Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan.
Department of Biochemistry, PMAS-Arid Agriculture University, Rawalpindi, Pakistan.
PLoS One. 2022 Mar 7;17(3):e0263875. doi: 10.1371/journal.pone.0263875. eCollection 2022.
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.
香蕉束顶病毒（BBTV）是一种多分体环状单链 DNA 病毒，属于 BABUVIRUS 属和 NANOVIRIDAE 科。它在世界范围内造成了重大的作物损失，在巴基斯坦也是如此。自 1988 年以来，BBTV 就存在于巴基斯坦，但到目前为止，该国只报道了大约二十个基因组成分的序列。为了深入了解巴基斯坦目前的遗传多样性，本研究对 57 个基因组成分进行了测序，其中包括 5 个完整基因组（由 DNA-R、-U3、-S、-M、-C 和 -N 组成）。对来自巴基斯坦的种群的遗传多样性分析表明，DNA-R 高度保守，其次是 DNA-N，而 DNA-U3 则高度多样化，其 BBTV 基因组中的共同区域茎环（CR-SL）最为多样化，这是一个功能区域，此前曾报道在巴基斯坦种群中发生过重组。利用所有成分的序列以及世界各地报道的基因组对分离株的整个基因组进行最大似然（ML）系统发育分析，更深入地了解了巴基斯坦疾病的起源。对巴基斯坦和世界各地整个 BBTV 种群的遗传多样性进行比较表明，遗传多样性与重组之间存在相关性。种群遗传学分析表明，选择压力的程度因地区和基因组成分而异。对各个成分和功能区域的重组进行详细分析表明，重组与 BBTV 基因组的功能部分密切相关，这些部分显示出较高的遗传多样性。遗传多样性和重组分析均表明，CR-SL 是所有 BBTV 基因组中的重组热点，在六个成分中，只有 DNA-U3 是广泛经历了种内和种间重组的重组成分。重组区域的多样性分析结果平均增加了一倍半，在某些情况下甚至增加了四倍，这是由于重组所致。这些结果表明，重组对世界各地的 BBTV 种群的遗传多样性有显著贡献。
