Circular DNA Enrichment Sequencing (CIDER-Seq) Facilitated the Discovery of a New World (NW) Begomovirus-Alphasatellite Complex Associated with Leaf Curl Disease of Tomato in Morelos, Mexico.

A circular DNA enrichment sequencing (CIDER-Seq) approach identified a New World (NW) begomovirus-alphasatellite complex associated with a leaf curl disease of tomato from plants collected in Morelos, México. Using one of 21 samples showing virosis-associated symptoms, CIDER-Seq data revealed the presence of various NW begomovirus species, namely Begomovirus solanumaureivariati (tomato golden mottle virus: ToGMoV), Begomovirus solanumseveri (tomato severe leaf curl virus: ToSLCV), and Begomovirus solanumlapazense (tomato chino La Paz virus: ToChLPV). Additionally, the alphasatellites Whiflysatellite guatemalaense (whitefly-associated Guatemala alphasatellite 1: WfaGA1) and Clecrusatellite guatemalaense (whitefly-associated Guatemala alphasatellite 2: WfaGA2) were identified, demonstrating that begomoviruses can co-infect with alphasatellites; however, the pathogenic implications of the alphasatellite-helper begomovirus association remain incompletely understood. PCR-based detection and Sanger sequencing of circular viral genomes revealed a high frequency of detection of mixed infections comprising all components of the begomovirus-alphasatellite complex, confirming the reliability of the CIDER-Seq approach in producing high-fidelity sequences. Molecular and biological analysis revealed the complex adaptation to tomato, the monopartite nature of ToSLCV/ToChLPV species, and the ability of these begomovirus species to act as helper viruses. To the best of our knowledge, this is the first report of leaf curl disease of tomato associated with a begomovirus-alphasatellite complex in Mexico.