Downloaded from www.microbiologyresearch.org by IP: 54.145.195.192 On: Sat, 10 Sep 2016 01:06:11 Genetic diversity and phylogeography of begomoviruses infecting legumes in Pakistan Muhammad Ilyas, Javaria Qazi, Shahid Mansoor and Rob W. Briddon Correspondence Rob W. Briddon rob.briddon@gmail.com National Institute for Biotechnology and Genetic Engineering, PO Box 577, Jhang Road, Faisalabad, Pakistan Received 26 January 2010 Accepted 1 April 2010 Grain legumes are an important source of dietary protein across southern Asia, but they suffer extensive losses due to several viruses that are members of the genus Begomovirus (family Geminiviridae), which are collectively known as legume yellow mosaic viruses (LYMVs). Despite their economic importance, little attention has been paid to LYMVs in Pakistan and only partial sequences of virus isolates originating from this country are available in the databases. Here, a survey of LYMVs occurring across Pakistan is described. Complete sequences of 44 components (23 DNA-A, 19 DNA-B and 2 betasatellites) were determined. The results show that only the mungbean yellow mosaic India virus (MYMIV) is of agricultural significance in Pakistan having been isolated from all cultivated grain legumes examined. Mungbean yellow mosaic virus, a significant crop pathogen in India, was only identified in a weed, which together with a novel species of LYMV we reported earlier, represents the first LYMV identified in non-cultivated plants. MYMIV was shown to occur as two types in Pakistan that show phylogeographical segregation. Additionally, two begomovirus species not considered pathogens of legumes and a betasatellite were isolated. This is of grave concern since it suggests that the presumed genetic isolation of the LYMVs in legumes may be being breached. LYMVs show little, if any, evidence of interspecific recombination with non-legume infecting begomoviruses. Thus, either recombination with non- legume viruses or interaction with betasatellites, which are host range and pathogenicity determining satellites of begomoviruses, could lead to the appearance of more aggressive virus variants/strains affecting legumes. INTRODUCTION The family Geminiviridae consists of viruses with circular, single-stranded (ss) DNA genomes that are transmitted from plant-to-plant by arthropod vectors. Taxonomically the family is divided into four genera based on host range, genome arrangement and insect vector (Stanley et al., 2005). The virus members of the genus Begomovirus are the most economically destructive and geographically the most widespread viruses, occurring throughout all the warmer parts of the world. Begomoviruses are transmitted exclusively by the whitefly Bemisia tabaci and have genomes consisting of either one or two ssDNA circles of ~2.8 kb. The two components making up the genomes of bipartite begomoviruses are known as DNA-A and DNA-B. So far only bipartite begomoviruses have been shown to be native to the New World, although a monopartite Old World (OW) begomovirus has been inadvertently intro- duced there recently (Polston et al., 1999). In the OW monopartite begomoviruses outnumber bipartite viruses and the vast majority of these monopartite viruses associate with DNA satellites that are symptom determining (Briddon & Stanley, 2006; Nawaz-ul-Rehman et al., 2009). The legume-infecting begomoviruses from the OW are amongst the most unusual of the begomoviruses. They are distinct from the numerous legume-infecting begomo- viruses that occur in the Americas and in phylogenetic analyses they segregate basal to the OW begomoviruses (Padidam et al., 1995; Fauquet et al., 2008). Qazi et al. (2007b) have suggested that the distinction between legume-infecting and other OW begomoviruses has arisen due to genetic isolation, there being either a host range barrier or lack of movement of whitefly vectors between legumes and non-leguminous plants preventing genetic exchange between these two groups of viruses. The bipartite begomoviruses mungbean yellow mosaic India virus (MYMIV; Mandal et al., 1997), mungbean yellow mosaic virus (MYMV; Morinaga et al., 1993), Dolichos yellow mosaic virus (DoYMV; Maruthi et al., 2006) and horsegram yellow mosaic virus (HgYMV) occur throughout southern Asia. They cause distinctive yellow The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are AM922485, AM948961, AM950268, AM992617, AM992618, FM161881, FM202439–FM202447, FM208833–FM208846, FM242701, FM242702, FM955598– FM955609 and FM958506 (see Table 1). Supplementary tables are available with the online version of this paper. Journal of General Virology (2010), 91, 2091–2101 DOI 10.1099/vir.0.020404-0 020404 G 2010 SGM Printed in Great Britain 2091