Molecular characterization of begomovirus-betasatellite-alphasatellite complex associated with okra enation leaf curl disease in Northern Sri Lanka

Abstract

Okra enation leaf curl is a newly emerging disease in commercial okra cultivation fields in Northern Sri Lanka. The present study aimed to identify and characterize the causative begomovirus and associated satellites. Okra plants showing the enation leaf curl disease symptoms were collected from Vavuniya and Jaffna districts of Northern Province. The PCR diagnostic and genome sequencing revealed that the symptomatic okra plants are associated with begomovirus, betasatellite, and alphasatellite complex. The begomovirus isolates shared 98.2-99.7% nucleotide identity with Okra enation leaf curl virus. The betasatellites showed 96-98.8% nucleotide identity with Bhendi yellow vein mosaic betasatellite which is usually associated with Bhendi yellow vein mosaic disease. Two distinct alphasatellite species, Okra leaf curl alphasatellite and Bhendi yellow vein mosaic alphasatellite, were identified in leaf samples with enation leaf curl disease. The disease was transmitted by whiteflies from diseased plants to healthy plants. Hybrid varieties were more susceptible to the disease compared to cultivated varieties.

Keywords: Alphasatellite; Begomovirus; Betasatellite; Okra enation leaf curl.

Fig. 1

a Symptoms exhibited by Okra enation leaf curl virus-infected okra plants in the field; severe upward leaf curling and associated vein thickening. b Disease incidence of OELCuD in different districts in Northern Province of Sri Lanka; the error bars are standard error of mean

Fig. 2

Colour-coded pairwise identity matrix generated from 54 different begomovirus DNA-As, including 2 OELCuV described in this work (with ‘*’ at the end of species name). See Supplementary Table 1 for details on the compared sequences. Each coloured cell represents a percentage identity score between two sequences. The coloured key indicates the correspondence between pairwise identities and the colours displayed in the matrix

Fig. 3

Molecular phylogenetic analysis for two OELCuV described in this work (with red colour text) with selected begomoviruses. The evolutionary history was inferred using the Maximum-Likelihood method based on the General Time Reversible model. The percentage of trees in which the associated taxa clustered together is shown next to the branches. A discrete Gamma distribution was used to model evolutionary rate differences among sites. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. All positions containing gaps and missing data were eliminated

Fig. 4

RDP analysis for recombination of the begomovirus isolates (a), betasatellites (b), and alphasatellites (c). For each of the isolates, recombinant fragments are shown as shaded bars with the origin (parental virus species) indicated where it could be determined. The orientation and approximate position of genes are shown as arrows at the top of the diagram

Fig. 5

Colour-coded pairwise identity matrix generated from 29 different betasatellite DNAs, including 2 BYVMB described in this work (with ‘*’ at the end of species name). See Supplementary Table 1 for details on the compared sequences. Each coloured cell represents a percentage identity score between two sequences. The coloured key indicates the correspondence between pairwise identities and the colours displayed in the matrix

Fig. 6

a Molecular phylogenetic analysis for two BYVMB described in this work (with red colour text) with selected betasatellites. The evolutionary history was inferred using the maximum-likelihood method based on the Tamura three-parameter model. b Molecular phylogenetic analysis for two alphasatellites described in this work (with bold text) with selected different alphasatellite species described by Briddon et al. (2018)

Fig. 7

Colour-coded pairwise identity matrix generated from 41 different alphasatellites, including two species described in this work (with ‘*’ at the end of species name). See Supplementary Table 1 for details on the compared sequences. Each coloured cell represents a percentage identity score between two sequences. The coloured key indicates the correspondence between pairwise identities and the colours displayed in the matrix