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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.

Banana bunchy top is one of the most damaging diseases in banana cultivation. However, the distribution and molecular diversity of banana bunchy top virus (BBTV) as well as its alternative hosts in Indonesia have not been reported since 1998. A total of 257 banana leaf samples were collected from the islands of Sumatra, Java, Kalimantan, Sulawesi, Maluku, Papua, Bali, Sumbawa, Timor, and Sumba from 2016 to 2019. The BBTV was detected through PCR in samples from all islands except Kalimantan. A molecular analysis showed that all BBTV isolates belonged to the South East Asian (SEA) subgroup. Based on the DNA-S and DNA-C analysis, the isolates from Sulawesi and Halmahera islands were closely related to those from the Philippines, while the remaining isolates were highly similar to those previously reported from Sumatra, Java, and Bali. Natural infection of BBTV was also recorded on abaca (Musa textilis), wild banana (M. acuminata subsp. sumatrana), ornamental pink banana (M. velutina), galangal (Alpinia galangal), and turmeric (Curcuma longa).

Bamboo mosaic virus belongs to the genus Potexvirus, family Alphaflexiviridae. Bamboo leaves with chlorotic mosaic were collected from Yogyakarta, Indonesia, and RT-PCR and sequence analyses determined that the causal agent was bamboo mosaic virus (BaMV). The genome, excluding the poly(A) tail, of Indonesian isolate BaMV-Yogya1 comprised 6364 nucleotides and 6365 nucleotides for BaMV-Yogya2. Both isolates had higher similarities to Taiwanese isolates than to Chinese isolates. A recombination detection program suggested that recombination occurred within the ORF1 and ORF5 regions of BaMV-Yogya1. This is the first report of the complete genome sequence of BaMV from Indonesia.