Characterization and complete nucleotide sequencing of Pepper Mild Mottle Virus infecting Bell Pepper in India
TL;DR: The first complete genome sequence of Indian isolate of PM MoV (HP-1) was elucidated and compared with other members of Virgaviridae family and PMMoV isolates showed that PMMov-HP1 isolate is more closely related to the PMMo V-J, the Japanese isolate.
Abstract: Capsicum (Capsicum annuum L var. grossum Sendt) commonly known as bell pepper or sweet pepper, is one of the most economical agricultural crop grown under both open and polyhouse conditions. The presence of Pepper mild mottle virus (PMMoV) from different districts of Himachal Pradesh was confirmed by double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) and RT-PCR using coat protein (CP) gene amplification. The first complete genome sequence of Indian isolate of PMMoV (HP-1) was elucidated and compared with other members of Virgaviridae family and PMMoV isolates. Sequence homology, multiple alignment and phylogenetic analysis on the basis of nucleotide and amino acid sequences showed that PMMoV-HP1 isolate is more closely related to the PMMoV-J, the Japanese isolate. Based on CP gene amino acid sequence analysis, the PMMoV-HP1 isolate showed 100 per cent identity with P12 pathotypes (capable of breaking L
2
gene mediated resistance in capsicum). This is the first report of the PMMoV complete genome organization intercepted in India.
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15 Oct 2018
TL;DR: Recent advancements in the understanding of the occurrence and persistence of PMMoV in natural and engineered water systems are reviewed and its advantages and limitations as a viral indicator for improved microbial water quality management are discussed.
Abstract: Pepper mild mottle virus (PMMoV) was recently found to be the most abundant RNA virus in human feces, and is a plant virus belonging to the genus Tobamovirus in the family Virgoviridae. When in human feces, it is of dietary origin from peppers and their processed products, and is excreted from a large proportion of healthy human populations, but rarely found in animal feces. Over the past decade, this virus has been increasingly attracting research attention as a potential viral indicator for human fecal pollution in aquatic environments and water treatment systems. Results presented in the literature reveal that PMMoV is globally distributed and present in various water sources in greater abundance than human pathogenic viruses, without substantial seasonal fluctuations. Several studies report that increased concentrations of PMMoV tend to be correlated with increased fecal contamination in general, along with more frequent detection of pathogenic enteric viruses. PMMoV also exhibits remarkable stability in water under various environmental conditions. Here, we review recent advancements in our understanding of the occurrence and persistence of PMMoV in natural and engineered water systems and discuss its advantages and limitations as a viral indicator for improved microbial water quality management.
181 citations
TL;DR: The combined results demonstrate that, unlike previously thought, the dominant PepMoV resistance in 9093 could be derived from C. annuum 'CM334', and that Pvr4 and Pvr7 should be considered as the same locus.
Abstract: Pepper mottle virus (PepMoV) is the most common potyvirus infection of pepper plants and causes significant yield losses. The Pvr7 gene from Capsicum chinense PI159236 and the Pvr4 gene from C. annuum CM334 both have been reported to confer dominant resistance to PepMoV. The Pvr7 locus conferring resistance to PepMoV in C. annuum ‘9093’ was previously mapped to chromosome 10. To develop a high-resolution map of the Pvr7 locus in 9093, we constructed an intraspecific F2 mapping population consisting of 916 individuals by crossing PepMoV-resistant C. annuum ‘9093’ and the PepMoV-susceptible C. annuum ‘Jeju’. To delimit the Pvr7 target region, single-nucleotide polymorphism (SNP) markers derived from the Pvr4 region were used for genotyping the F2 population. Molecular mapping delimited the Pvr7 locus to a physical interval of 258 kb, which was the same region as Pvr4 on chromosome 10. Three SNP markers derived from Pvr4 mapping perfectly cosegregated with PepMoV resistance. Sequencing analyses of the Pvr7 f...
13 citations
TL;DR: Chilli pepper (Capsicum annuum) is an important cash crop in Pakistan which is cultivated on an area of 62,500 ha with an annual yield of 145,100 tonnes (Farooq, 2014).
Abstract: Chilli pepper ( Capsicum annuum ) is an important cash crop in Pakistan which is cultivated on an area of 62,500 ha with an annual yield of 145,100 tonnes (Farooq, 2014). Pepper mild mottle virus (PMMoV) is a single-stranded RNA virus…
6 citations
References
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TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
70,111 citations
"Characterization and complete nucle..." refers methods in this paper
...checked manually using bioEdit software (Altschul et al. 1997)....
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...The sequences were also checked manually using bioEdit software (Altschul et al. 1997)....
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TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
Abstract: Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.
39,110 citations
"Characterization and complete nucle..." refers methods in this paper
...The multiple alignment of the present isolate was done using ClustalW (www.ebi.ac.uk/ Tools/msa/clustalw2/) and phylogenetic trees were constructed using MEGA5 program (Tamura et al. 2011) using the Neighbor-Joining method....
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01 Jan 2005
4,979 citations
TL;DR: The method enabled the highly sensitive detection of a number of morphologically different viruses in purified preparations and in unclarified extracts of herbaceous hosts and of infected crop plants.
Abstract: Some characteristics of a microplate method for the detection and assay of plant viruses using enzyme-labelled antibodies are described. The method enabled the highly sensitive detection of a number of morphologically different viruses in purified preparations and in unclarified extracts of herbaceous hosts and of infected crop plants. Virus concentrations were estimated by photometric measurement of the colour intensity of the hydrolysed substrate. The suitability of the tehcnique for various field and research applications is considered.
4,773 citations
"Characterization and complete nucle..." refers methods in this paper
...…different viruses viz., CMV, PepMoV, PMMoV, TMVand Tomato mosaic virus (ToMV) through DAS-ELISA (Bioreba, Switzerland) using polyclonal antibodies (Clark & Adams 1977) and the samples found positive for PMMoVantiserum were maintained on susceptible bell pepper variety “California wonder” through…...
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Book•
01 Jan 1996
TL;DR: Viruses of plants : descriptions and lists from the VIDE database, Viruses of Plants :descriptions and list from the VIDEO database, etc.
Abstract: Viruses of plants :descriptions and lists from the VIDE database , Viruses of plants :descriptions and lists from the VIDE database , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
384 citations
"Characterization and complete nucle..." refers background in this paper
...The virus is highly contagious and like other tobamoviruses also transmitted through seed and soil (Komuro & Iwaki 1969; Lanter et al. 1982; Brunt et al. 1996; Tan et al. 1997; Ikegashira et al. 2004; Toyoda et al. 2004)....
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