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Identification and molecular characterization of a new recombinant begomovirus and associated betasatellite DNA infecting Capsicum annuum in India

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Abstract

Capsicum annuum (Chilli) is a perennial herbaceous plant that is cultivated as an annual crop throughout the world, including India. Chilli leaf curl disease (ChiLCD) is a major biotic constraint, causing major losses in chilli production. During 2014, leaf samples of chilli plants displaying leaf curl disease were collected from the Ahmedabad district of Gujarat, India. These samples were used to isolate, clone and sequence viral genomic DNA and an associated betasatellite DNA molecule. Sequence analysis showed 90.4 % nucleotide sequence identity to the previously reported chilli leaf curl virus-[India:Guntur:2009] (ChiLCV-[IN:Gun:09]. As per ICTV nomenclature rules, ChiLCV-Ahm represents a new species of begomovirus, and we therefore propose the name chilli leaf curl Ahmedabad virus-[India:Ahmedabad:2014] (ChiLCAV-[IN:Ahm:14]). The associated betasatellite DNA showed a maximum of 93.5 % nucleotide sequence identity to a previously reported tomato leaf curl Bangladesh betasatellite and may be named tomato leaf curl Bangladesh betasatellite-[India:Ahmedabad:Chilli:2014].

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Acknowledgments

This work was supported by a research grant provided to AKS by the SERB, Government of India (SR/FT/LS-142/2010), and the central instrumentation facility supported by CUG, Gandhinagar, Gujarat.

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    Authors and Affiliations

    1. School of Life Sciences, Central University of Gujarat, Gandhinagar, 382030, India

      Bhavin S. Bhatt, Fenisha D. Chahwala, Sangeeta Rathod & Achuit K. Singh

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    1. Bhavin S. Bhatt
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    2. Fenisha D. Chahwala
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    3. Sangeeta Rathod
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    4. Achuit K. Singh
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    Correspondence to Achuit K. Singh.

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    This paper is in compliance with ethical standards for research. The authors declare no conflicts of interest.

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    B. S. Bhatt and F. D. Chahwala contributed equally to this work.

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    705_2016_2769_MOESM1_ESM.docx

    Fig.S1 Graphical representation of percentage pairwise genome scores and nucleotide identity plot of full genomes of studied begomovirus with other begomoviruses from Indian subcontinent prepared using MUSCLE parameter of SDTv1.0 (Species Demarcation Tool; http://web.cbio.uct.ac.za/SDT) [17, 18] in three color mode with cut-off 1 is 90 and cut-off 2 is 78. The begomovirus sequences used for comparisons and phylogenetic analysis were obtained from GenBank, NCBI. GenBank accession numbers are indicated to the right of each virus name and abbreviations are as per Brown JK et. al. [20] (DOCX 61 kb)

    Supplementary material 2 (DOCX 18 kb)

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    Bhatt, B.S., Chahwala, F.D., Rathod, S. et al. Identification and molecular characterization of a new recombinant begomovirus and associated betasatellite DNA infecting Capsicum annuum in India. Arch Virol 161, 1389–1394 (2016). https://doi.org/10.1007/s00705-016-2769-z

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