Phylogenetic analysis and molecular characterization of BBTV DNA-R of wild and cultivated banana isolates from East Java, Indonesia

Banana bunchy top virus (BBTV) molecular detection and understanding its origin are important issues for mitigating future spread. The aim of this study was to molecularly detect BBTV infection and analyze the characteristic also phylogenetic of banana isolates from East Java Indonesia. Two BBTV asymptomatic wild bananas and two BBTV symptomatic banana cultivars were examined. PCR amplifications were accomplished using BBTV DNA-R primers for master replication initiation protein. Sequences evaluations were conducted in SeqScanner. Sequences identification was performed in nucleotide BLAST. Translation of ORFs was determined using ORF Finder server tool. Protein identification was conducted in protein BLAST. Sequences polymorphisms were analyzed using  DnaSP6. Phylogenetic analysis was employed using Neighbor-Joining algorithm with Kimura two-parameter (K2P) substitution model in MEGA7. Results showed that BBTV DNA-R components were detected in all isolates and confirmed as Rep protein. The sequences length were varied from 616 to 1,074 bp, low GC content (42.90%) and low conservation (56.47%). Asymptomatic wild bananas generated shorter length and more variable sequences, presumably related to the resistance mechanism. Phylogenetic analysis of BBTV DNA-R East Java with other 38 homolog sequences worldwide were found clustered in Asian Group, closely related to Vietnam, Thailand, and China. Hence, it presumably originated from China mainland via Malay Peninsula route.