title: Complexity of begomovirus and betasatellite populations associated with chilli leaf curl disease in India.
abstract: Chilli, which encompasses several species in the genus Capsicum, is widely consumed throughout the world. In the Indian subcontinent, production of chilli is constrained due to chilli leaf curl disease (ChiLCD) caused by begomoviruses. Despite the considerable economic consequences of ChiLCD on chilli cultivation in India, there have been scant studies of the genetic diversity and structure of the begomoviruses that cause this disease. Here we report on a comprehensive survey across major chilli-growing regions in India. Analysis of samples collected in the survey indicates that ChiLCD-infected plants are associated with a complex of begomoviruses (including one previously unreported species) with a diverse group of betasatellites found in crops and weeds. The associated betasatellites neither enhanced the accumulation of the begomovirus components nor reduced the incubation period in Nicotiana benthamiana. The ChiLCD-associated begomoviruses induced mild symptoms on Capsicum spp., but both the level of helper virus that accumulated and the severity of symptoms were increased in the presence of cognate betasatellites. Interestingly, most of the begomoviruses were found to be intra-species recombinants. The betasatellites possess high nucleotide variability, and recombination among them was also evident. The nucleotide substitution rates were determined for the AV1 gene of begomoviruses (2.60 × 10- 3 substitutions site- 1 year- 1) and the βC1 gene of betasatellites [chilli leaf curl betasatellite (ChiLCB), 2.57 × 10- 4 substitution site- 1 year- 1; tomato leaf curl Bangladesh betasatellite (ToLCBDB), 5.22 × 10- 4 substitution site- 1 year- 1]. This study underscores the current understanding of Indian ChiLCD-associated begomoviruses and also demonstrates the crucial role of betasatellites in severe disease development in Capsicum spp.
authors.affiliation: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India.
authors.forename: R Vinoth
authors.initials: RV
authors.lastname: Kumar
authors.affiliation: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India.
authors.forename: Achuit Kumar
authors.initials: AK
authors.lastname: Singh
authors.affiliation: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India.
authors.forename: Ashish Kumar
authors.initials: AK
authors.lastname: Singh
authors.affiliation: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India.|Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, USA.
authors.forename: Tribhuwan
authors.initials: T
authors.lastname: Yadav
authors.affiliation: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India.|Department of Entomology, University of Nebraska, Lincoln, USA.
authors.forename: Saumik
authors.initials: S
authors.lastname: Basu
authors.affiliation: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India.
authors.forename: Nirbhay
authors.initials: N
authors.lastname: Kushwaha
authors.affiliation: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India.
authors.forename: Brotati
authors.initials: B
authors.lastname: Chattopadhyay
authors.affiliation: Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India.
authors.forename: Supriya
authors.initials: S
authors.lastname: Chakraborty
mesh_terms: D053839:Begomovirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D002212:Capsicum / Q000821:virology*; D014644:Genetic Variation; D007194:India; D008969:Molecular Sequence Data; D059645:Mutation Rate; D010935:Plant Diseases / Q000821:virology*; D011995:Recombination, Genetic; D012526:Satellite Viruses / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA; D014026:Nicotiana / Q000821:virology