molecular characterization of tospoviruses infecting
TRANSCRIPT
Indian Journal of Biotechnology
Vol. 19, July 2020, pp 182-191
Molecular characterization of tospoviruses infecting Capsicum annuum L.
Rajamanickam S1*
, Haokip B D1, Caroline R
2 and Nakkeeran S
1
1Department of Plant Pathology, 2Department of Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University,
Coimbatore - 641 003, India
Received 15 April 2020; revised & accepted 26 May 2020
Chilli (Capsicum annuum L) a prime vegetable cum spice crop is infected by tospoviruses, which has become a serious
threat to it's cultivation worldwide. A survey was conducted for infection of tospoviruses on the basis of chlorotic and
necrotic symptoms in chilli growing areas of Tamil Nadu. The symptomatic leaves were positive for tospovirus-specific
antiserum tested through direct antigen coating - enzyme linked immunosorbent assay (DAC-ELISA), dot blot
immunobinding assay (DIBA) and tissue blot immunobinding assay (TIBA). The samples with typical symptoms were
successfully established for the chlorotic and necrotic lesions in assay host, cowpea and chilli upon artificial inoculation of
tospoviruses. Further, an expected complementary DNA (cDNA) fragment sequence of about 840 bp and 1.2 kb were
positively amplified using PCR correspond to coat protein (CP) gene of the respective viruses, which confirmed the
presence of groundnut bud necrosis virus (GBNV), capsicum chlorosis virus (CaCV) in chilli. However, there is a lack of
standard method to understand the genetic information of tospoviruses infecting chilli which requires the reliable, sensitive
and specific method. To address this issue, we have investigated an application based on CP gene of GBNV and CaCV to
perform molecular profiling. The nucleotide sequences of GBNV and CaCV showed maximum identity between the isolates
and amino acid sequences had more than 90% similarity. However, superimposed 3D prediction structures constructed using
MODELLER software revealed the single variation at 259th position comprising of glutamine and valine respectively. The
protein profiling of CP gene provides the basic knowledge on properties of CP proteins of two tospoviruses infecting chilli
and their structural relationships.
Keywords: Chilli, tospoviruses, serodiagnosis, CP gene sequences, 3D prediction structures
Introduction
Chilli (Capsicum annuum L.) belongs to the
Solanaceae family known as red pepper, is an
important condiment cum vegetable crop in India.
The chilli is known for its flavor, pungency and for its
medicinal value. India has produced around 8 lakh
tonnes of dry chilli from an area of 9.3 lakh hectares
from major chilli producing states of India including
Andhra Pradesh, Tamil Nadu, Karnataka, Kerala and
Maharashtra1-2
. As with other crops, chilli is affected
by various pathogen and pest that can cause
comprehensive loss in production. Among the various
pathogens infecting chilli, around 10 viruses cause a
serious threat affecting the yield3. The viral disease of
chilli causes 50-100 per cent yield reduction during
early stage of infection and often has social
consequences4-5
. The literature survey revealed that,
groundnut bud necrosis virus (GBNV) is an
economically important virus with a broad host range
and widespread distribution throughout the world. In
India, necrosis disease in vegetables is caused by a
virus collectively known as tospovirus group.
Tospoviruses are important among the plant viruses
worldwide causing significant economic losses in the
cultivation of chilli and other vegetable crops6. In the
early 2000, chilli leaf curl virus (ChiLCV), the type
species of geminivirus and potyviruses caused
significant losses on chilli in northern part of India7. In
the late 2000, a new tospovirus, GBNV, which caused
severe losses in the production of chilli and other
vegetable crops in India. The virus was first recorded
on groundnut during 1968 and it has become a major
constraint to the cultivation of several leguminous and
solanaceous hosts such as potato, tomato and chilli8-10
.
The another tospovirus, capsicum chlorosis virus
(CaCV) was reported for the first time in tomato in
northern India during 2007 and subsequently it has
been reported in peppers cultivated at southern India11
.
In addition, the distribution of CaCV infecting tomato in
southern and central India belongs to watermelon silver
mottle virus (WSMoV) serogroup. The tospoviruses are
known to be transmitted by different species of thrips in
a persistent and propagative manner. Tospoviruses form
——————
*Author for correspondence:
RAJAMANICKAM et al MOLECULAR ANALYSIS OF TOSPOVIRUSES INFECTING CHILLI
183
pleomorphic, spherical particles within plant cells and
are surrounded by a lipid envelope with two surface
glycoproteins projections, enclosing three nucleocapsids.
The virus consists of a tripartite genome with S, M and
L RNA segments.
The symptoms produced by CaCV mimic the same
as that of GBNV in chilli which includes, circular
chlorotic and necrotic spots on the leaves, stunting of
plants and misshapen leaves under field conditions.
So far, only morphological and symptom based
studies have been conducted on necrosis disease in
chilli and other vegetable crops. Furthermore, CaCV
can react to all the serogroup of GBNV, therefore it is
difficult to differentiate the specificity of tospovirus
infecting chilli through serological reactions11
. There
are few investigations focused on the molecular
characterization on different viruses infecting chilli
under field conditions. Strategies for the management
of viral diseases normally include control of vector
population using insecticides, use of virus-free
propagating material, appropriate cultural practices
and use of resistant cultivars. Recently, plant
virologists have focused their attention to develop
virus resistance transgenic plants or triggered the
host plant resistance against plant viruses through
different molecular approaches worldwide12-13
. The
enhancement of host plant resistance appears as one
of the best options because it offers an easy, cheap
and sustainable technology. Several researchers find
the active sites present in the viral genome which can
positively interact with the several proteins from
plants and microbial origin which leads to
enhancement of plant immunity14-15
. Under these
circumstances, it is highly imperative to develop
biological and molecular tools for the detection of
tospoviruses infecting chilli in Tamil Nadu. Hence,
the present study was aimed in serological, molecular
detection and computational analysis to find out the
protein profiling of tospoviruses infecting chilli.
Materials and Methods
Survey and Collection of Virus Infected Samples
Field survey was conducted during 2017-18 by
covering major chilli growing areas viz., Coimbatore,
Dharapuram, Pollachi and Udumalapet of Tamil Nadu
state to document the virus diseases. The per cent
disease incidence was recorded by counting the total
number of plants and virus infected plants in each and
every field of different areas. The plant samples
showing characteristic tospovirus-like symptoms were
collected separately for further analyses. Ten samples
from each field were collected in zip-loc bags and
labeled. Samples were transported to the laboratory
on ice and kept at 4°C. All samples were processed
within 24 h after collection.
Serological Assay of Tospovirus Isolates
The chilli plants showing the characteristic
symptoms of necrosis diseases were subjected to
direct antigen coating-enzyme linked immunosorbent
assay (DAC-ELISA) using the polyclonal antibodies
specific to tospoviruses16
. The polyclonal antibody
was diluted in antibody buffer and experiment was
carried out with standard protocol. The results were
quantitatively recorded in an ELISA reader at 405 nm
(Biotek EL X 800). The positive samples were further
tested through dot blot immunobinding assay (DIBA).
The infected tissue was extracted (1:10 w/v) in
antigen extraction buffer and filtered through double
layer of cheese cloth. The samples (5-10 µl) were
spotted on nitrocellulose membrane, air-dried and
tested17
. The results were assessed by comparing the
intensity of colour and photographed.
Inoculums Preparation and Mechanical Transmission
The positive samples of tospovirus in DAC-ELISA
were used for transmission studies in cowpea and
chilli hosts by mechanical sap inoculation. Cowpea
cv. C152 and chilli var. syngenta bullet were used as
propagating host for the virus inoculation. Cowpea
and chilli express typical chlorotic and necrotic lesion
within 3-4 days and 10 days after inoculation,
respectively. The plants were raised in the glass house
and maintained under insect-proof conditions. The
virus extract was prepared by macerating infected
chilli plant tissue with 0.1M sodium phosphate
buffer (pH 7.0) containing 0.1% β-mercaptoethanol,
using ice tray. Inoculation was carried out by gentle
rubbing with inoculum using broad end of the pestle
on the cotyledonary leaves on six day old cowpea
plants and in young leaves of one month old chilli
plants, which were previously dusted with 600 mesh
carborundum powder. After few min, the excess
inoculum was washed with a jet of sterile distilled
water using wash bottle. The inoculated plants were
incubated at room temperature for 3-7 days for
cowpea and for 10 days in case of chilli plants for
studying the expression of symptoms18
.
Total RNA Extraction, cDNA Synthesis and Amplification of
Coat Protein (CP) Genes
Total RNA of ~50 μg/μl concentration was
extracted from 100 mg leaves of infected chilli using
INDIAN J BIOTECHNOL, APRIL 2020
184
trizol plant extraction kit (Sigma Chemicals, USA)
according to the manufacturers protocol and
resuspended in 50 μl nuclease-free water. The total
RNA isolated from the virus infected field chilli
samples were subjected to PCR in
50 µl reaction volume containing cDNA and 2 units
of enzyme mix along with the primers specific
to GBNV (CPF-ATGTCTAACGTYAAGCAGCTC;
CPR-TTACAACTCTAGCGAAGGAC) and CaCV
(CPF-AACCAATAGTTTGCCTCCG; CPR - AGA
GCAATCGAGGCACTA) corresponding to coat
protein gene of GBNV and CaCV, respectively, to
amplify the complete coding region of CP genes19
.
The PCR settings comprised of 35 cycles of
amplification including denaturation at 94°C for
2 min, annealing at 52°C (GBNV) and 60°C (CaCV)
for 30 s, extension at 72°C for 1 min and a final
extension at 72°C for 10 min. PCR reaction was
carried out in Eppendorf master cycler gradient ES.
The amplified products were analysed on 1% agarose
gel, stained with ethidium bromide and photographed
under UV-gel doc system (Alpha Imager).
Prediction of CP Gene at Sequence Level
The amplicons of CP gene fragments were purified
using QIAGEN gel extraction kit (Qiagen Inc.,
Chatsworth, CA, USA), cloned into pGEM-T Easy
vector and transformed into Escherichia coli DH5α
following standard protocol20
. Plasmid DNA from
positive clones were sequenced, edited using the
BIOEDIT software. The nucleotide and amino acid
sequences were aligned with selected sequences from
National Centre for Biotechnology Information (NCBI)
database using MEGA 721-22
. Phylogenetic tree was
constructed using the neighbour-joining method with
bootstrap value of 1,000 replicates23
. Tomato zonate
spot virus was used as a reference out-group member
of the genus tospovirus for rooting the phylogenetic
tree. The protein sequences of GBNV and CaCV
were retrieved from NCBI with accession numbers
MK424873 and MK507959, respectively. The
sequence level comparison was carried by performing
pair-wise alignment and DOTPLOT was used for
performing this pair-wise alignment24
. The classical dot
plot algorithm uses a pair-wise comparison between
two sequences, and the results are presented as a dot-
matrix. A sliding window is often used to filter the
output for better visualization25
.
3D Structure Prediction
To compare the structure of GBNV and CaCV, a
protein model was generated using MODELLER
software26
. To model the protein structure, the target
sequence was aligned with the template structure
using 2D scripts in MODELLER and models for the
target were generated with discrete optimized protein
energy (DOPE) score. The modeled 3D structures
were visualized using PyMOL, an independent
software development project of DeLano Scientific, a
sole proprietorship based in San Carlos, California,
USA27
. The 3D structures were superimposed and
compared to find the structural difference.
RAMPAGE server was used for validating the
protein structure based on Ramachandran plot. The
Ramachandran plot displays the main chain
conformation angles (φ and Ψ) of the polypeptide
chain of a protein molecule28
.
Results
Serodiagnosis of Virus Isolates
During the survey, a highest per cent disease
incidence of tospovirus was recorded in Dharapuram
area of Tirupur district of Tamil Nadu state. The
severe disease symptoms of tospovirus infection were
observed under field condition in young plants, before
the flowering stage. During the field plants infected
by tospovirus showed the diagnostic symptoms of
chlorotic and necrotic ring spots on the leaves and
stems (Fig. 1). Further analysis, the infected samples
showed strong positive reaction with approximately
five-fold increase in absorbance values than the
apparently healthy samples analyzed through DAC-
ELISA. The positive samples were further tested
through dot blot immunobinding assay (DIBA) and
tissue blot immunobinding assay (TIBA). The
positive signals were detected by the development of
purple color on blotted area of nitrocellulose
membrane, while no such color development was
observed in the apparently healthy samples against
tospovirus antiserum. The result was assessed by
visual observation by comparing the intensity of
colour and photographed.
Biological Assay for Proliferation of Virus
Chilli plant samples showing the characteristic
symptoms of tospovirus were collected from field was
propagated on cowpea cv. C152 plants separately
through mechanical sap inoculation. The assay host
plant cowpea cv. C152 expressed distinct local
chlorotic lesions after 4 days post inoculation (dpi).
The inoculated cowpea cotyledonary leaves
developed necrotic lesions and then the systemic
veinal necrosis occurred. The veinal necrosis resulted
RAJAMANICKAM et al MOLECULAR ANALYSIS OF TOSPOVIRUSES INFECTING CHILLI
185
in severe stem necrosis and led to the death of
inoculated plants. Similarly, the assay host plant chilli
expressed distinct local lesions on 10 days after
inoculation. The inoculated leaves developed circular
necrotic lesions and necrotic patches. The systemic
infection was noticed after one month of expression
of local lesions on the inoculated leaves (Fig. 1c). The
virus produced brown necrotic rings spots and
necrosis symptoms after 10 days of inoculation and
100 per cent transmission of virus was recorded.
Identification of CP Genes
The cDNA derived from the extracted RNA
of chilli samples collected from field were used for
PCR amplification of CP genes of tospovirus.
The amplified PCR products from infected
samples with an amplicon size of approximately
840 bp and 1.2 kb corresponding to CP gene
of GBNV and CaCV respectively (Fig. 2). The
nucleotide sequence analysis using NCBI BLAST
confirmed the association of GBNV/CaCV. The CP
gene sequences of GBNV isolates were submitted in
NCBI GenBank database bearing the Accession
Nos. MK424873 and MK424874. Similarly, CP gene
sequences of CaCV isolates were submitted in
NCBI GenBank database bearing the Accession
Nos. MK507959 and MK507960.
Fig. 1 — Chilli plants expressing symptoms of necrosis disease caused by tospovirus (a and b); circular chlorotic patches on leaves of
inoculated cowpea upon artificial inoculation (c)
Fig. 2 — Amplification GBNV (a) and CaCV (b) from infected samples. Where, Lane 1 - 100 bp ladder; Lane 2 & 3 - Infected samples;
Lane 4 - Healthy control; Lane 5 - Positive control
INDIAN J BIOTECHNOL, APRIL 2020
186
Multiple Sequence Alignment and Analysis of CP Genes Analysis of CP gene sequences of GBNV and
CaCV isolates were compared to the reference sequence of with other tospovirus isolates at the nucleotide and amino acid sequence levels. The GBNV sequences of our isolates showed cent per cent sequence similarity between the isolates. Though, the nucleotide sequence recorded the maximum of 98.30% nucleotide homology with tomato GBNV isolate reported in India (AY463968). This was followed by sequence of our isolates had 97.8%, 97.7% and 92.70%, nucleotide homology with chilli GBNV isolate reported in India (AY882002, KX244330 and AY882001), respectively. Analysis of CP gene of CaCV of our isolates revealed that, the nucleotide sequences had 97.50% nucleotide homology between the isolates. The Coimbatore (MK507959) isolate exhibited the maximum of 96.40% nucleotide homology with CaCV (KY308186) reported in India. This sequence also had 96.0, 96.1 and 95.8% similarity from peanut and tomato CaCV (DQ022745, AY626762 and FJ947156) reported from Thailand, respectively. Similarly, Dharapuram isolate (MK507960) exhibited the maximum of 96.2% nucleotide homology with other groundnut-CaCV (KX078567) reported from China. Further, Dharapuram isolate showed 94.4, 94.3 and 94.2% nucleotide homology with other chilli-GBNV (DQ022745, AY626762 and FJ947156) reported from Thailand respectively (Table 1). Multiple nucleotide sequence alignment and phylogenetic analysis revealed very high homologies between the GBNV and CaCV isolates (Fig. 3). The tospoviruses formed two different clusters. Where, cluster I is comprised of GBNV isolates and cluster II is comprised of CaCV isolates. Further sequence analysis, higher homology between the nucleotide sequence of chilli, peanut and tomato isolates were observed. Multiple Sequence Alignment and Protein Level Comparison of CP Genes
The alignment and visualization of GBNV/CaCV sequences using MULTALIN programme revealed more than 90% amino acid sequence similarity between two tospoviruses (Fig. 4). Further, dotplot analysis revealed that CP gene of GBNV and CaCV had substantial region similarity, several dots align to form diagonal lines and local regions exhibited the long diagonal lines. The analysis also showed the other features such as repeats (which form parallel diagonal lines), insertions or deletions (which form
RAJAMANICKAM et al MOLECULAR ANALYSIS OF TOSPOVIRUSES INFECTING CHILLI
187
breaks or discontinuities in the diagonal lines). The
amino acid sequences exhibited more than 90%
sequence similarity formed a long diagonal line.
3D Structure Comparison of CP Genes
The template structure, 5IP2A chain was retrieved
using PDB BLAST based on the maximum query
coverage (87%) with more than 30% sequence
identity. Further, modelling process with the Python
script for model in MODELLER resulted in selection
of 3 best constructed models based on atomic charges,
Van der waals interaction and hydrophilicity. The
software generates the model with DOPE score and
the model with least DOPE scores of -25038.51 and -
24820.74 was selected as the best one for the targets
GBNV and CaCV, respectively. The generated 3D
structures visualized using PyMOL software revealed
the single amino acid variation at 259th
position and
was represented as ball and sticks in the model. The
modeled structure of GBNV was comprised with
glutamine and CaCV was comprised with valine at
259th position (Fig. 5).
Fig. 3 — Neighbour joining phylogenetic tree based on the nucleotide sequences of CP gene of GBNV, CaCV and tomato zonate spot
virus as a for out group
INDIAN J BIOTECHNOL, APRIL 2020
188
Discussion
Studies on emerging tospoviruses infecting chilli in
Tamil Nadu state are important since it causes crop
loss in terms of yield and quality, provides the basic
knowledge on disease diagnosis and genetic
information of the virus. The infected chilli samples
showed symptoms of tospoviruses including necrosis
and chlorosis on leaves and stems. Initially small
concentric rings appeared on the leaves, which later
coalesced to produce mosaic pattern in older leaves.
In some plants, circular necrotic rings were observed
on the young leaves, later which spread to the
terminal buds leading to complete drying of leaves
under field conditions. In advance stage, necrotic
streaks were observed on the tender part of the stem,
mimicking the GBNV as like that of infected tomato.
The chilli exhibiting typical symptoms of
tospovriuses were inoculated on cowpea cv. C152
plants, resulted in production of typical circular
chlorotic lesions on inoculated primary leaves on
4 dpi; advanced stage of infection led to death of
plants under glasshouse conditions. The development
of circular chlorotic and necrotic lesions on cowpea
are the characteristic symptoms of tospoviruses by
mechanical inoculation29
. In India, CaCV a genus in
tospovirus was first reported in tomato during the year
2007 and subsequently this virus also reported from
chilli since the virus has a wide host range. In our
study, chilli produced local and as well systemic
infection by developing concentric necrotic lesions on
the inoculated leaves, later coalesce to form large
patches, stunting of plants with small size leaves with
systemic infection irrespective of isolates upon
artificial inoculation with CaCV and GBNV. This
Fig. 4 — Protein sequence alignment of GBNV and CaCV using MultAlin
Fig. 5 — 3D structure representations of GBNV model (a) and CaCV model (b) and superimposed modelled structure (c)
RAJAMANICKAM et al MOLECULAR ANALYSIS OF TOSPOVIRUSES INFECTING CHILLI
189
result was supported by Kunkalikar et al. (2010) who
reported that tospovirus produced symptoms of
cholorotic and necrotic lesions in many plant species
which belong to Solanaceae, Amaranthaceae,
Leguminaceae and Fabaceae. They also stated the
symptoms produced by CaCV resemble those induced
by GBNV under field and greenhouse conditions,
which indicates the possible occurrence of CaCV for
long time in India. Recently, Haokip et al. (2016)
observed that CaCV from chilli produced circular
chlorotic and necrotic lesions on cowpea and
concentric necrotic rings on chilli.
Serological or immunological assays have been
adopted for the detection of plant viruses for a long
time. Infected chilli samples collected from field were
found to be positive for polyclonal antibody specific
to tospoviruses. However, chilli sample infected with
CaCV was found to react strongly than the one
infected with GBNV. This type of results were
supported by Kunkalikar et al. (2010) who reported
that CaCV infected tomato and chilli samples showed
strong reaction with CaCV-PAb, but were found to
react weakly with PBNV-PAb in ELISA. Similarly,
Haokip et al. (2016) raised the polyclonal antiserum
against the CaCV and reported the positive reaction of
infected samples of chilli in ELISA. In our study,
virus preparation has reacted with the antiserum
specific to tospoviruses and samples were also
produced positive reaction in DIBA and TIBA. This
suggested that it is difficult to differentiate the virus
infecting chilli under the genus tospovirus group
through symptomatology and serodiagnosis. This was
supported by the results of Jain et al. (2005) who
developed the antiserum specific to GBNV and
detected the virus from infected chilli under field
condition30
. Similarly, Gopal et al. (2011) surveyed
for GBNV infection in chilli under field condition at
Ranga Reddy district of Andhra Pradesh and they
confirmed the infection of GBNV using DAC-
ELISA31
. Sharma and Kulshrestha (2016) also
detected the GBNV infection in bell pepper from
Himachal Pradesh, through DAC-ELISA using
polyclonal antiserum specific to GBNV32
.
The present investigation was attempted for accurate
and highly specific molecular characterization of two
tospoviruses from chilli based on molecular profiling
of CP gene. During our survey in Tamil Nadu, chilli
plants were found to be diseased autonomously with
GBNV and CaCV, but there were no mixed infections.
In disparity, CaCV and TSWV infected the tomato
plant as mixed infection33
. The results of our study
represented the amplification of approximately
840 bp and 1.2 kb corresponding to CP gene of
GBNV and CaCV using specific primers. The GBNV
isolates shared 98.3% identities with tomato isolate
(AY463968) reported from India. The results were in
line with those obtained by Pavithra et al. (2016), who
diagnosed the presence of GBNV from chilli collected
from the farmer fields and characterized the CP gene
of GBNV using specific primers. Further, the
sequence analysis revealed more than 96% sequence
similarity with GBNV isolate reported from India.
The present study also demonstrated that, CaCV
isolates shared maximum of 97.50% and 96.4%
identities with Indian isolates. In earlier studies,
higher level of identities was obtained from CaCV
isolates with similarity of more than 98% and
99-100% at nucleotide and amino acid levels,
respectively
(Haokip et al. 2016). Similarly,
CaCV isolates from chilli and tomato are genetically
similar showing 96-100 % similarity with N gene
amino acid, indicated the wider host range with
possible spread of virus from one host to another
(Kunkalikar et al. 2010).
In our study, a combined phylogenetic tree
constructed by NJ algorithm using tospoviruses
revealed the formation of two different clusters. The
phylogenetic analysis enabled to describe the
relatedness of viruses infecting crops by generating a
distinct cluster and their gradual evolution34
. We have
investigated the molecular characterization and
profiling of CP gene of GBNV and CaCV isolates
involved in disease outbreaks in chilli. Since the
relative sequence analysis CP gene soft tospoviruses
infecting chilli and structural study of genes through
3D prediction structure provides precise identification
of variability at molecular level and provided a simple
method of classification of emerging viruses. This
type of study was conducted in mixed infection of
chilli vein mottle virus and chilli leaf curl virus (Sahu
et al. 2016) and cucumber mosaic virus (Biswas et al.
2013). In our study, GBNV and CaCV isolates were
exhibited the minimum level of similarities between
the viruses, which concluded that both viruses are
dissimilar at nucleotide levels. Whereas, MULTALIN
programme revealed that both the viruses had 90%
similarity at amino acid levels, which confirms the
presence of little variation between CaCV and GBNV
isolates. They were exhibited a single variation in
259th position at amino acid levels consisting of
INDIAN J BIOTECHNOL, APRIL 2020
190
glutamine and valine in GBNV and CaCV,
respectively. Similarly, Chavhan et al. (2018) also
documented the protein profiling of tobacco streak
virus, represented the active pocket site at 177th
amino
acid residue. The three dimensional model from ßC1
pathogenicity region of cotton leaf curl virus
suggested that plant flavonoid have strong binding
active site, as these molecules binds with active site at
viral protein which leads to plant defense against viral
infection (Sarwar et al. 2019). This study concludes
the occurrence of GBNV and CaCV in chilli at
serological and molecular levels. The sequence
structure analysis highlights the key residues involved
in the confirmation of the protein structure. It would
enhance the power of the analysis by drawing a
connection between primary sequence, 3D structure
and its function. Predicted 3D structures of viral
proteins allowed to find a consistent location
for conserved residues among all members of
tospovirus, which could be useful in developing
novel virus control strategies targeting the localized
residues in future.
Acknowledgements
Authors gratefully acknowledge the School of Post
Graduate Studies, Tamil Nadu Agricultural
University, Coimbatore, India for the financial
support of the project under Dr. A.P.J. Abdul Kalam
Fellowship. Also, acknowledge the DST-FIST, GOI,
New Delhi for providing infrastructure facilities.
References 1 Vinoth Kumar R, Singh A K & Chakraborty S A, new
monopartite begomovirus species, Chilli leaf curl Vellanad
virus, and associated betasatellites infecting chilli in the
Vellanad region of Kerala, India, New Disease Reports, 2
(2012) 20.
2 Chandrasekhar Rao V & Kesava Rao G V, An insight
into chilli cultivation and risk management procedures
with special reference to Karnataka & Andhra Pradesh,
Int J Business and Admin Res Rev, 2 (3) (2014) 144-155.
3 Biswas K, Hallan V, Zaidi A A & Pandey P K, Molecular
evidence of Cucumber mosaic virus subgroup II infecting
Capsicum annuum L. in the Western region of India, Current
Discovery, 2 (2) (2013) 97-105.
4 Kunkalikar S R, Sudarsana P, Rajagopalan P, Zehr U B &
Ravi K S, Biological and molecular characterization of
Capsicum chlorosis virus infecting chilli and tomato in India,
Arch Virol (2010) doi. 10.1007/s00705-010-0681-5.
5 Sushmitha C & Bhat S K, Pepper vein banding virus-an
over view, International Journal of Scientific Research, 3 (6)
(2014) 30-31.
6 Prins M & Goldbach R, The emerging problem of tospovirus
infection and non-conventional methods of control,
Trends Microbiol, 6 (1), (1998) 31-35.
7 Sahu A K, Chitra N, Mishra R, Verma R & Gaur R K,
Molecular evidence of Chilli vein mottle virus and Chilli leaf
curl virus simultaneously from naturally infected chilli plant
(Capsicum annuum L.), Indian Journal of Biotechnology
15 (2016) 266-268.
8 Bhat A I, Jain R K, Varma A & Lal S K, Nucleocapsid
protein gene sequence studies suggest that soybean bud
blight is caused by a strain of Groundnut bud necrosis virus,
Curr Sci, 82 (2002) 1389-139.
9 Jain R K, Paul Khurana S M, Bhat A I & Chaudhary V,
Nucleocapsid protein gene sequence studies confirm that
potato stem necrosis is caused by a strain of Groundnut bud
necrosis virus, Indian Phytopath, 57 (2004) 169-173.
10 Pavithra B S, Krishnareddy M & Rangaswamy K T,
Detection and partial characterization of Groundnut bud
necrosis virus in chilli, International Journal of Science &
Nature, 7 (4) (2016) 843-847.
11 Krishnareddy M, Rani R, Kumar K, Reddy K & Pappu H,
Capsicum chlorosis virus (Genus Tospovirus) infecting
chili pepper (Capsicum annuum) in India, Plant Disease,
92 (2008) 1469.
12 Rajamanickam S, Raveendran M & Karthikeyan G,
Conserved sequence of replicase gene mediated resistance in
Nicotiana tabacum L. cv Abirami through RNA silencing,
European Journal of Plant Pathology, 142 (4) (2015)
865-874.
13 Zhao Y, Yang X, Zhou G & Zhang T, Engineering plant
virus resistance: from RNA silencing to genome editing
strategies, Plant Biotechnology Journal, 18 (2020) 328-336.
14 Sarwar M W, Riaz A, Nahid N, Al Qahtani A, Ahmed N et
al, Homology modeling and docking analysis of ßC1 protein
encoded by Cotton leaf curl Multan betasatellite with
different plant flavonoids, Heliyon, 5 (2019) e01303.
15 Vanthana M, Nakkeeran S, Malathi V G, Renukadevi P &
Vinodkumar S, Induction of in planta resistance by
flagellin (Flg) and elongation factor-TU (EF-Tu) of
Bacillus amyloliquefaciens (VB7) against groundnut bud
necrosis virus in tomato. Microbial Pathogenesis, 137 (2019)
103757.
16 Hobbs H A, Reddy D V R, Rajeshwari R & Reddy A S, Use
of direct antigen coating and protein A coating ELISA
procedures for detection of three peanut viruses, Plant
Disease, 71 (1987) 747-749.
17 Dijkstra J & De Jager C P, Practical Plant Virology, in
protocols and exercises (Springer, New York) 1998, 45-60
18 Subramanian K S & Narayanasamy P, Mechanical
transmission of Whitefly borne yellow mosaic virus of
Lablabniger Medikus, Current Science, 47 (1973) 92-93.
19 Haokip BD, Alice D, Nagendran K, Renukadevi P &
Karthikeyan G, Detection of Capsicum chlorosis virus
(CaCV), an emerging virus infecting chilli in Tamil Nadu,
India, Vegetos, 29 (2016) 1-4.
20 Sambrook J, Fritsch E F & Maniatis T, Molecular cloning:
A laboratory manual (Cold Spring Harbor, New York) 1989,
405-413.
21 Larkin M A, Blackshields G, Brown N P, Chenna R,
McGettigan P A et al, Clustal W and Clustal X version 2.0,
Bioinformatics, 23 (2007) 2947-2948.
22 Saitou N & Nei M, The neighbour-joining method: A new
method for reconstructing phylogenetic trees, Mol Biol Evol,
4 (1987) 406-425.
RAJAMANICKAM et al MOLECULAR ANALYSIS OF TOSPOVIRUSES INFECTING CHILLI
191
23 Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al,
MEGA5: Molecular evolutionary genetics analysis using
maximum likelihood, evolutionary distance, and maximum
parsimony methods, Mol Biol Evol, 28 (2011) 2731-2739.
24 Cabanettes F & Klopp C, D-GENIES: dot plot large
genomes in an interactive, efficient and simple way, Peer J,
6 (2018) e4958.
25 Maizel J V & Lenk R P, Enhanced graphic matrix analysis of
nucleic acid and protein sequences, Proc Natl Acad Sci USA,
78 (1981) 7665-7669.
26 Fiser A & Sali A, Modeller: Generation and refinement of
homology-based protein structure models. in Methods in
enzymology (Academic Press, New York) 2003, 461-491.
27 DeLano W L, Pymol: An open-source molecular graphics
tool, CCP4 Newsletter on Protein Crystallography, 40
(2002) 82-92.
28 Gopalakrishnan K, Sowmiya G, Sheik S S & Sekar K,
Ramachandran plot on the web (2.0), Protein and Peptide
Letters, 14 (2007) 669-671.
29 Ramiah M, Bhat A I, Jain R K, Pant R P, Ahlawat Y S et al,
Partial characterization of an isometric virus causing
sunflower necrosis disease, Indian Phytopathology, 54
(2001) 246-250.
30 Jain R K, Pandey A N, Krishnareddy M & Mandal B,
Immunodiagnosis of groundnut and watermelon bud
necrosis viruses using polyclonal antiserum to recombinant
nucleocapsid protein of Groundnut bud necrosis virus,
Journal of Virological Methods, 130 (1-2) (2005)
162-164.
31 Gopal K, Muniyappa V & Jagadeeshwar R, Weed and crop
plants as reservoirs of peanut bud necrosis tospovirus and its
occurrence in South India, Archives of Phytopathology &
Plant Protection, 44 (12) (2011) 1213-1224.
32 Sharma A & Kulshrestha S, Molecular characterization of
tospoviruses associated with ringspot disease in bell pepper
from different districts of Himachal Pradesh, Virus Disease,
27 (2) (2016) 188-192.
33 McMichael L A, Persley D M & Thomas J E, A new
tospovirus serogroup IV species infecting capsicum and
tomato in Queensland, Australia, Aust Plant Pathol, 31
(2002) 231-239.
34 Chavhan R L, Verma M K, Hinge V R, Kadam U S,
Kokane S B et al, Sequence analysis of coat protein and
molecular profiling of sunflower necrosis virus (SNV) strains
from Indian subcontinent, J Plant Biochem Biotechnol, 27
(2018) 28-35.