Evidence of inter-component recombination, intra-component recombination and reassortment in banana bunchy top virus

Abstract

Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component, ssDNA virus, which causes widespread banana crop losses throughout tropical Africa and Australasia. We determined the full genome sequences of 12 BBTV isolates from the Kingdom of Tonga and analysed these together with previously determined BBTV sequences to show that reassortment and both inter-and intra-component recombination have all been relatively frequent occurrences during BBTV evolution. We found that whereas DNA-U3 components display evidence of complex inter-and intra-component recombination, all of the South Pacific DNA-R components have a common intra-component recombinant origin spanning the replicationassociated protein gene. Altogether, the DNA-U3 and DNA-M components display a greater degree of inter-component recombination than the DNA-R, -S, -C and -M components. The breakpoint distribution of the inter-component recombination events reveals a primary recombination hotspot around the 59 side of the common region major and, in accordance with recombination hotspots detectable in related ssDNA viruses, a secondary recombination hotspot near the origin of virion-strand replication.

Genetic structure and diversity of the Banana bunchy top virus population on Sumatra Island, Indonesia

“…On the other hand, DNA-U3 was notable for having the highest diversity of all BBTV components (Hyder 2009), but the DNA-U3 of Sumatra isolates had high identity (Table S3). This is similar to the results for the Pakistan and Tonga populations (Hyder et al 2011;Stainton et al 2012). Since the nucleotide sequence of DNA-U3 had not been determined in Indonesia isolates until now, our data will be especially useful for the investigation of BBTV in Indonesia.…”

“…Sumatra isolates have a high identity to isolates of the Asian group (Table S3). Previous studies have shown that the nucleotide and amino acid sequences of DNA-R and DNA-S are generally conserved at a high level (Stainton et al 2012). Similarly, the sequence identity of DNA-R and DNA-S on Sumatra Island were more than 98 and 99 %, respectively.…”

“…The PCR conditions consisted of 1 cycle of 94°C for 2 min, followed by 40 cycles of 94°C for 1 min, the annealing temperature of each primer pair for 1 min, and 72°C (Ex Taq) or 68°C (Platinum® Pfx) for 2 min, and a final extension for 10 min at 72°C (Ex Taq) or 68°C (Platinum® Pfx). Previous studies showed that the phylogenetic trees deduced from the sequences of all six DNA components showed the same hereditary patterns across individual isolates (Vishnoi et al 2009;Stainton et al 2012). Moreover, since DNA-R (encoding Rep) and DNA-S (encoding CP) were important for the multiplication of viral genomes and the formation of a virion, respectively and DNA-U3 is known to have high diversity compared with other components, we used DNA-R, -U3, and -S for genetic analysis in this study.…”

The global distribution ofBanana bunchy top virusreveals little evidence for frequent recent, human-mediated long distance dispersal events

“…Towards this end, the CD was analyzed for evidence of reassortment using RDPv4.27 (Martin et al. 2010), with manual identification of reassortment events as detected recombination events that had inferred breakpoint locations spanning entire components (Stainton et al. 2012).…”

“…Given that this analysis involved almost four times more full genomes than previous BBTV reassortment analyses, it is not surprising that of the seventy-five isolates detected as reassortants, only 10 had been detected previously (Hu et al. 2007; Stainton et al. 2012).…”