Viruses virus (ChiLCINV), Chilli leaf curl Kanpur virus (ChiLCKV),

Viruses are considered as a major
constraint to agriculture production in India. Chilli is an important field
crop grown in Rajasthan province and infection of begomoviruses in chilli has
high agronomic impact by inhibiting plant growth and reduced fruit quality. In
India, Chilli leaf curl Ahmedabad virus
(ChiLCAV), Chilli leaf curl virus
(ChiLCuV), Chilli leaf curl India virus
(ChiLCINV), Chilli leaf curl Kanpur virus
(ChiLCKV), Chilli Leaf curl Vellanad
virus (ChiLCVV), Pepper leaf curl
Bangladesh virus (PepLCBV), Tomato
leaf curl New Delhi virus (ToLCNDV), Papaya
leaf curl virus (PaLCuV), Radish leaf
curl virus (RaLCuV), Tomato leaf curl
virus (ToLCuV) and Tomato leaf curl
Joydebpur virus (ToLCJ) have been reported in chilli crop, thereby
depicting leaf curl disease (Malathi et al. 2017), but so far there is no
report have been found on association of ChiLCuV, ToLCuV, and CLCuRV. We
reported here, the presence of representatives of three distinct begomoviruses,
ChiLCuV, ToLCuV, and CLCuRV (DNA-A segments) and their satellite molecules in
chilli, concomitantly analyse their sequence variability, phylogeny and
recombination potential. The high degree of genetic variability was observed in
DNA-A segment of ToLCuV as compare to DNA-A segment of ChiLCV and CLCuRV
isolates. Furthermore, the dN/dS ratio of DNA-A segment of Chili
leaf curl virus and cotton leaf curl virus is higher than the tomato leaf curl
virus, these results suggests that the DNA-A segment is under less evolutionary
constraint then the other DNA segments. Low nucleotide diversity, evolutionary
divergence and lower number recombination breakpoints were observed in alpha
satellite DNA segment. The dN/dS ratio of alpha satellite molecules was
significantly lower (table 1) consistent with other variation analysis. These
results imply that the alpha satellite molecules are under robust evolutionary
limitation then other DNA segments. Computing the transitions/transversions
bias (R) is very significant for correct inference of phylogeny, divergence
time estimation and for understanding the evolution of genomes (Yang and Yoder
1999; Verma et al. 2016) as it allows us to verify the presence of bias in the
nucleotide substitutions. In our datasets, the transitions/transversions bias
(R) is equal to one was consistent with the principle that transitions were
more frequent than transversion in analysed sequences. Phylogenetic analysis
revealed that the DNA-A segment of CLCuRV and ToLCuV as well as betasatellite
and alphasatellite molecules grouped with other Indian isolates, whereas the
DNA-A segment of ChiLCuV showed grouping with the isolates reported from Oman.
Higher negative Tajima values of DNA-A of CLCuRV and associated alphasatellite
molecules (Table 1) implies an excess of low frequency polymorphisms,
concomitantly the Tajima D value near to zero of DNA-A segment of ChiLCuV shows
neutral selection and positive Tajima D value of DNA-A segment of ToLCuV
exhibit the balancing selection in analysed sequences.

Emergence of new begomoviruses relies on how frequently begomoviruses
recombine with each other and eventually acquire satellite molecules to further
complicate the story (Zaffalon et al. 2011; Nawaz-ul-Rehman & Fauquet
2009). Begomoviruses not only recombine with each other but they can also
experience recombination with satellite molecules or DNA-B (Venkataravanappa et
al. 2011; Nawaz-ul-Rehman & Fauquet 2009). Majority of recombination
breakpoint were found in the AC1 and AV1 region of DNA-A segments of all the
identified isolates as supported by previous results of Kumar et al. (2015).
Cotton leaf curl Rajasthan virus had showed recombination events between (Cotton
leaf curl Multan virus (CLCuMuV) and cotton leaf curl Khokhran virus (CLCuKoV) at
AV1 and CP region (Table 2) (Kumar et al. 2015; Saleem et al. 2016) similarly,
we too observed seven recombination breakpoints in Cotton leaf curl Rajasthan
virus including CP/Rep/MP regions (Table 2). In support of the findings,
recombination in the DNA-A segments have higher nucleotide divergence and high
rate of nucleotide substitutions (Table1).

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Several
reports such as geminiviruses infecting cassava in Africa (Pita et al. 2001), harbouring
bean/tomato in several other countries (Chakraborty et al. 2008; Alves et al.
2009), suggests that mixed infections are potential source of geminivirus
variability due to recombination events (Rentería-Canett et al. 2011). Mixed
virus infections are significant to virus evolution because they provide the
precondition for recombination, which may contribute to the appearance of more
severe virus strains or new begomovirus species (Ala-Poikela et al.
2005; Ribeiro et al.
2003). Numerous studies exposed the mixed infection of begomoviruses in various
crops worldwide, such as mixed infection of begomoviruses infecting tomato,
pepper and cucurbit crops in Nicaragua (Ala-Poikela et al. 2005); Pepper huasteco yellow vein virus and Pepper golden mosaic virus on pepper in
Mexico (Renteria-Canett et al. 2011); association of Tomato leaf curl new Delhi virus, Squash leaf curl China virus and Tomato leaf curl Palmpur virus infecting pumpkins in India (Jaiswal
et al. 2012);  Cotton leaf curl virus (CLCuRV) and Okra yellow vein mosaic virus (OYVMV) on cotton and other
malvaceous species in Pakistan (Sanz et al. 2000) ; Pepper yellow leaf curl Indonesia virus (PepYLCIV), Tomato yellow leaf curl Kanchanaburi virus(TYLCKaV),
and Ageratum yellow vein virus (AYVV)
on pepper plants in Indonesia (Koeda et al. 2016) and; association of Chili vein mottle virus and Chilli leaf curl virus in chilli plant
in India (Sahu et al. 2016); Tomato leaf
curl New Delhi virus and a Tomato
yellow leaf curl Thailand betasatellite on potato in Pakistan (Hameed et
al. 2017). Mixed infections of ChiLCV and PepLCBV were also noticed in eastern
Uttar Pradesh (Ghazipur) and the Bihar (Chhapra) region (Kumar et al. 2015). In
India, the most prevalent betasatellites associated with ChiLCD have been
reported from tomato and chilli rather than from weeds (Chattopadhyay et al. 2008;
Kumar et al. 2011). These reports suggest that mixed infection is the major
influential force in the emergence and spread of begomoviruses.  Here, we report association of Chilli leaf curl virus (ChiLCuV), Tomato leaf curl virus (ToLCuV), and Cotton leaf curl Rajasthan virus (CLCuRV)
infection together in chilli plants. This means that the expanded frequency and
extension in the host range of begomovirus disease complexes, can posture
genuine future threat to agriculture practices in India.