Low genetic diversity of Banana bunchy top virus, with a sub-regional pattern of variation, in Democratic Republic of Congo

Mukwa, Lyna Fama Tongo; Gillis, Annika; Vanhese, V.; Romay, Gustavo; Galzi, Serge; Laboureau, Nathalie; Kalonji-Mbuyi, A.; Iskra-Caruana, Marie-Line; Bragard, Claude

doi:10.1007/s11262-016-1383-1

Cited by 10 publications

(13 citation statements)

References 21 publications

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“…Recombination is a major contributor to genetic diversity [ 18 , 74 ] and genetic variations [ 75 ] in ssDNA viruses. Recombination analysis of BBTV components based on nucleotide sequence showed that DNA-U3 exhibits complex intra- and inter recombination patterns ( Fig 3 ) with a recombination occurrence ( Table 7 ) of about 16.8% which is about 9 times more than the least recombined DNA-S component (1.8%).…”

Section: Discussionmentioning

confidence: 99%

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

Bashir

Naqvi

Muhammad³

et al. 2022

PLoS ONE

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

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Section: Discussionmentioning

confidence: 99%

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

Bashir

Naqvi

Muhammad³

et al. 2022

PLoS ONE

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“…Thus, this study was performed to investigate the genetic structure and diversity of the BBTV isolates in the Philippines. Here, the partial DNA-R region of BBTV was sequenced due to its wide application in assessing genetic diversity and other molecular analyses (Bell et al, 2002; Furuya et al, 2005; Amin et al, 2007; Kumar et al, 2011; Shekhawat et al, 2012; Banerjee et al, 2014; Chiaki et al, 2015; Mukwa et al, 2016). Survey and sample collection were conducted in banana growing areas in various regions in the Philippines for BBTV detection and diversity analysis.…”

Section: Discussionmentioning

confidence: 99%

“…In-depth studies on the diversity of BBTV from various countries were already reported, such as in Democratic Republic of Congo (Mukwa et al, 2016), Pakistan (Amin et al, 2007), sub-Saharan Africa (Kumar et al, 2011), Indonesia (Chiaki et al, 2015), Japan (Furuya et al, 2005) and India (Banerjee et al, 2014). The information on the degree of genetic diversity and distribution of BBTV in these countries provided useful and fundamental information to control BBTD through various pest management approaches.…”

Section: Introductionmentioning

confidence: 99%

Genetic Structure and Diversity of Banana Bunchy Top Virus (BBTV) in the Philippines

Cortaga

et al. 2021

Preprint

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Banana bunchy top virus (BBTV) is an important disease of banana in the Philippines and in other banana-producing countries. This study was conducted to investigate the genetic structure and diversity of Philippine BBTV isolates which remain unexplored in the country. BBTV-infected plant tissues were sampled from banana-growing provinces (i.e., Cagayan, Isabela, Quirino, Batangas, Laguna, Rizal, Quezon, Palawan, Cebu, Leyte, and Davao del Sur) and the partial DNA-R gene of BBTV was sequenced. Analysis of all local BBTV isolates showed a nucleotide diversity (π) of 0.00721, average number of nucleotide differences (k) of 5.51984, and haplotype diversity (hd) of 0.971. Neutrality tests using Fu′s Fs and Tajima′s D showed significant and highly negative values which suggest an excess number of rare alleles due to recent population expansion or from genetic hitchhiking. Haplotype network and phylogenetic analyses revealed that the local BBTV isolates were closely related to Southeast Asian (SEA) group and exhibited a monophyletic clade with distinct haplotype grouping from other SEA sequences. However, some Indonesian and Indian reference sequences were also clustered within the Philippine BBTV group suggesting sequence homology. Results also showed that the local BBTV isolates may be categorized into three major haplotype groups (HA, HB, and HC) but only the HC group remained distinct upon comparison with other Philippine and SEA reference sequences. BBTV isolates from Quezon were the most diverse while isolates from Palawan displayed low genetic diversity indices and belonged only in the HC group. The assessment of the degree of variability among Philippine BBTV isolates will provide a reference towards the development of high-throughput BBTV detection systems as well as enable to devise plant breeding strategies to manage the current BBTV spread and variations.

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“…One of the most important cases is the banana streak viruses (BSVs), because the cultivated banana species are only reproduced by vegetative propagation and BSVs remain inserted into genome indefinitely. Along with BSVs, Banana bunchy top virus (BBTV, family Nanoviridae ) are the most economically important viruses for banana production worldwide (Rybicki, 2015; Mukwa et al, 2016). Interestingly, BBTV is a DNA virus that could be directly targeted using the same transgene-free GES approach.…”

Section: Ges-mediated Plant Virus Defenses Vis-à-vis Gmo Regulationsmentioning

confidence: 99%

Antiviral Defenses in Plants through Genome Editing

Romay

Bragard

2017

Front. Microbiol.

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Plant–virus interactions based-studies have contributed to increase our understanding on plant resistance mechanisms, providing new tools for crop improvement. In the last two decades, RNA interference, a post-transcriptional gene silencing approach, has been used to induce antiviral defenses in plants with the help of genetic engineering technologies. More recently, the new genome editing systems (GES) are revolutionizing the scope of tools available to confer virus resistance in plants. The most explored GES are zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats/Cas9 endonuclease. GES are engineered to target and introduce mutations, which can be deleterious, via double-strand breaks at specific DNA sequences by the error-prone non-homologous recombination end-joining pathway. Although GES have been engineered to target DNA, recent discoveries of GES targeting ssRNA molecules, including virus genomes, pave the way for further studies programming plant defense against RNA viruses. Most of plant virus species have an RNA genome and at least 784 species have positive ssRNA. Here, we provide a summary of the latest progress in plant antiviral defenses mediated by GES. In addition, we also discuss briefly the GES perspectives in light of the rebooted debate on genetic modified organisms (GMOs) and the current regulatory frame for agricultural products involving the use of such engineering technologies.

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Low genetic diversity of Banana bunchy top virus, with a sub-regional pattern of variation, in Democratic Republic of Congo

Cited by 10 publications

References 21 publications

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

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

Genetic Structure and Diversity of Banana Bunchy Top Virus (BBTV) in the Philippines

Antiviral Defenses in Plants through Genome Editing

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