High-Throughput Sequencing Identified Distinct Bipartite and Monopartite Begomovirus Variants Associated with DNA-Satellites from Tomato and Muskmelon Plants in Saudi Arabia

Abstract

The studies on the prevalence and genetic diversity of begomoviruses in Saudi Arabia are minimal. In this study, field-grown symptomatic tomato and muskmelon plants were collected, and initially, begomovirus infection was confirmed by the core coat protein sequences. Four tomato and two muskmelon plants with viral infections were further evaluated for Illumina MiSeq sequencing, and twelve sequences (2.7–2.8 kb) equivalent to the full-length DNA-A or DNA-B components of begomoviruses were obtained along with eight sequences (~1.3–1.4 kb) equivalent to the begomovirus-associated DNA-satellite components. Four begomovirus sequences obtained from tomato plants were variants of tomato yellow leaf curl virus (TYLCV) with nt sequence identities of 95.3–100%. Additionally, two tomato plants showed a mixed infection of TYLCV and cotton leaf curl Gezira virus (CLCuGeV), okra yellow crinkle Cameroon alphasatellite (OYCrCMA), and okra leaf curl Oman betasatellite (OLCuOMB). Meanwhile, from muskmelon plants, two sequences were closely related (99–99.6%) to the tomato leaf curl Palampur virus (ToLCPalV) DNA-A, whereas two other sequences showed 97.9-100% sequence identities to DNA-B of ToLCPalV, respectively. Complete genome sequences of CLCuGeV and associated DNA-satellites were also obtained from these muskmelon plants. The nt sequence identities of the CLCuGeV, OYCrCMA, and OLCuOMB isolates obtained were 98.3–100%, 99.5–100%, and 95.6–99.7% with their respective available variants. The recombination was only detected in TYLCV and OLCuOMB isolates. To our knowledge, this is the first identification of a mixed infection of bipartite and monopartite begomoviruses associated with DNA-satellites from tomato and muskmelon in Saudi Arabia. The begomovirus variants reported in this study were clustered with Iranian isolates of respective begomovirus components in the phylogenetic dendrogram. Thus, the Iranian agroecological route can be a possible introduction of these begomoviruses and/or their associated DNA-satellites into Saudi Arabia.

Artificial microRNA-mediated resistance against Oman strain of tomato yellow leaf curl virus

“…Tomato yellow leaf curl disease (TYLCD), caused by tomato yellow leaf curl virus (TYLCV), is one of the most devastating begomoviral diseases infecting the tomato crop in diverse tropical, subtropical, and temperate regions around the globe. TYLCV has become the most economically important tomato-invading pathogen, originating from the Middle East and spreading into different countries and regions ( Czosnek and Laterrot, 1997 ; Polston et al., 1999 ; Font et al., 2000 ; Moriones and Navas-Castillo, 2000 ; Lefeuvre et al., 2010 ; Just et al., 2014 ; Ramos et al., 2019 ; Shahid, 2020 ; AlHudaib et al., 2022 ). TYLCV is a member of the genus Begomovirus of the Geminiviridae family, which is distributed globally, and it is difficult to control or eradicate this virus.…”