Ageratum yellow vein alphasatellite and tomato leaf curl Java betasatellite association with begomoviruses infecting crops and weeds in Indonesia

Symptomatic samples were taken from five districts in Yogyakarta and Central Java provinces of Indonesia to survey the genetic diversity of Begomovirus, α and β satellites. A total of 14 samples were tested positive by PCR for tomato leaf curl New Delhi virus (ToLCNDV), pepper yellow leaf curl Indonesia virus (PepYLCIV), mungbean yellow mosaic India virus (MYMIV), and ageratum yellow vein China virus (AYVCNV) infections. Besides that, ageratum yellow vein alphasatellite (AYVA) was identified for the first time in Indonesia, and tomato leaf curl Java betasatellite (ToLCJaB) were detected for the first time in different hosts. Partial genome sequences of begomoviruses and complete sequences of the α and β satellites were recovered and registered in NCBI GenBank (OP846592-OP846615). Phylogenetic study showed that AYVA and ToLCJaB each had two separate lineages. Polymorphism and diversity analyses confirmed other reports that βC1 coding region of ToLCJaB genome is highly conserved. Comparison of phylogroups 1 and 2 of ToLCJaB produced a high FST value, indicated genetic isolation between them. This report could be a basis for future works on the less studied genetic variation of α and β satellites in Indonesia and other countries.