Discovery of a novel alphasatellite of the genus Clecrusatellite associated with a wide array of New World tomato-infecting begomoviruses

A new alphasatellite was discovered via high-throughput sequencing in mixed infections with five distinct tomato-infecting begomoviruses in central Brazil, and the presence of this alphasatellite in tomato leaf samples was confirmed by PCR and Sanger sequencing. It has a circular genome of 1,321 nucleotides with typical features of alphasatellites belonging to the subfamily Geminialphasatellitinae, including a replication-associated hairpin sequence (TAGTATTAC) and an open reading frame encoding a replication-associated protein. Pairwise sequence comparisons and phylogenetic analysis indicated that this alphasatellite represents a new species, with 69–77% sequence identity to other members of the genus Clecrusatellite. Tomato golden vein virus (TGVV) was the only begomovirus present in all six positive samples. However, it was not possible to determine which of these viruses can function as a helper virus for the alphasatellite. The species name "Clecrusatellite solanumbrasiliensis" is proposed to classify this alphasatellite associated with endemic Brazilian begomoviruses. To our knowledge, this is the first report of a tomato-associated alphasatellite in the New World.