Distribution, molecular characterization and diversity of banana bunchy top virus in Tripura, India

Abstract

Banana bunchy top virus (BBTV) is a serious threat to banana (Musa spp.) production in India. Generally, BBTV isolates within the country share very low genetic diversity. However, in India, relatively greater diversity has been observed between isolates from north-eastern (NE) region (Meghalaya) and rest of India. Tripura is situated in the south-west corner of NE India and shares international border with Bangladesh. During 2014-2015, diagnostic surveys were conducted in seven districts of Tripura and polymerase chain reaction based detection established that BBTD is widely prevalent in all parts of Tripura showing an average incidence of 22.02%. Among the cultivars, maximum BBTV infection (27.03%) was recorded in 'Chini Champa', followed by plantain (24.29%). A representative population (31 isolates) of BBTV from Tripura was characterized based on DNA R and DNA S. Phylogenetic analysis based on BBTV DNA R and DNA S generated two broad clusters of Pacific-Indian Oceans (PIO) and south-east Asian groups including all Tripura isolates within PIO cluster. The clustering pattern and genetic diversity of BBTV population from Tripura suggested monophyletic origin of majority of representative isolates from a common ancestor of PIO group. The exchange of vegetative propagules within and in between countries could have contributed to the geographical expansion of PIO isolates in Tripura. However, four variant BBTV isolates has been identified from North Tripura and Khowai districts possessing somewhat unique variability than that of distinct isolate (BBTV-Umiam) reported from NE India (Meghalaya).

Keywords: Banana bunchy top virus; North-east India; Phylogeny; Population genetics; Tripura.

Fig. 1

Geographical location of Tripura. The collection sites of BBTV suspected samples are indicated by blue circles with actual geographical coordinates

Fig. 2

Circular cladogram representing phylogenetic relationship based on nucleotide sequences of DNA R of 31 BBTV isolates from Tripura along with previously reported PIO and SEA isolates of BBTV rooted with ABTV. The evolutionary history was inferred using the neighbour-joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches (shown only when > 50%). The evolutionary distances were computed using the ‘Maximum Composite Likelihood’ method and are in the units of the number of base substitutions per site. Each sequence is labelled with the GenBank accession number followed by origin and isolate name. The blue coloured branches indicate the ABTV isolates, the orange coloured branches indicate PIO isolates and the green coloured branches indicate SEA isolates of BBTV

Fig. 3

Circular cladogram representing phylogenetic relationship based on nucleotide sequences of DNA S of 31 BBTV isolates from Tripura along with previously reported PIO and SEA isolates of BBTV rooted with ABTV. The evolutionary history was inferred using the neighbour-joining method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches (shown only when > 50%). The evolutionary distances were computed using the ‘Maximum Composite Likelihood’ method and are in the units of the number of base substitutions per site. Each sequence is labelled with the GenBank accession number followed by origin and isolate name. The blue coloured branches indicate the ABTV isolates, the orange coloured branches indicate PIO isolates and the green coloured branches indicate SEA isolates of BBTV