Banana bunchy top virus genetic diversity in Pakistan and association of diversity with recombination in its genomes

Sana Bashir,Syed Muhammad Saqlan Naqvi,Aish Muhammad,Muhammad Zeeshan Hyder,Sumaira Farrakh,Kazim Ali,Iqbal Hussain,Tayyaba Yasmin,Muhammad Ramzan Khan,Rajarshi Gaur

doi:10.1371/journal.pone.0263875

Sana Bashir, Syed Muhammad Saqlan Naqvi + Show 8 more

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https://doi.org/10.1371/journal.pone.0263875

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Abstract

Banana Bunchy top virus (BBTV) is a multipartite circular single strand DNA virus that belongs to genus Babuvirus and family Nanoviridae. It causes significant crop losses worldwide and also in Pakistan. BBTV is present in Pakistan since 1988 however, till now only few (about twenty only) sequence of genomic components have been reported from the country. To have insights into current genetic diversity in Pakistan fifty-seven genomic components including five complete genomes (comprises of DNA-R, -U3, -S, -M, -C and -N components) were sequenced in this study. The genetic diversity analysis of populations from Pakistan showed that DNA-R is highly conserved followed by DNA-N, whereas DNA-U3 is highly diverse with the most diverse Common Region Stem-loop (CR-SL) in BBTV genome, a functional region, which previously been reported to have undergone recombination in Pakistani population. A Maximum Likelihood (ML) phylogenetic analysis of entire genomes of isolates by using sequence of all the components concatenated together with the reported genomes around the world revealed deeper insights about the origin of the disease in Pakistan. A comparison of the genetic diversity of Pakistani and entire BBTV populations around the world indicates that there exists a correlation between genetic diversity and recombination. Population genetics analysis indicated that the degree of selection pressure differs depending on the area and genomic component. A detailed analysis of recombination across various components and functional regions suggested that recombination is closely associated with the functional parts of BBTV genome showing high genetic diversity. Both genetic diversity and recombination analyses suggest that the CR-SL is a recombination hotspot in all BBTV genomes and among the six components DNA-U3 is the only recombined component that has extensively undergone inter and intragenomic recombination. Diversity analysis of recombinant regions results on average one and half fold increase and, in some cases up to four-fold increase due to recombination. These results suggest that recombination is significantly contributing to the genetic diversity of BBTV populations around the world.

Highlights

Banana bunchy top disease (BBTD) is the most common and devastating viral disease of Banana, predominantly found in Pacific and Asian regions
BBTD is caused by Banana Bunchy top Virus (BBTV), which belongs to genus Babuvirus in the family Nanoviridae [3]
BBTV infected plant material showing typical BBTD symptom was collected from district Tandojam, Sindh province in 2006 for P.TJ1 isolate (for which DNA-R was previously reported by Hyder and colleagues (2007)), and in 2007, for P.BS1 & 2, P.GH1 & 2, P.HD1 & 2, P

Summary

Introduction

Banana bunchy top disease (BBTD) is the most common and devastating viral disease of Banana, predominantly found in Pacific and Asian regions. It has been considered one of the most important plant viral diseases around the world [1]. In Pakistan, BBTD was first observed in 1988 in Sindh province. Later, based on symptomology it was identified in 1991 [2]. BBTD is caused by Banana Bunchy top Virus (BBTV), which belongs to genus Babuvirus in the family Nanoviridae [3]. BBTV is transmitted persistently by the aphid Pentalonia nigronervosa Coq, its sole known vector, and infects only the members of Musaceae [4]

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