Characterization of Begomoviruses Sampled during Severe Epidemics in Tomato Cultivars Carrying the Ty-1 Gene

Abstract

Tomato yellow leaf curl virus (TYLCV, genus Begomovirus, family Geminiviridae) is a major species that causes a tomato disease for which resistant tomato hybrids (mainly carriers of the Ty-1/Ty-3 gene) are being used widely. We have characterized begomoviruses severely affecting resistant tomato crops in Southeast Spain. Circular DNA was prepared from samples by rolling circle amplification, and sequenced by massive sequencing (2015) or cloning and Sanger sequencing (2016). Thus, 23 complete sequences were determined, all belonging to the TYLCV Israel strain (TYLCV-IL). Massive sequencing also revealed the absence of other geminiviral and beta-satellite sequences. A phylogenetic analysis showed that the Spanish isolates belonged to two groups, one related to early TYLCV-IL isolates in the area (Group 1), and another (Group 2) closely related to El Jadida (Morocco) isolates, suggesting a recent introduction. The most parsimonious evolutionary scenario suggested that the TYLCV isolates of Group 2 are back recombinant isolates derived from TYLCV-IS76, a recombinant virus currently predominating in Moroccan epidemics. Thus, an infectious Group 2 clone (TYLCV-Mu15) was constructed and used in in planta competition assays against TYLCV-IS76. TYLCV-Mu15 predominated in single infections, whereas TYLCV-IS76 did so in mixed infections, providing credibility to a scenario of co-occurrence of both types of isolates.

Use of High-Throughput Sequencing and Two RNA Input Methods to Identify Viruses Infecting Tomato Crops

“…A BLASTn analysis of these sequences revealed a nucleotide similarity above 97% with other TYLCV sequences belonging to the Israel strain (TYLCV-IL). No insertion characterizing the TYLCV-IS76 isolates was detected in the non-coding intergenic region of these sequences [ 26 ]. Based on qRT-PCR of individual samples, TYLCV was detected in seven out of 20 samples.…”

Enhanced Age-Related Resistance to Tomato Yellow Leaf Curl Virus in Tomato Is Associated With Higher Basal Resistance

“…However, to date genetic resources against TYLCV have been found in only a few wild relatives of cultivated tomato and introgression of resistance into tomato cultivars may take years and end up unsuccessful ( Dhaliwal et al, 2019 ). More importantly, resistance break-down has been found in southeast Spain where severe epidemics of TYLCV in tomato cultivars carrying the Ty-1 gene were reported ( Torre et al, 2018 ). Therefore, alternative measures to improve the resistance in tomato plants are needed.…”

Preliminarly Survey Results and Phylogenetic Analysis for Tomato Yellow Leaf Curl Virus and Potato Leaf Roll Virus on Tomato Grown in Adana

“…Tobacco Mosaic Virus (TMV) (Mayer et al 2009 (Czosnek and Laterrot, 1997). The spread of TYLCV is primarily caused by infected plant material movement or by whiteflies that have TYLCV (Torre et al, 2018). The virus was first spoted in Jordan and Israel in 1939 (Avidov, 1944).…”