; Sadik et al., 1999).The viron consists of at least six components of circular ssDNA each component of the BBTV genome contains one large (monocistronic) transcriptional active open reading frame (ORF) except BBTV DNA 1 contains two ORFs one master replication protein (Rep) ORF (Hafner et al., 1997) and a small ORF internal to major ORF (Beetham et al., 1997). Additionally, two conserved region: stem-loop common region (CR-SL) and major common region (CR-M), potential TATA box at 3 ' of the stem-loop and polyadenylation signal (Burns et al., 1995; Beetham et al., 1997 and 1999).The nucleotide sequence of the component six of Australian isolate BBTV has 1089 nt. (Burns et al., 1995). The encoded protein of BBTV DNA-6 is a nuclear shuttle protein and is preferentially targeted to the nucleus when expressed alone however in the presence of the movement protein it targeted to the cell periphery (Wanitchakorn et al., 2000a).The aim of this study is to amplify, clone and sequence the full length of BBTV DNA-6 and compare it with other published sequences of the corresponding sequence.

Molecular Characterization of Geographically Different Banana bunchy top virus Isolates in India

Banana bunchy top disease (BBTD) caused by Banana bunchy top virus (BBTV) is one of the most devastating diseases of banana and poses a serious threat for cultivars like Hill Banana (Syn: Virupakshi) and Grand Naine in India. In this study, we have cloned and sequenced the complete genome comprised of six DNA components of BBTV infecting Hill Banana grown in lower Pulney hills, Tamil Nadu State, India. The complete genome sequence of this hill banana isolate showed high degree of similarity with the corresponding sequences of BBTV isolates originating from Lucknow, Uttar Pradesh State, India, and from Fiji, Egypt, Pakistan, and Australia. In addition, sixteen coat protein (CP) and thirteen replicase genes (Rep) sequences of BBTV isolates collected from different banana growing states of India were cloned and sequenced. The replicase sequences of 13 isolates showed high degree of similarity with that of South Pacific group of BBTV isolates. However, the CP gene of BBTV isolates from Shervroy and Kodaikanal hills of Tamil Nadu showed higher amino acid sequence variability compared to other isolates. Another hill banana isolate from Meghalaya state had 23 nucleotide substitutions in the CP gene but the amino acid sequence was conserved. This is the first report of the characterization of a complete genome of BBTV occurring in the high altitudes of India. Our study revealed that the Indian BBTV isolates with distinct geographical origins belongs to the South Pacific group, except Shervroy and Kodaikanal hill isolates which neither belong to the South Pacific nor the Asian group.

First report of Banana bunchy top virus infecting banana in Iran

Banana bunchy top disease is one of the most serious diseases of bananas (Musa spp.) worldwide. The disease is caused by Banana bunchy top virus (BBTV), the type species of the Babuvirus genus; (family Nanoviridae). The genome of BBTV is comprised of at least six circular single-stranded DNA (ssDNA) components, each approximately 1 Kb in size. Symptoms of BBTV infection include plant stunting, foliar yellowing and most characteristically, dark green streaks on the pseudostem, petioles and leaves (Harding et al. 1993; Vetten et al., 2005). From 2004 to 2006, a series of field surveys were conducted in the major banana-growing areas in Iran: Mazandaran province (Sari, Babol, Behshahr, and Ghaemshahr) in the north and Hormozgan province (Jask and Varz-Abad) in the south. A total of 164 banana plant samples with bunchy top, stunting and leaf samples with green streak symptoms were collected. Samples were tested for the presence of BBTV with a double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) using positive control and polyclonal antibodies against BBTV, according to the supplier's instructions (Bio-Rad). Of the samples tested, 27 were positive for BBTV using DAS-ELISA. To confirm BBTV identification, polymerase chain reaction (PCR) was carried out using samples that previously tested positive by ELISA. Forward [F3: 5′-GGAAGAAGCCTCTCATCTGCTTCAGAGAR C-3′; nts 287 to 258] and reverse [FPCR4: 5′-TTCCCAGGCGCACACCTTGAGAAACGA AAG-3′; nts 284 to 313] primers were used to amplify complete BBTV DNA-1 (Furuya et al., 2005). PCR analysis showed fragments of approximately 1 Kb in 19 samples. Furthermore, using primer pairs designed to differentiate BBTV strains (Su et al., 2003), Iranian BBTV isolates were divided into two distinct strains. This is the first report of the occurrence of BBTV in Iran.

Banana bunchy top virus DNA-2 to 6 are monocistronic

Banana bunchy top virus (BBTV) DNA-3 to 6 have each previously been shown to contain one large open reading frame in the virion sense, whereas no large ORF had been identified in BBTV DNA-2. RNAs transcribed from the BBTV genome were mapped using northern hybridisation and 3' RACE. One mRNA was transcribed from each of BBTV DNA-2 to 6 and four of these mRNAs mapped to the ORFs previously identified in BBTV DNA-3 to 6. The mRNA of BBTV DNA-2 was transcribed from a virion sense ORF probably using a TATA box sequence different to that in BBTV DNA-1, and DNA-3 to 6. This ORF encoded a 10 kDa protein of unknown function. The 3' untranslated region of the five mRNAs varied from 25 nucleotides (BBTV DNA-6) to 167 nucleotides (BBTV DNA-4) and each contained putative polyadenylation signals with associated GT rich sequence together with a possible termination signal (C/T/A)TGTAA conserved in all five mRNAs.

Evidence that banana bunchy top virus has a multiple component genome.

A 93 nucleotide sequence was found to be strongly conserved between two ssDNA genomic components of banana bunchy top virus (BBTV). Two outwardly extending degenerate primers were designed from this sequence and used in a polymerase chain reaction (PCR) with DNA extracted from purified BBTV virions. PCR amplified products consisting of at least seven distinct bands all approximately 1 kb and possibly representing full-length BBTV dsDNA were resolved. The PCR amplified products were cloned and the clones screened by restriction enzyme analysis. Four distinct restriction analysis groups were identified. These results confirm that the genome of BBTV contains at least five components and that it belongs to a previously undescribed group of plant viruses which may also contain subterranean clover stunt virus.

Nucleotide sequence of one component of the banana bunchy top virus genome contains a putative replicase gene

One DNA component of the banana bunchy top virus (BBTV) genome was cloned and sequenced. This component is present as a circular, ssDNA in the virions and consists of 1111 nucleotides. It contains one large open reading frame (ORF) of 858 nucleotides in the virion sense; this ORF encodes a putative replicase based on the presence of a dNTP-binding motif (GGEGKT). Two smaller ORFs (249 and 366 nucleotides), in the complementary orientation, could not be assigned any obvious function. Neither of these ORFs had significant sequence homology with any known DNA plant virus gene or gene product. Computer analysis of this component-predicted a strong stem-loop structure in the virion sense putative untranslated region; a nonanucleotide sequence in the loop was nearly identical to the nonanucleotide invariant loop sequence of geminiviruses and coconut foliar decay virus. There is strong evidence that the genome of BBTV consists of more than one component because no ORF was found that would encode a protein the size of the BBTV coat protein. BBTV has some characteristics in common with geminiviruses but cannot be classified as one. Rather, BBTV probably belongs to an undescribed plant virus group which could also include subterranean clover stunt virus and coconut foliar decay virus.