Identification and characterization of a distinct banana bunchy top virus isolate of Pacific-Indian Oceans group from North-East India.
Banana bunch top virus (BBTV) is considered to be a serious threat to banana production. A new isolate of the virus (BBTV-Umiam) was identified and characterized from local banana mats growing in mid-hills of Meghalaya in North-East India. The complete nucleotide sequence analysis revealed the presence of six full-length ssDNA components (DNA R, DNA U3, DNA S, DNA M, DNA C and DNA N) sharing major common region (CR-M) and a stem-loop common region (CR-SL). BBTV-Umiam showed a unique deletion of 20 nucleotides in the intergenic region of DNA R, the absence of predicted open reading frame (ORF) in DNA U3 and probability for a small ORF in DNA U3 expecting functional evidence at transcriptional level. Phylogenetic analysis based on 88 complete nucleotide sequence of BBTV DNA R available in GenBank generated two broad clusters of Pacific-Indian Oceans (PIO) and South-East Asian (SEA) groups including BBTV-Umiam within PIO cluster. However, BBTV-Umiam was identified as the most distinct member of the PIO group with 100% bootstrap support. This was further supported by the phylogenetic grouping of each genomic component of BBTV-Umiam at the distant end of PIO group during clustering of 21 complete BBTV sequences. BBTV-Umiam shared relatively less nucleotide identity with PIO group for each genomic component (85.0-95.4%) and corresponding ORF (93.8-97.5%) than that of earlier PIO isolates (91.5-99.6% and 96.0-99.3%, respectively). Recombination analysis revealed two intra-component and five inter-component recombination events in BBTV-Umiam, but none of them was unique. Moreover, the isolate was identified as major parental sequence for intra-component recombination event spanning the replication-associated protein encoding region in Tongan BBTV DNA R. The current study indicated differential evolution of BBTV in North-East India (Meghalaya). The natural occurrence of hybrids of Musa balbisiana and M. acuminata in this geographically isolated region could be the contributing factor in accumulating genetic distinctiveness in BBTV-Umiam which need further characterization.
Division of Crop Improvement, ICAR Research Complex for NEH Region, Umiam 793 013, Meghalaya, India. Electronic address: amrita.ars@gmail.com.
Amrita
A
Banerjee
National Bureau of Plant Genetic Resources, Regional Station, Umiam 793 013, Meghalaya, India.
Somnath
S
Roy
Division of Crop Improvement, ICAR Research Complex for NEH Region, Umiam 793 013, Meghalaya, India.
Ganesh T
GT
Behere
ICAR Research Complex for NEH Region, Manipur Centre, Lamphelpat 795 004, Manipur, India.
Subhra Saikat
SS
Roy
ICAR Research Complex for NEH Region, Mizoram Centre, Kolasib 796 081, Mizoram, India.
Sudip Kumar
SK
Dutta
Division of Crop Improvement, ICAR Research Complex for NEH Region, Umiam 793 013, Meghalaya, India.
S V
SV
Ngachan
D052658:Babuvirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D016000:Cluster Analysis; D004279:DNA, Viral / Q000737:chemistry* / Q000235:genetics*; D019143:Evolution, Molecular; D016679:Genome, Viral; D007194:India; D008969:Molecular Sequence Data; D028521:Musa / Q000821:virology; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
D004279:DNA, Viral
Banana bunchy top virus; Complete genome sequence; North-East India; Phylogeny; Recombination analysis