Recombination analysis of Maize dwarf mosaic virus (MDMV) in the Sugarcane mosaic virus (SCMV) subgroup of potyviruses

Abstract

Recombination among RNA viruses is a natural phenomenon that appears to have played a significant role in the species development and the evolution of many strains. It also has particular significance for the risk assessment of plants which have been genetically modified for disease resistance by incorporating viral sequences into their genomes. However, the exact recombination events taking place in viral genomes are not investigated in detail for many virus groups. In this analysis, different single-stranded positive-sense RNA potyviruses were compared using various in silico recombination detection methods and new recombination events in the Sugarcane mosaic virus (SCMV) subgroup were detected. For an extended in silico recombination analysis, two of the analyzed Maize dwarf mosaic virus full-length genomes were sequenced additionally during this work. These results strengthen the evidence that recombination is a major driving force in virus evolution, and the emergence of new virus variants in the SCMV subgroup, paired with mutations, could generate viruses with altered biological properties. The intra- and interspecific homolog recombinations seem to be a general trait in this virus group, causing little or no changes to the amino acid of the progenies. However, we found a few breakpoints between the members of SCMV subgroup and the weed-infecting distant relatives, but only a few methods of the RDP3 package predicted these events with low significance level.

Occurrence and Evolutionary Analysis of Coat Protein Gene Sequences of Iranian Isolates of Sugarcane mosaic virus

“…Subsequently, further spread of SCMV within Iran could have occurred via movement of contaminated vegetative cuttings across provinces to other host plants such as maize, sorghum, and so on and within provinces via aphid vectors. Mutation and recombination are two main sources of genetic variation in RNA viruses (Gell et al, 2015; Mangrauthia et al, 2008; Moreno et al, 2004; Padhi and Ramu, 2011). Recombination events are common in Potyvirus evolution and can be detected throughout the genome (Chare and Holmes, 2006; Revers et al, 1996; Sztuba-Solińska et al, 2011; Valli et al, 2007).…”

Molecular characterization of two sugarcane streak mosaic virus isolates from Iran with emphasis on its population structure

“…As SCSMV can be transmitted through vegetative set, it seems that Iranian isolates have been introduced into the country from sugarcane-producing Asian countries such as India and Pakistan via contaminated vegetative cuttings. In RNA viruses, viral genome evolutions are directed by recombination and mutation events, which are two important sources of genetic variation (Roossinck, 1997;Posada et al, 2002;Gell et al, 2015). Recombination occurs frequently among members of the family Potyviridae (Revers et al, 1996;Chare and Holmes, 2006;Valli et al, 2007;Padhi and Ramu, 2011;Sztuba-Solin' ska et al, 2011;Gell et al, 2015), however, no recombination event was found in Iranian SCSMV isolates and also other members of group II, suggesting that probably this evolutionary force has not shaped the emergence of SCSMV group II variants (in contrast to group I (Liang et al, 2016)).…”

Himalayan wild cherry (Prunus cerasoides) as a new natural host of Cherry necrotic rusty mottle virus (CNRMV) and a possible role of insect vectors in their transmission

“…Owing to this deletion the CP of the Indian isolates is 266 amino acids instead of 267 as in case of all other isolates. In case of RNA viruses it is a well‐known fact that the virus populations may be variable within a given plant because of the constant occurrence of replication errors leading to changes, mutations and recombination (Gell, ). Although there was no recombination event detected in the Indian isolates (analyzed by RDP3; Martin et al , ), this missing triplet could be a result of a deletion which has been selected in nature and is being passed on to further generations, probably suited to virus multiplication in this Hwc and bamboo (Awasthi et al , ).…”