Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA

Abstract

The nucleotide sequence of 17 variants of the satellite RNA of cucumber mosaic virus (CMV-satRNA) isolated from field-infected tomato plants in the springs of 1989, 1990, and 1991 was determined. The sequence of each of the 17 satRNAs was unique and was between 334 and 340 nucleotides in length; 57 positions were polymorphic. There was much genetic divergence, ranging from 0.006 to 0.141 nucleotide substitutions per site for pairwise comparisons, and averaging 0.074 for any pair. When the polymorphic positions were analyzed relative to a secondary structure model proposed for CMV-satRNAs, it was found that there were significantly different numbers of changes in base-paired and non-base-paired positions, and that mutations that did not disrupt base pairing were preferred at the putatively paired sites. This supports the concept that the need to maintain a functional structure may limit genetic divergence of CMV-satRNA. Phylogenetic analyses showed that the 17 CMV-satRNA variants clustered into two subgroups, I and II, and evolutionary lines proceeding by the sequential accumulation of mutations were apparent. Three satRNA variants were outliers for these two phylogenetic groups. They were shown to be recombinants of subgroup I and II satRNAs by calculating phylogenies for different molecular regions and by using Sawyer's test for gene conversion. At least two recombination events were required to produce these three recombinant satRNAs. Thus, recombinants were found to be frequent ( approximately 17%) in natural populations of CMV-satRNA, and recombination may make an important contribution to the generation of new variants. To our knowledge this is the first report of data allowing the frequency of recombinant isolates in natural populations of an RNA replicon to be estimated.

Molecular Population Genetics of Cucumber Mosaic Virus in California: Evidence for Founder Effects and Reassortment

“…Thus, the absence of detectable recombinants in our study may also be explained by two alternative scenarios: either (i) recombination events occurred between two closely related isolates and are difficult to detect by the methods we used here or (ii) recombination events did occur, but the resulting recombinants were not favored and subsequently were selected out. Indeed, recombination events in the CMV genome and CMV satellite RNA have been described recently in both experimental systems and natural populations (1,2,4,10,16,18,37). Estimation of various population genetics parameters showed that coding regions on RNA2 (2a and 2b) were more variable, suggesting that the resultant proteins were more tolerant to amino acid changes than were regions on RNA1 (1a) and RNA3 (MP and CP) ( Table 4).…”

The promiscuous evolutionary history of the family Bromoviridae

“…Proportionally, the amount of genetic variability produced after a single recombination event is larger than that produced by single point mutations. Although the importance of recombination was underappreciated in early studies of virus genome evolution, it is now recognized as a widespread phenomenon among positive-strand RNA viruses in animals (Grassly & Holmes, 1997;Holmes et al, 1999;Wilson et al, 1988) and plants (Nagy & Bujarski, 1993;Revers et al, 1996;Aranda et al, 1997;Olsthoorn et al, 2002;Bousalem et al, 2003;Cheng & Nagy, 2003;Moreno et al, 2004;Tan et al, 2004;Bonnet et al, 2005;Urbanowicz et al, 2005;Chare & Holmes, 2006;Weng et al, 2007), as well as in retroviruses such as human immunodeficiency virus type 1 Prljic et al, 2004;Althaus & Bonhoeffer, 2005;Galetto & Negroni, 2005), although it is a rare or even non-existent phenomenon among negativestrand viruses (Chare et al, 2003). There are several mechanisms by which RNA recombination may take place, the most common of which is homologous recombination (Lai, 1992).…”

The AU-Rich RNA Recombination Hot Spot Sequence of Brome Mosaic Virus Is Functional in Tombusviruses: Implications for the Mechanism of RNA Recombination

“…RNA recombination plays a major role during the evolution of plus-strand RNA viruses (1,6,10,29,35). New viruses or strains may emerge via recombination between different viral RNAs or between viral and host RNAs (29,35).…”