Ageratum yellow vein alpha satellite and tomato leaf curl Java beta satellite association with begomoviruses infecting crops and weeds in Indonesia

The 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. Fourteen samples tested positive by PCR for infections of tomato leaf curl New Delhi virus, pepper yellow leaf curl Indonesia virus, mungbean yellow mosaic India virus, and ageratum yellow vein China virus. For the first time, the Ageratum yellow vein alpha satellite (AYVA) was identified in Indonesia and the tomato leaf curl Java beta satellite (ToLCJaB) was detected in different hosts. The partial genome sequences of begomoviruses and complete sequences of the α and β satellites were obtained and deposited in NCBI GenBank (OP846592-OP846615). The phylogenetic study revealed that AYVA and ToLCJaB each had two separate lineages. Coherent with the other reports, the polymorphism and diversity analyses confirmed that the βC1 coding region of the ToLCJaB genome is highly conserved. The comparison of phylogroups 1 and 2 of ToLCJaB produced a high Fixation index (FST) value, indicating genetic isolation between them. This report could serve as a basis for future work on the poorly studied genetic variation of α and β satellites in Indonesia and other countries.