Genetically Diverse Variants of Sugarcane bacilliform virus Infecting Sugarcane in India and Evidence of a Novel Recombinant Badnavirus Variant

2014 ◽  
Vol 162 (11-12) ◽  
pp. 779-787 ◽  
Author(s):  
Govind P. Rao ◽  
Susheel K. Sharma ◽  
Deepti Singh ◽  
Meenakshi Arya ◽  
Priyanka Singh ◽  
...  
Keyword(s):  
Sugarcane Bacilliform Virus

Comparison of pcr and dac-elisa for the diagnosis of sugarcane bacilliform virus in sugarcane

Sugar Tech ◽  
2005 ◽  
Vol 7 (4) ◽  
pp. 119-122 ◽  
Author(s):  
M. Balamuralikrishnan ◽  
R. Viswanathan
Keyword(s):  
Sugarcane Bacilliform Virus

Genetic diversity of Sugarcane bacilliform virus isolates infecting Saccharum spp. in India

Virus Genes ◽  
2013 ◽  
Vol 46 (3) ◽  
pp. 505-516 ◽  
Author(s):  
R. Karuppaiah ◽  
R. Viswanathan ◽  
V. Ganesh Kumar
Keyword(s):  
Genetic Diversity ◽  
Saccharum Spp ◽  
Sugarcane Bacilliform Virus ◽  
Virus Isolates

True Seed Transmission of Sugarcane bacilliform virus (SCBV) in Sugarcane

Sugar Tech ◽  
2021 ◽  
Author(s):  
Sanju Balan ◽  
K. Nithya ◽  
K. Anita Cherian ◽  
R. Viswanathan
Keyword(s):  
Seed Transmission ◽  
True Seed ◽  
Sugarcane Bacilliform Virus

Sugarcane bacilliform virus encapsidates genome concatamers and does not appear to integrate into the Saccharum officinarum genome

2004 ◽  
Vol 149 (4) ◽  
pp. 791-798 ◽  
Author(s):  
R. J. Geijskes ◽  
K. S. Braithwaite ◽  
G. R. Smith ◽  
J. L. Dale ◽  
R. M. Harding
Keyword(s):  
Saccharum Officinarum ◽  
Sugarcane Bacilliform Virus

Prevalence and RT/RNase H Genealogy of Sugarcane Bacilliform Virus Isolates from China

2016 ◽  
Vol 164 (9) ◽  
pp. 595-607 ◽  
Author(s):  
Xiao-Bin Wu ◽  
Olufemi J. Alabi ◽  
Mona B. Damaj ◽  
Sheng-Ren Sun ◽  
Theodore Erik Mirkov ◽  
...  
Keyword(s):  
Rnase H ◽  
Sugarcane Bacilliform Virus ◽  
Virus Isolates

scholarly journals An Algorithmic framework for genome-wide identification of Sugarcane (Saccharum officinarum L.)-encoded microRNA targets against SCBV

2020 ◽  
Author(s):  
Muhammad Aleem Ashraf ◽  
Xiaoyan Feng ◽  
Xiaowen Hu ◽  
Fakiha Ashraf ◽  
Linbo Shen ◽  
...  
Keyword(s):  
Single Molecule ◽  
Hypothetical Protein ◽  
Saccharum Officinarum ◽  
Potential Candidate ◽  
Candidate Mirnas ◽  
Microrna Targets ◽  
Genome Wide ◽  
Algorithmic Framework ◽  
Sugarcane Bacilliform Virus

AbstractSugarcane Bacilliform Virus (SCBV) is considered an economically the most damaging pathogen for sugarcane production worldwide. Three ORFs are characterized in a single molecule of circular, ds-DNA genome of the SCBV, encoding for hypothetical protein (ORF1), DNA binding protein (ORF2) and Polyprotein (ORF3). The study was aimed to predict and comprehensively evaluate sugarcane miRNAs for the silencing of SCBV genome using in-silico algorithms. Computational methods were used for prediction of candidate miRNAs from sugarcane (S. officinarum L.) to silence the expression of SCBV genes through translational inhibition by mRNA cleavage. Mature sugarcane miRNAs were retrieved and were assessed to hybridization with the SCBV genome. A total of fourteen potential candidate miRNAs from sugarcane were computed by all the algorithms used for the silencing of SCBV. A consensus of three algorithms predicts hybridization sites of sof-miR159e at common locus 5534. The miRNA-mRNA interaction was estimated by computing free-energy of miRNA-mRNA duplex using RNAcofold algorithm. Regulatory network of predicted candidate miRNAs of sugarcane with SCBV ORFs, generated using Circos, identify novel targets. Consequently, detecting and discarding inefficient amiRNAs prior to cloning would help suppressed mutants faster. The efficacy of predicted candidate miRNAs was evaluated to test the survival rate of the in vitro amiRNA-mediated effective badnaviral silencing and resistance in sugarcane cultivars.

scholarly journals First Report of Rubus yellow net virus on Rubus idaeus in Alberta, Canada

Plant Disease ◽  
2008 ◽  
Vol 92 (6) ◽  
pp. 974-974 ◽  
Author(s):  
M. L. Kalischuk ◽  
L. M. Kawchuk ◽  
F. Leggett
Keyword(s):  
Pcr Amplification ◽  
Rubus Idaeus ◽  
Ribonuclease H ◽  
Specific Primers ◽  
First Report ◽  
Transmission Electron ◽  
Pcr Product ◽  
Southern Alberta ◽  
Sugarcane Bacilliform Virus ◽  
Amphorophora Agathonica

In North America, Rubus yellow net virus (RYNV), a member of the genus Badnavirus, family Caulimoviridae, is vectored in a semipersistent manner by the large raspberry aphid (Amphorophora agathonica Hottes) and is responsible for producing net-like chlorosis of tissue along the leaf veins (2). Red raspberry (Rubus idaeus L.) is commonly grown in Canada and after the dry, hot summer of 2006 in southern Alberta, a group of garden raspberry plants located near Lethbridge, Alberta exhibited interveinal chlorosis resembling viral symptoms. Nonenveloped, 140 × 30 nm, bacilliform particles typical of badnaviruses were observed in infected leaves by transmission electron microscopy. The presence of RYNV was confirmed by immunocapture of virions from extracts of symptomatic leaves using Sugarcane bacilliform virus polycolonal antiserum (Agdia Incorporated, Elkhart, IN) followed by PCR amplification of a 451-bp fragment with RYNV-specific primers based on the highly conserved region of the reverse transcriptase and ribonuclease H genes (5′-ATCCTCAAAGGGTTACGTAGCTGGTT-3′ and 5′-TTCAAGCCACCTTACCCTCGAAGGTTT-3′). Sequence of clones from the PCR product (GenBank Accession No. EU327346) showed 87% identity to a previously sequenced isolate of RYNV (GenBank Accession No. AF468454) (1). To our knowledge, this is the first report of RYNV in Alberta, Canada, and as an important component of raspberry veinbanding disease, it poses a new threat to the Alberta raspberry industry. References: (1) A. T. Jones et al. Ann. Appl. Biol. 141:1, 2002. (2) R. Stace-Smith. Can. J. Bot. 33:269, 1955.

scholarly journals Dynamics of genetic diversity among Indian Sugarcane bacilliform virus species and implications of associated recombination events in the virus

2021 ◽  
Author(s):  
PK Janiga ◽  
K. Nithya ◽  
Rasappa Viswanathan
Keyword(s):  
Protein Sequence ◽  
Low Frequency ◽  
Purifying Selection ◽  
Virus Species ◽  
Efficient Tool ◽  
Over Expression ◽  
Evolutionary Changes ◽  
Sugarcane Bacilliform Virus ◽  
Neutrality Tests ◽  
Virus Isolates

Abstract Sugarcane bacilliform virus (SCBV), a plant pararetrovirus causing leaf fleck disease in sugarcane across the globe. Since the virus occurs throughout the sugarcane growing areas and germplasm in India, we have assessed the genetic divergences among the virus isolates from 104 isolates infecting germplasm and Saccharum hybrid varieties. With the evidence gathered from phylogenetic analysis and sequence demarcation tool, five novel genotypes are being proposed: SCBV-U, SCBV-V, SCBV-W, SCBV-X and SCBV-Y. SCBV-W: CBJ 46, due to the divergence in the nucleotide and protein sequence with existing isolates, established itself as a novel candidate in SCBV species. In comparison with the existing database of SCBV and conclusion from the present study, SCBV isolates from India exhibited maximum diversity in comparison with other regions. SCBV-U, SCBV-W, SCBV-X which turned out as potent recombinants along with other six recombinants in the study, directs at the plausible heterogeneity and genetic exchange happened within SCBV species over time which lead to the evolution of new variants. Neutrality tests indicate the existence of low-frequency polymorphism and Selection pressure of < 1 pointed out at purifying selection. Codon usage bias acted as an efficient tool for identifying patterns in SCBV, in which non-randomness in mutational events might lead to the over expression of codon AGA. The current study on characterization and evidence of nucleotidal variation within SCBV species will lead to devising robust diagnostics of the virus in quarantine and improving the knowledge on the evolutionary changes in SCBV species.

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