Complete nucleotide sequence of watermelon chlorotic stunt virus originating from Oman

Abstract

Watermelon chlorotic stunt virus (WmCSV) is a bipartite begomovirus (genus Begomovirus, family Geminiviridae) that causes economic losses to cucurbits, particularly watermelon, across the Middle East and North Africa. Recently squash (Cucurbita moschata) grown in an experimental field in Oman was found to display symptoms such as leaf curling, yellowing and stunting, typical of a begomovirus infection. Sequence analysis of the virus isolated from squash showed 97.6-99.9% nucleotide sequence identity to previously described WmCSV isolates for the DNA A component and 93-98% identity for the DNA B component. Agrobacterium-mediated inoculation to Nicotiana benthamiana resulted in the development of symptoms fifteen days post inoculation. This is the first bipartite begomovirus identified in Oman. Overall the Oman isolate showed the highest levels of sequence identity to a WmCSV isolate originating from Iran, which was confirmed by phylogenetic analysis. This suggests that WmCSV present in Oman has been introduced from Iran. The significance of this finding is discussed.

Keywords: Begomovirus; Oman; WmCSV; squash.

Figure 1

Arrangement of the genomic components of WmCSV (A). The positions and orientations of genes are shown with colored arrows. The position of the predicted stem-loop structure (containing the nonanucleotide sequence; TAATATTAC) is indicated. An alignment of the common region sequences of the DNA A and DNA B components of WmCSV isolates from Oman is shown in (B). Spaces (-) are introduced to optimize the alignment. Differences in sequences are indicated with boxes. Stem and loop sequences (pink highlighting and pink text, respectively) of the predicted stem-loop structure, position of iterons (red text) and TATA box (highlighted in green) of the Rep promoter are indicated.

Figure 2

Alignment of CR sequences of the DNA B components of WmCSV from Oman and the database sequences from different origins. Spaces (-) are introduced to optimize the alignment. Differences in the sequences are highlighted. Oman isolates are marked as bold.

Figure 3

Neighbor joining phylogenetic dendrogram based upon alignments of the sequences of the genomes for DNA A components (A) and DNA B components (B) of WmCSV and selected other begomoviruses from the databases. In each case the database accession number is given. The numbers at nodes represent percentage bootstrap confidence scores (1000 replicates). The alignment was arbitrarily rooted on outgroup Bean golden yellow mosaic virus (BGYMV), a distantly related begomovirus. Begomovirus acronyms used are Mungbean yellow mosaic virus (MYMV), Mungbean yellow mosaic India virus (MYMIV), Tomato leaf curl New Delhi virus (ToLCNDV), Squash leaf curl China virus (SLCCNV), African cassava mosaic virus (ACMV), South African cassava mosaic virus (SACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Zanzibar virus (EACMZV), East African cassava mosaic Kenya virus (EACMKV), Tomato yellow leaf curl virus (TYLCV) and Tomato leaf curl Oman virus (ToLCOMV). The isolates characterized here are indicated with white text on black background. Other begomoviruses from Oman are highlighted by a gray background. Additionally the begomoviruses originating from the Middle East, Africa and southern Asia are indicated by colored boxes.

Figure 4

Symptoms of plants infected with WmCSV. A non-inoculated healthy N. benthamiana plant (A); N. benthamiana plants inoculated with the clones of WmCSV (B–D) and squash plants in the field infected with WmCSV (E).