Genetic diversity and phylogeography of begomoviruses infecting legumes in Pakistan

Abstract

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.

Genomic sequence characterization of Begomovirus infecting soybean and molecular evolutionary genomics of Legume yellow mosaic viruses (LYMVs)

“…The hypothesis of genetic isolation of legume yellow mosaic viruses (LYMVs) has been put forward hence genetic recombination or genomic components exchanges are rare (Qazi et al, 2007;Ilyas et al, 2010). Supporting the hypothesis, all the recombination events detected in this study are between Old World begomoviruses (Fig 3a and Fig 3b and Supplementary table 3 and Supplementary table 4).…”

“…The situation warrants serious management techniques to tackle YMD disease of soybean in central India. In this context, it is pertinent to mention begomoviruses and their beta satellites which were not considered as pathogens of grain legumes were found to involve in genetic recombination while analyzing genetic diversity and phylogeography in Pakistan (Ilyas et al, 2010). Likewise, a novel legumovirus Soybean chlorotic blotch virus (SbCBV) found to be infecting soybean in Nigeria was characterized with genomic components identical to the virus infecting wild species Centrosema pubescens (Alabi et al, 2010).…”

Molecular characterization of a new begomovirus infecting a leguminous weed Rhynchosia minima in India

“…Many reports have demonstrated that weeds would serve as a reservoir or alternative hosts for begomoviruses survival and spread [4,11]. The possible contribution of weeds in the evolution of cropinfecting begomoviruses via genetic recombination [12] strongly underscores the importance of characterization of begomoviruses infecting weeds.…”

“…Begomoviruses belonging to OW are further differentiated into viruses from Africa, India, Asia, and Japan. Two groups of viruses, those infecting legumes in Africa, India, and South East Asia (Legumoviruses) [4] and viruses that infect sweet potato are distinct from all other OW begomoviruses.…”

Molecular Evidence for the Occurrence of Abutilon mosaic virus, A New World Begomovirus in India

“…Although weeds do not appear to be significant reservoirs of crop-infecting viruses, they are found to be natural reservoirs for some of the agriculturally significant begomoviruses [7][8][9][10]. Considering the importance of weeds harboring many begomoviruses [11,12], during the year 2010, a study was undertaken for the identification and characterization of the begomovirus species which are associated with native weeds.…”