Genome characterisation of a distinct species of Begomovirus causing leaf curl disease in sweetpotato [Ipomoea batatas L. (Lam)] in India

ABSTRACT

A novel species of monopartite begomovirus was detected in sweetpotato [Ipomoea batatas L (Lam)] originating from the experimental field of ICAR-AICRP on Tuber Crops (West Bengal), India. The plants showed a typical upward curling of leaves symptoms and reduction in plant height and was easily transmitted through the tuber and vine cuttings of infected plant. PCR-mediated detection using specific primers confirmed the presence of begomovirus in the infected sweetpotato plants. The virus isolate was characterised genome level with 2823 nucleotide in size (GenBank accession FN432356) and designated as Sweet potato leaf curl Bengal virus (SPLCV) (India:West Bengal). The comparative analysis showed that SPLCV (India:West Bengal) clustered with distinct isolate of previously reported 35 SPLCV in the world. Six ORFs of the isolate were highly divergent from equivalent regions of other isolates. Sequence comparisons and population structure analysis of 35 SPLCV isolates revealed that SPLCV (India:West Bengal) showed 85–90% nucleotide sequence identity. Systematic examination revealed that SPLCV (India:West Bengal) isolate was shown to have a recombinant in origin. The results of the current study have uncovered the diversity and genetic structure of sweetpotato leaf curl virus and generated potentially useful information for developing management strategies for this virus.

KEYWORDS:

• Sweetpotato leaf curl virus
• genome
• characterisation
• phylogeny
• population structure

Acknowledgments

The first and corresponding authors thankfully acknowledge Indian Council of Agricultural Research-All India Coordinated Research Project on Tuber Crops, ICAR-CTCRI, Sreekariyam, Thiruvananthapuram - 695 017, Kerala, India.

Disclosure statement

Mr. Manoj Kumar worked under the supervision of Dr. Jayanta Tarafdar and his work was financially supported by ICAR-All India Coordinated Research Project on Tuber Crops, Kalyani centre, Directorate of Research, Bidhan Chandra Krishi Visswavidyalaya, Kalyani 741235, West Bengal, India. Mr. Kumar also has consulted for Dr. Jayanta Tarafdar, Dr. Nayan Adhikary and Miss Sarbani Das declare no potential conflict of interest.

Additional information

Funding

This work was supported by the ICAR-AICRP on Tuber Crops, Kalyani Centre, Directorate of Research, BCKV, West Bengal, India [2019 AICRPTC/PC].